Science & Engineering Catalog...The OGI School of Science & Engineering remains committed to its...

03/04Catalog

OGI School ofScience & Engineering

www.ogi.edu/catalog

20000 N.W. Walker Road • Beaverton, OR • 97006-8921phone (503) 748-1027 toll free (800) 685-2423 fax (503) 748-1285

e-mail [email protected] URL www.ogi.edu

www.ogi.edu/catalog

0803

OGI School ofScience & Engineering

TA B L E O F C O N T E N T S | O G I

W E L C O M E T O T H E O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G

L E T T E R F R O M T H E D E A N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

H I S T O R I C A L B A C K G R O U N D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

M I S S I O N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

E Q U A L O P P O R T U N I T Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

A C A D E M I C C A L E N D A R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

A B O U T T H I S C ATA L O G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

O V E R V I E W

A C A D E M I C D E P A R T M E N T S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

D E G R E E P R O G R A M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

C E R T I F I C AT E P R O G R A M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

S T U D E N T S N O T S E E K I N G D E G R E E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

A C C R E D I TAT I O N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

A D M I S S I O N S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

T U I T I O N & F I N A N C E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

C O U R S E N U M B E R S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

A C A D E M I C P O L I C I E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

T H E C A M P U S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 0

O V E R V I E W O F O G I A C A D E M I C P R O G R A M S

B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y P R O G R A M . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3

B I O M E D I C A L E N G I N E E R I N G P R O G R A M . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3

C O M P U T E R S C I E N C E A N D E N G I N E E R I N G P R O G R A M . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3

E L E C T R I C A L E N G I N E E R I N G P R O G R A M . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3

E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G P R O G R A M . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4

M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G Y P R O G R A M . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 4

A C A D E M I C D E P A R T M E N T S / P R O G R A M S / R E S E A R C H / FA C U LT Y

B I O M E D I C A L E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 5

C O M P U T E R S C I E N C E A N D E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3

E L E C T R I C A L E N G I N E E R I N G P R O G R A M I N S E M I C O N D U C T O R E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1

E N V I R O N M E N TA L A N D B I O M O L E C U L A R S Y S T E M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 5

M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 1

C R O S S - I N S T I T U T I O N A L P R O G R A M S A N D C O U R S E S

P R O G R A M S O F S T U D Y I N S P O K E N L A N G U A G E U N D E R S TA N D I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 7

A P P L I E D C O M P U T I N G C O U R S E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 7

A P P L I E D M AT H E M AT I C S C O U R S E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 7

G E N E R A L E D U C AT I O N C O U R S E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 7

C O U R S E D E S C R I P T I O N S

A P P L I E D C O M P U T I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 9

B I O M E D I C A L E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 9

C O M P U T E R S C I E N C E A N D E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1

E N V I R O N M E N TA L A N D B I O M O L E C U L A R S Y S T E M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 6

E L E C T R I C A L E N G I N E E R I N G C O U R S E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 9

A P P L I E D M AT H E M AT I C S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 4

M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 5

O R E G O N M A S T E R O F S O F T W A R E E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 8

Photography by Jerome Hart, David Moore, Rick Rappaport, Anne Rybak and Jeff Schilling.3

O G I | L E T T E R F R O M T H E D E A N

A L E T T E R F R O M T H E D E A N

It’s about the connections between ahealthy environment and a healthypopulation. It’s about computers that thinklike people do, and are reliable enough totrust with the safety of our communities.It’s about helping our seniors live longer,more satisfying lives. It’s about cultivatingbusiness leaders who can guide Oregon’shigh-technology companies through today’stough markets. At the OGI School ofScience & Engineering, it’s all aboutbuilding healthier, better-informed andmore secure communities in Oregon andbeyond. Virtually everything we do - be itgraduate education, research, industrialcollaboration, or community outreach - isaimed at solving important societalproblems, and at putting these solutionsinto the hands of those that need themmost. Are you interested in expanding yourscience and engineering knowledge in thistype of environment? As a component ofOregon Health & Science University, ourschool welcomes high-caliber students whoseek to apply advanced technologies inreal-world situations. This electroniccatalog is designed to tell you everythingyou need to know about pursuing agraduate degree at OGI.

As you scroll through the catalog, you maybe surprised at the wide range of programsoffered through such a small school. SinceOGI’s inception 40 years ago, the school’ssmall size has been one of its key strengths.We offer an enviable faculty/student ratio of1/1.9 for Ph.D. students. Despite our size,OGI awards a significant percentage ofOregon’s graduate degrees in high-technology fields, and our highly productivefaculty attract approximately $18 million in

research support each year fromgovernment and industrial sources. In fact, our Department of Computer Scienceand Engineering ranks an impressive 15th in the nation, based on federalresearch grants. OGI is small enough toremain responsive to changing needs inthe fields we serve, and to fostercollaborative, interdisciplinary researchacross a broad — yet synergistic — rangeof scientific endeavors.

Accredited M.S. degrees are offeredthrough four academic departments:Biomedical Engineering (BME), ComputerScience and Engineering (CSE),Environmental and Biomolecular Systems(EBS) and Management in Science andTechnology (MST). Students can earnaccredited doctoral degrees through theBME, CSE and EBS departments. Studentscan also obtain an electrical engineeringM.S. or Ph.D. degree by selecting EEspecialization areas within the BME or CSEdepartments. These specialization areasinclude computer engineering, signalprocessing, medical optics and sensors.OGI also offers graduate-level certificatesin Management in Science and Technologyand Health Care Management. We areproud of our diverse population of full- andpart-time students, who learn in anenvironment where fundamental knowledgeis balanced with a focus on practicalproblem solving. OGI is committed tofollowing discoveries from concept all theway through to fruition, leveraging thecommercial potential of our technologieswherever possible to serve the broadestpossible cross-section of the public.

At OGI, it’s all about making a difference.I’ve tried to give you an idea of how wemake a difference in our region and beyond.Now, I invite you to read for yourself howOGI can make a difference to you.

Ed Thompson, Ph.D.OHSU Vice-President and DeanOGI School of Science & Engineering

WELCOME

HISTORICAL BACKGROUND

The OGI School traces its origins to the early1960s, when Mark Hatfield, then Oregon’sgovernor, and an advisory committee ofindustrial and educational leadersrecommended creating an independentinstitution for graduate education andresearch in the Portland area. In 1963 theyestablished the Oregon Graduate Center forStudy and Research. In 1989, the center wasrenamed the Oregon Graduate Institute ofScience and Technology.

Over the next decade, OGI awarded morethan 1,000 graduate degrees, offeredhundreds of continuing education classes andworkshops, and pursued more than $100million in research, most of it federallyfunded. Now in its third year as a school ofOregon Health & Science University, OGIcontinues as a premier provider of high-quality graduate science and engineeringeducation, with more than 500 studentsworking full- or part-time toward master’s orPh.D. degrees, and more than $18 million inresearch annually.

OHSU is a health and research universitydedicated to graduate education, researchand health care. The university educatessome 3,000 students each year and in 2001brought in more than $212 million inresearch dollars - a figure that is expected togrow by 15 to 20 percent annually. About1,500 scientists are working on basic andapplied research projects throughout OHSU.Its merger with OGI has broadened themission of the institution to encompass newresearch frontiers where technology andengineering converge with health care andbiomedicine.

The OGI School of Science & Engineeringremains committed to its historical purpose:to educate students and conduct high-qualityresearch in science and engineering and toserve as a resource for Oregon’s high-technology industry. The merger bothstrengthens OGI’s traditional research-basedprograms and enables the school to expand innew directions. In 2002, with a $4 milliongrant from the M.J. Murdock Charitable Trust,the school established a Department of

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Biomedical Engineering, the new curriculumof which is published here for the first time.The merger also facilitates cross-disciplinary collaboration, especially in thebiosciences, environmental sciences andinformation technology.

OGI is part of OHSU’s West Campus, whichalso includes the Vaccine and Gene TherapyInstitute, the Neurological Sciences Instituteand the Oregon National Primate ResearchCenter. The West Campus is about 12 milesfrom OHSU’s central campus on Portland’sMarquam Hill.

MISSION

The mission of the OGI School of Science &Engineering is to carry out advancedresearch in science, engineering andmanagement that responds to importantsocial, environmental and industry needs; tooffer outstanding graduate and professionaleducational opportunities; and, by so doing,to contribute to the region’s economy andwell-being.

T O A C C O M P L I S H T H I S M I S S I O N ,T H E O G I S C H O O L :

• provides students with the necessaryknowledge, skills and breadth for leader-ship in a technological society;

• supports, through research, education andtraining, the people, industries and organi-zations that drive the economic growth ofthe Pacific Northwest;

• attracts and develops high-quality faculty,students and staff.

EQUAL OPPORTUNITY

Oregon Health & Science University and theOGI School of Science & Engineering arefirmly committed to a policy of affirmativeaction and equal opportunity. Thisencompasses all employment, education andpatient service activities connected withOHSU. No patient, employee, student,trainee, beneficiary or potential beneficiaryof the hospitals and clinics or the universityshall be unlawfully discriminated against onthe basis of race, color, sex, sexualorientation, religion, creed, national origin,age, marital status, disability, veteran statusor another applicable basis in law.

AC A D E M I C C A L E N DA R | O G I

*Management in Science and Technology weekend and Distance Learning courses haveunique late registration and add/drop deadlines. Please refer to OGI’s quarterly courseschedule for the specific MST registration information.

A C A D E M I C C A L E N D A R 2 0 0 3 | 2 0 0 4

FALL QUARTER 2003

August 11 Registration begins for Fall Quarter

September 22-26 New student orientation week

September 28 Last day to register without late fees

September 29 Fall Quarter instruction begins

October 6 Student account balances due

October 24 Last day to add/drop classes

November 10 Registration begins for Winter Quarter

November 27-28 Thanksgiving holiday (no classes, OGI offices closed)

December 8-12 Final exams

December 25 Christmas holiday (OGI offices closed)

WINTER QUARTER 2004

November 10 Registration begins for Winter Quarter

January 1 New Year’s holiday (OGI offices closed)

January 4 Last day to register without late fees

January 5 Winter Quarter instruction begins

January 12 Student account balances due

January 19 Martin Luther King Jr.’s Birthday(no classes, OGI offices closed)

January 30 Last day to add/drop classes

February 9 Registration begins for Spring Quarter

February 16 President’s Day (no classes, OGI offices closed)

March 16-19 Final exams (Monday, March 15th will be a regular class dayto account for two Monday holidays earlier this quarter)

SPRING QUARTER 2004

February 9 Registration begins for Spring Quarter

March 28 Last day to register without late fees

March 29 Spring Quarter instruction begins

April 5 Student account balances due

April 23 Last day to add/drop classes

May 3 Registration begins for Summer Quarter

May 31 Memorial Day holiday (no classes, OGI offices closed)

June 6 Commencement

June 7-11 Final exams

SUMMER QUARTER 2004

May 3 Registration begins for Summer Quarter

June 20 Last day to register without late fees

June 21 Summer Quarter instruction begins

June 28 Student account balances due

July 5 Independence Day holiday (no classes, OGI offices closed)

July 16 Last day to add/drop classes

August 30 Final examsSeptember 3

September 6 Labor Day holiday (no classes, OGI offices closed)

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O G I | O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G

ABOUT THIS CATALOG

This catalog is as accurate as possible as ofSeptember 1, 2003. Information containedin the catalog may be changed during thecourse of any academic year, including butnot limited to changes in policies, fees,course offerings and requirements. Thisdocument should not be construed asforming the basis of a contract.

Additional student and academic policiesare listed in the OGI Student Handbooklocated at www.ogi.edu/students/studenthandbook.pdf.

OVERVIEW

A C A D E M I C D E P A R T M E N T S

The OGI School of Science & Engineeringhas four academic departments: BiomedicalEngineering (BME), Computer Science andEngineering (CSE), Environmental andBiomolecular Systems (EBS) andManagement in Science and Technology(MST). Students benefit from cross-disciplinary research and education asfaculty members take part in researchprojects outside their main department. Thisencourages the exchange of ideas acrossrelated research areas and provides thefullest use of the wide range ofinstrumentation available at the school.

D E G R E E P R O G R A M S

The OGI School of Science & Engineeringoffers M.S. and Ph.D. degrees in:

• Biochemistry and Molecular Biology• Biomedical Engineering

• Computer Science and Engineering

• Electrical Engineering

• Environmental Science and Engineering

• Management in Science and Technology

(M.S. degree only)

C E R T I F I C AT E P R O G R A M S

Certificate programs are available throughour Department of Management in Scienceand Technology in:

• Health Care Management • Management in Science and Technology

S T U D E N T S N O T S E E K I N G D E G R E E S

Any qualified student may take courses atOGI, in a part-time capacity, withoutenrolling in a degree program. Students maytake a full-time course load for only onequarter while waiting for a decisionregarding admission to a degree program.Up to 21 credits completed prior tomatriculation (enrollment in a degreeprogram), either taken at OGI or transferredfrom another institution, may be acceptedtoward degree requirements. Departmentalregulations may be more restrictive.

ACCREDITATION

Oregon Health & Science University and theOGI School of Science & Engineering areaccredited by the Commission on Colleges ofthe Northwest Association of Schools andColleges, an institutional accrediting bodyrecognized by the Council for HigherEducation Accreditation and/or the U.S.Department of Education. The address is: Commission on Colleges, NWASC,8060 165th Avenue NE, Suite 100,Redmond, WA 98052.

ADMISSIONS

A D M I S S I O N S R E Q U I R E M E N T S

Individual academic programs have specificrequirements in addition to those shownbelow. These are found in the departmentsections of the catalog.

• To enroll in any degree program at theOGI School, an applicant must have pre-viously earned a four-year bachelor’s, orequivalent, degree, although a studentmay be provisionally admitted prior tothat time. An international applicant witha three-year bachelor’s degree from a for-eign country should have his/heracademic credentials evaluated by anexternal evaluation company in order todetermine equivalency to a four-year,U.S. bachelor’s degree.

• The Graduate Record Examination (GRE) may be required. See Departmentsection for specific requirements.

• Official transcripts from each college oruniversity attended.

• Three original letters of recommendation.The letters should attest to the student’sability to succeed in a graduate program.Recommendation letters must be signedand preferably mailed directly from theauthor. If sent in by the student, therecommendation letter must be in a sealedenvelope. Alternatively, a recommendationform is available to use (see www.ogi.edu/grad-ed/pdf/recommendation_letter.pdf).

A D D I T I O N A L R E Q U I R E M E N T S F O RI N T E R N AT I O N A L S T U D E N T S

To be considered for admission to the OGI School for a full course of study,international students must also providedocumentation to show that they meet thefollowing requirements:

• Evidence of adequate financial resourcesto pay for their OGI education and theircost of living.

• Written TOEFL scores for all applicantswhose native language is not English,except for those who have earned a degreefrom a U.S. institution. The OGI School willaccept both the paper-based test and thecomputer-based test. Required scores forindividual programs are discussed in thedepartment sections of this catalog. Formore information on the TOEFL pleasevisit www.toefl.org.

A P P L I C AT I O N P R O C E D U R E S

For degree programs, the following items mustbe submitted:

• Completed OGI School of Science &Engineering application form.

• $65 nonrefundable application fee, whichis valid for one year and cannot be waivedor deferred.

• Official transcripts from each college oruniversity attended. The transcripts mustarrive in a sealed envelope and should bemailed directly to the Department ofGraduate Education (see address below).

• Three letters of recommendation.

• Official GRE scores (if applicable, seeDepartment). The institutional code forOGI is 4592.

• TOEFL scores (if applicable, see above).

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O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G | O G I

For certificate programs, the following items mustbe submitted:

• Completed OGI certificate program appli-cation form.

• $25 nonrefundable application fee, whichis valid for one year and cannot be waivedor deferred.

Completed applications, transcripts andother application materials should besent to:

Department of Graduate EducationOGI School of Science and Engineering20000 N.W. Walker RoadBeaverton, Oregon 97006-8921

Phone: 503 748-1382Toll-free: 800 685-2423Fax: 503 748-1285E-mail to: [email protected]

Due dates: Applications are considered on ayear-round basis. It is highly recommendedthat domestic students submit theirapplications 10 weeks prior to the quarterin which they would like to begin, 15 weeksfor international students. NOTE: priority isgiven in the admission and financial supportprocesses to those applications received byMarch 1.

Start date: The academic year formally beginsin September and students are encouragedto start the academic program at that time.However, mid-year admissions may be offer-ed. Generally, Ph.D. students are admittedfor Fall quarter and as full-time students.

S T U D E N T V I S A S

Information on student visas and otherimmigration services can be found on the Website for OGI’s Office of International Studentsand Scholars, www.ogi.edu/immigration.

TUIT ION AND FINANCES

T U I T I O N A N D F E E S

For the 2003-2004 academic year, tuitionfor full-time matriculated students (definedas nine or more credit hours per quarter) is$5,355. Part-time tuition for regular OGISchool of Science & Engineering courses is$595 per credit hour or audit unit. Pleasenote that there is no full-time tuition ratefor non-matriculated students, except whenan admission decision is pending. Tuition

includes OHSU’s activity fee, building fee,technology fee and incidental fee.

• Environmental and Biomolecular Systemsstudents pay tuition on an annual basis,which may be paid in full at the beginningof the year or in quarterly installments.

• Deposits. Upon admission as a master’sstudent, applicants in the Environmentaland Biomolecular Systems departmentmust deposit $100 to reserve a place inthe program. Deposits will be appliedtoward tuition and are nonrefundable.

H E A LT H I N S U R A N C E

Full-time, matriculated students enrolled inan OGI degree program are eligible forgroup student medical insurance throughthe school. In fact, eligible students musteither enroll in OGI’s insurance plan orprovide proof of other medical insurancecoverage. OGI pays the entire premium forfull-time Ph.D. students and two-thirds ofthe premium for full-time master’s students.Insurance for family members may bepurchased for an additional charge. Contactthe Graduate Education Department forcurrent premium rates.

F I N A N C I A L A I D

Entering full-time Ph.D. students may beeligible for financial support through acombination of tuition scholarships, OGIfellowships, named fellowships and graduateresearch assistantships. Offers of supportare initiated by the individual academicdepartments. Part-time Ph.D. students maybe eligible for some of the above. Partialtuition scholarships may be awarded by theschool or individual academic departmentsto entering full-time M.S. students. Noadditional application is required.

Subsidized and Unsubsidized FederalStafford Loans are available to eligiblestudents who are formally admitted to amaster’s or Ph.D. program at the OGI Schoolof Science & Engineering. Students must beenrolled for at least five credits eachquarter, and must be either U.S. citizens oreligible non-citizens. For applicationmaterials and additional information,contact the Financial Aid Office at OHSU at503 494-7800 or 800 775-5460 [email protected]. Information about

financial aid may also be found on OHSU’sWeb site, www.ohsu.edu/finaid/.

The “Free Application for Student Aid”(FAFSA) forms may be found atwww.fafsa.ed.gov/. Hard-copy forms areavailable from the OHSU Financial AidOffice. Use Federal School Code 004883when completing the FAFSA form.

COURSE NUMBERS

Effective Fall Quarter 2003, the OGI Schoolhas renumbered many of its courses tobetter align course numbers with theOregon Health & Science Universitystandard numbering scheme. To assist inrelating the new course numbers to coursesoffered in the past, a course number“crosswalk” is available online atwww.ogi.edu/schedule/crosswalk.shtml.Additionally, the following guidelines willhelp you understand the standardizedfeatures of our new numbering system.

5xx Graduate courses offered primarilyin support of master’s programs. May be used towards a doctoral program as appropriate.

6xx Graduate courses offered primarilyin support of doctoral programs. May be used towards a master’s program as appropriate.

Courses listed as 5xx/6xx are applicable toboth a master’s program as well as adoctoral program. Master’s and certificatestudents should register for the 5xx classand doctoral students should register for the6xx class when available.

The following standard course numbers may be included in each program’s courseofferings. Refer to the individual programfor further details.

501/601 Master’s Non-Thesis Research/PhDPre-qualifying Research

502/602 Independent Study

503/603 Master’s Thesis Research/PhD Dissertation Research

504/604 Internship

505/605 Reading and Conference

506/606 Special Topics Courses

507/607 Seminar

508/608 Workshop

509/609 Practicum7


ACADEMIC POLICIES

The following is a summary of selected OGISchool of Science & Engineering academicpolicies. A more comprehensive listing canbe found in the OGI School StudentHandbook at www.ogi.edu/students/studenthandbook.pdf.

A U D I T I N G A C O U R S E

OGI courses are offered for graded graduatecredit hours or ungraded audit units.Students may register to audit a course on aspace available basis. Students taking acourse for credit have priority over studentsauditing a course. Audits are recorded onthe student’s transcript at the discretion ofthe instructor, based upon a reasonableexpectation of attendance and minimalparticipation determined by the instructor.Audits are charged at the standard tuitionrate. Audit units do not count toward astudent’s full-time status. Instructors have final discretion over allowing audits of their classes and defining their academic expectations.

C O N F I D E N T I A L I T Y O F S T U D E N T R E C O R D S

With the passage of the Federal FamilyEducational Rights and Privacy Act (FERPA) of 1974, Oregon Health & ScienceUniversity adopted rules to govern thecollection, use and disclosure of studentrecords with the goal of ensuring theirprivacy. Students have the right to inspecttheir educational records that aremaintained by OGI/OHSU, the right to ahearing to challenge the contents of thoserecords when they allege the recordscontain misleading or inaccurateinformation, and the right to give theirwritten consent before their records arereleased to any person, agency ororganization other than OGI/OHSU officials and certain authorized federal and state authorities.

Directory Information. OGI/OHSU can releasecertain public domain information, known asdirectory information, unless a student filesa written request in the OGI GraduateEducation Department or the OHSURegistrar’s Office to restrict the disclosureof all directory information. The school

limits directory information to the student’sfull name, address(es) — including but notlimited to e-mail address, telephonenumber(s), major field of study, date(s) ofattendance, degrees and dates received, andthe fact of enrollment, including whether thestudent is enrolled full- or part-time. Theschool does not make this informationavailable to vendors.

Each student has the right to designatedirectory information as not being subject to release without his or her consent, except as otherwise permitted by law.The University Registrar’s Office shallprovide to each student a form entitled“Request to Restrict Directory Information”to be used by the student to designate that directory information may not bereleased without the student’s consent. Ifthe student does not submit the completedform by the date indicated, the Universitymay release directory informationpertaining to that student.

C O N T I N U O U S E N R O L L M E N T

A Ph.D. or M.S. student who has begun workon their dissertation or thesis must registerand pay for at least one credit hour ofresearch per quarter in order to maintainmatriculated status. If all requirements havenot been satisfied at the end of fourconsecutive academic quarters ofregistering for only one credit per quarter,or if an alternate plan of completion has notbeen approved by the department and theEducational Policy Committee, matriculatedstatus may be terminated. If the studentwishes to return to his/her program at alater date, it will be necessary to reapply foradmission. Continuous enrollment is notrequired of master’s students not pursuing athesis, nor of master’s or Ph.D. studentswho have not yet begun working on theirthesis or dissertation. However, allmatriculated students are required toregister for classes or to indicate temporaryinactive status by filing a TemporaryInactive Status form with the Department ofGraduate Education Department.

C R E D I T L O A D P E R Q U A R T E R

Twelve credits per quarter are considered anormal course load for full-time students,

although nine or more is considered full-time status. A student may not register formore than 12 credits in a quarter withouthis or her academic department’s approval.Up to 18 credits plus four audit units maybe taken with the approval of the student’sacademic department. Registering for morethan 18 credits plus four audit unitsrequires Educational Policy Committee(EPC) permission and will incur anadditional tuition cost.

G R A D I N G / S AT I S FA C T O R Y A C A D E M I C P R O G R E S S

Most OGI School courses are graded with aletter grade. Research work may be gradedwith either a Pass/No Pass or letter grade asdetermined by each academic department.

Transfer credits and Pass/No Pass gradesare not counted in students’ Grade PointAverages (GPAs). The GPA is a weightedaverage of all eligible credits and gradevalue points.

The following value point scale is employedat the OGI School:

A = 4.00 B = 3.00 C = 2.00

A- = 3.67 B- = 2.67 C- = 1.67

B+= 3.33 C+ = 2.33 F = 0.00

The grading system is defined as:

A = Excellent

B = Satisfactory

C = Below graduate standard

F = Failure

The following marks are also used:

AU = Audit, no credit

P = Satisfactory completion

NP = No credit, unsatisfactory

I = Incomplete

PI = Permanent Incomplete

W = Withdrawn (after the add/drop period)

Matriculated students must maintain acumulative GPA of 3.0. Failure to do so willresult in academic probation, and if the GPAis not improved, may lead to dismissal.

Incompletes. An Incomplete must be completedby the end of the quarter following thequarter in which the Incomplete wasawarded. In cases where the Incomplete is

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not completed, the instructor has the choiceof assigning a grade or converting theIncomplete into a Permanent Incomplete.The grade may be an “F” but instructorshave the option of assigning another grade ifthey feel quality and quantity of workaccomplished warrants it. If a studentwants an extension of this one quarterdeadline, the student may petition theEducational Policy Committee (EPC)showing the instructor’s support of theextension (a separate letter, e-mail orsignature on the petition will suffice). Thepetition should be specific, include a date bywhich the grade will be assigned andsubmitted to the Graduate EducationDepartment in writing.

L E A V E O F A B S E N C E

In special circumstances, leaves of absencefrom a graduate program may be allowed.A student considering a leave should firstdiscuss the issue with his/her advisor ordepartment academic coordinator. If thedepartment supports the leave of absence,the student then submits a petition to theschool’s Educational Policy Committee(EPC) for approval. International studentsshould consult with OGI’s Manager ofInternational Students and Scholars beforeconsidering a leave of absence.

M AT R I C U L AT E D V S . N O N - M AT R I C U L AT E D

A matriculated student is admitted andenrolled in a degree program. A non-matriculated student has not applied andbeen admitted to a degree program. Full-time matriculated students carry aminimum of nine credits per quarter. Auditunits do not count toward the nine-creditminimum. Academic departments mayrequire students to carry more than ninecredits per quarter as a condition ofeligibility for a stipend and/or tuitionscholarship. Part-time matriculatedstudents are admitted to a degree program,carry fewer than nine credits per quarterand pay tuition at the per-credit rate. Non-matriculated students pay tuition at the per-credit rate and must register forfewer than nine credits unless they haven application under review during that quarter.

M E A S L E S I M M U N I Z AT I O N P O L I C Y

Every full-time student who was born on orafter January 1, 1957, must provide the OGISchool with evidence of having received asufficient measles vaccination (Rubeola).Students are expected to submit acompleted Immunization Form when theyfirst register for classes at OGI. Studentswho do not provide the needed evidence onthis form will not be allowed to register forclasses for the second or succeedingquarters following their initial registration.The complete Measles Immunization Policyand Immunization Form are available fromthe of Graduate Education Department.

O N - S I T E ( R E S I D E N C Y ) P H . D . R E Q U I R E M E N T S

The OGI School has a two-year on-siteresidency requirement for Ph.D. programs.Full-time Ph.D. students usually meet thisrequirement by an on-site dissertationproject under the advisement of an OGIfaculty member. Part-time Ph.D. studentscan satisfy the first year of the on-siterequirement by attendance in classes on theOGI campus. Because part-time Ph.D.students, by definition, are not on campusfull time, the student’s academic departmentwill determine residency requirements forthe second year.

In exceptional circumstances (e.g.,dissertation topics requiring access tospecial facilities only available elsewhere),other arrangements may be proposed to thestudent’s academic department for writtenapproval. There is no on-site programrequirement for M.S. or certificateprograms at OGI.

P R E - M AT R I C U L AT I O N C R E D I T S A P P L I E DT O W A R D A D E G R E E

A maximum of 21 credits earned beforematriculation at OGI may be applied towarddegree requirements. This maximum mayinclude a combination of up to 12 (up to 18from Portland State University, theUniversity of Oregon and Oregon StateUniversity) transfer credits and creditstaken at OGI. Individual departmentalregulations may be more restrictive. Ifnecessary, a student may petition theEducational Policy Committee (EPC) for anexception to this policy.

R E G I S T R AT I O N

Any qualified student may take courses atthe OGI School of Science & Engineering, ina part-time capacity, without enrolling in adegree program. Non-matriculated studentsmay take a full-time course load for only onequarter, while waiting for a decisionregarding admission to a degree program.

Each quarter a class schedule is publishedwith the specific courses being offered withthe dates, times and locations. To access acurrent class schedule online, visitwww.ogi.edu/schedule/. All studentsattending a class must be registered for thatclass. A student will not earn a grade orcredits for the class if s/he is not registeredfor that class.

A student may register for classes online at www.ogi.edu/studentaccounts/. Onlineregistration is available seven days a weekduring established registration times.Alternatively, if a student prefers to registerin person, he or she may do so at the OGIGraduate Education Department.

T I M E L I M I T S T O C O M P L E T E A D E G R E E

An M.S. degree must be completed within seven years from the quarter ofmatriculation. A Ph.D. degree must becompleted within five years from the timethe student passes the Ph.D. qualifyingexam. Petitions for extensions to the time limit must first be approved by the department and then submitted to the Educational Policy Committee for final approval.

T R A N S C R I P T S

An official transcript is a formal, writtenrecord of a student’s OGI School of Science& Engineering educational experience. Allcourses taken at the OGI School and otherOHSU schools are recorded on it, as are allgrades and degrees earned while atOGI/OHSU. Requests for transcripts must bein writing with a signature, submitted eitherby fax, mail or in person to the OHSURegistrar’s office. Official transcripts are onspecial paper and have the official OHSUseal. Official transcripts cost $8 per copywhen ordered 48 hours in advance. Forquicker service or a faxed official transcript

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the fee is $10. A request form for anofficial transcript can be found atwww.ohsu.edu/registrar/transcriptreq.pdf.

T R A N S F E R C R E D I T

The OGI School of Science & Engineeringaccepts transfer credits from accreditedinstitutions that have not previously beenapplied toward another degree. Up to 12credits may be transferred to OGI (up to 18from Portland State University, University ofOregon and Oregon State University).Credits transferred to OGI must typicallycome from courses completed beforematriculation at OGI. The specific credits, if any, which will be accepted as transfercredits into OGI and applied toward degreerequirements are determined solely by theacademic department. Only courses with aB or better grade may be transferred to astudent’s OGI academic record. Transfercredit grades are not calculated in the OGIgrade point average. Credits graded on aPass/No Pass basis may not be transferred.

THE CAMPUS

G E O G R A P H I C S E T T I N G

The greater-Portland metropolitan area hasa population of about 1 million, nearly halfthe population of Oregon. It provides diversecultural activities including art, music,entertainment and sports. Portland has anextensive park system, including the largestwilderness park within the limits of any cityin the United States. The OGI School ofScience & Engineering is located 12 mileswest of downtown Portland, in an areaknown as the “Silicon Forest”. OGI’sneighbors include Intel’s largest researchand development facility, Tektronix, IBM,Hewlett-Packard, Mentor Graphics, Nike,Adidas and hundreds of other technology-based companies.

We are the newest school within OregonHealth & Science University (OHSU), joiningthe Schools of Medicine, Dentistry andNursing, which are located on the MarquamHill Campus in downtown Portland. OGI ispart of OHSU’s 300-acre West Campus,which also includes the NeurologicalSciences Institute, the Oregon NationalPrimate Research Center and the Vaccine

and Gene Therapy Institute. The OGIcampus consists of modern buildings thatprovide spacious laboratories, faculty andadministrative offices and a research library.

Providing a striking setting for collaborative,interdisciplinary research and education,the 80,000 square-foot Bronson CreekBuilding is the newest addition to OGI’scampus landscape. Acquired by OHSU in2002, the modern three-story brickstructure is the new home of the OGIadministration, members of the WestCampus Services team, and OGI’sdepartments of Biomedical Engineering andComputer Science and Engineering. Takingits name from a scenic stream nearby, thenew building serves as a physical focal pointof the entire West Campus.

L I B R A R Y

The Samuel L. Diack Library’s collectionincludes more than 21,000 monographictitles (including 4,000 electronic books incomputer science and business) and over500 current print and electronic journalsubscriptions. These support the teachingand research efforts at the OGI School byproviding texts, conference proceedings,reference materials, journals and researchmonographs in the subject areas ofcomputer science, electrical engineering,environmental science, biochemistry,molecular biology and management asrelated to science and technology. Theseresources are supplemented by the OHSULibrary’s holdings of more than 74,000monographs and 1,200 print and electronicjournal subscriptions. OGI students canaccess the OHSU Library’s electroniccollections from OGI and can use the printcollections by visiting the hill campus orrequesting materials be sent to OGI. A proxyserver allows access to the libraries’electronic collections from off campus.Materials unavailable from the OHSUlibraries are obtained on interlibrary loanfor faculty, staff and students at no cost. Anonline catalog, acquisitions and circulationsystem is in place. The library is a memberof two consortia that provide access to othercollege and university collections. The OrbisCascade Alliance allows for direct-requestborrowing from 26 institutions in Oregonand Washington, including the University of

Oregon, Oregon State University, PortlandState University and the six baccalaureateinstitutions in Washington, e.g., Universityof Washington and Washington StateUniversity. The PORTALS consortiumincludes libraries in the Portlandmetropolitan area such as Portland StateUniversity and Reed College.

The library’s public workstations not onlyprovide for searching the catalog and thelibrary’s databases but also provide entry toWeb resources for faculty, staff andstudents. The librarians will performsearches on the systems and databases thatare not available directly to students.Library orientation is part of theintroduction to OGI for new students, andclasses on library research methods areoffered throughout the year.

C O M P U T E R FA C I L I T I E S

The OGI School of Science & Engineering’scomputing environment gives members ofthe community access to a rich array oftechnologies and information resources.Many of these resources, including networks and telecommunications, are the responsibility of OHSU’s centralInformation Technology Group (ITG). Inaddition, many OGI departments andlaboratories maintain their own computingfacilities. Most OGI computers connect to aschool-wide local area network and to theInternet, providing convenient access to theWorld Wide Web. The local area network isconnected to the Internet through two high-speed data paths. In addition, it is alsoconnected to the Internet 2 (Internet2.edu)resources. The Internet 2 connection wasmade possible through an alliance of localacademic institutions.

H O U S I N G

Although the OGI School has no on-campushousing, it is situated amid a very largeresidential area. There are numerousapartment complexes, rental houses, busand light-rail lines and shopping areasnearby. The Graduate EducationDepartment maintains a list of localapartment buildings, available athttp://www.ogi.edu/students/ housing.shtml.Additionally, the Student Council has a Web site for current, new and prospective


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OGI students who are looking for housinginformation,roommates, etc. This serviceis found at http://cse.ogi.edu/council/forums.html.

S T U D E N T C O U N C I L

The OGI Student Council serves as theliaison between the student body and thefaculty and administration, and strives toimprove the quality of life for OGI students.Student representatives make themselvesavailable to students in their department toforward comments, ideas and concerns tothe Student Council and to promoteinvolvement in student-body activities.Representatives also disseminate pertinentinformation to other students in theirdepartments. As liaisons, members of theStudent Council represent the student bodyand student interests on a variety of schooltask forces and committees, including theEducational Policy Committee and theSafety Committee. Two Student Councilmembers are also representatives onOHSU’s All-Hill Council to represent OGI’sstudent body to the larger institution. Thisyear, one of OGI’s own students, DanGareau, is president of the All-Hill Council.

The Student Council sponsors andcoordinates at least one major social eventeach quarter, open to everyone at theschool. These events have included acoffeehouse with live music performed bypeople from the school community, anannual International Food and Cultural Fair,the fall orientation picnic and numerouseducational forums. Periodic skiing andrafting trips have also been arranged. Many student events throughout OHSU are open to all students at the four OHSUschools. More information on StudentCouncil is available on their Web site,http://cse.ogi.edu/concil or by e-mail [email protected].

P E T S O N C A M P U S

The school enjoys the presence of well-behaved pets on our campus and has adetailed pet policy that can be found atwww.ogi.edu/policies/pets.html. We considerit a privilege, and not a right, to bring petsonto the campus with certain restrictions.The rights of students, employees andvisitors of the school are primary to those of

pets and pet owners. Following is asummary of the policy: Anyone with amedical condition, fear of animals or relatedcondition is responsible for notifying the petowner and the owner is obligated to respectthe individual’s concerns and requests. Petsare not allowed in specified areas of thecampus, including eating areas, classrooms,laboratories, restrooms and the library; theymust be leashed outside a private office.Pets are allowed in private offices only

when the owner posts a notice alertingpeople to the presence of a pet; the pet doesnot bark, hiss or otherwise annoy others;the pet is caged, on a leash or behind a gatewhenever left unsupervised; and the owneraccommodates any individual who is notcomfortable with the pet. In addition,owners must clean up after their pet, petsmust be in good health with currentimmunizations, and animals in heat are notallowed. Students, faculty, staff or visitorswho violate the policy are notified that theirpet can no longer be brought to any part ofthe campus. Our policy does not apply toseeing/hearing or personal assistantanimals for individuals with disabilities.

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1

OVERVIEW OF OGIACADEMIC PROGRAMSOGI prepares its graduates tobecome leaders in knowledge-driven professions by providing a learning environment stronglyfocused on collaborative,interdisciplinary research. OGIstudents learn to reach acrosstraditional academic boundariesto seek the knowledge andresources needed to solveimportant technological problems.Our curriculum is organized tofacilitate this type of educationalexperience, where students maychoose from a number ofchallenging paths to reach theirgoal of a degree in a particulardiscipline. This program-focusedcurriculum encourages studentsto work closely with theiradvisors to select a course ofstudy that matches their specificneeds, strengths and careerobjectives. The following listingsummarizes OGI’s currentacademic programs and directsthe reader to the correspondingacademic department(s) offeringthat program.

O V E R V I E W O F O G I AC A D E M I C P R O G R A M S | O G I

BIOCHEMISTRY AND MOLECULAR BIOLOGY PROGRAMSee Department of Environmental and Biomolecular Systems, page 45

Doctor of Philosophy in Biochemistry and Molecular Biology

Master of Science in Biochemistry and Molecular Biology

BIOMEDICAL ENGINEERING PROGRAMSee Department of Biomedical Engineering, page 15

Doctor of Philosophy in Biomedical Engineering

Master of Science in Biomedical EngineeringBiomaterials TrackBiomedical Optics TrackNeuroengineering TrackSpeech and Language Engineering Track

COMPUTER SCIENCE AND ENGINEERING PROGRAMSee Department of Computer Science and Engineering, page 23

Doctor of Philosophy in Computer Science and Engineering

Master of Science in Computer Science and EngineeringAdaptive Systems TrackComputer Security TrackData-Intensive Systems TrackHuman-Computer Interfaces TrackNetworking TrackSoftware Engineering TrackSoftware Engineering for Industry Professionals TrackSpoken Language Systems TrackSystems Software Track

ELECTRICAL ENGINEERING PROGRAM

Doctor of Philosophy in Electrical EngineeringSee Department of Biomedical Engineering, page 15See Department of Computer Science and Engineering, page 23See Electrical Engineering Program in Semiconductor Engineering, page 41

Master of Science in Electrical Engineering

B I O M E D I C A L E N G I N E E R I N G C O N C E N T R AT I O N :

See Department of Biomedical Engineering, page 15

Biomaterials TrackBiomedical Optics TrackNeuroengineering TrackSpeech and Language Engineering Track

C O M P U T E R E N G I N E E R I N G A N D D E S I G N C O N C E N T R AT I O N :

See Department of Computer Science and Engineering, page 23

Computer Architecture TrackCircuit Design TrackSignal Processing Track

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OGI ’s annua l Open House prov ides studentswith a f r iend ly introduct ion to the school ’snumerous graduate degree opt ions .

14

O G I | O V E R V I E W O F O G I AC A D E M I C P R O G R A M S

Master of Science in Electrical Engineering (cont’d)

S E M I C O N D U C T O R E N G I N E E R I N G C O N C E N T R AT I O N :

See Electrical Engineering Program in Semiconductor Engineering, page 41

MEMS and Sensors TrackSemiconductor Devices and Circuits TrackSemiconductor Materials and Device Characterization TrackSemiconductor Processing and Materials Track

S I G N A L S A N D S Y S T E M S C O N C E N T R AT I O N :

See Department of Computer Science and Engineering, page 23

Signal and Image Processing TrackMachine Learning TrackSpeech Processing Track

ENVIRONMENTAL SCIENCE AND ENGINEERING PROGRAMSee Department of Environmental and Biomolecular Systems, page 45

Doctor of Philosophy in Environmental Science and Engineering

Master of Science in Environmental Science and EngineeringEnvironmental Information Technology TrackEnvironmental Health Systems Track

MANAGEMENT IN SCIENCE AND TECHNOLOGY PROGRAMSee Department of Management in Science and Technology, page 61

Master of Science in Management in Science and TechnologyManaging the Technology Company TrackManaging in the Software Industries Track

THE DEPARTMENT OF BIOMEDICAL

ENGINEERING integrates thedisciplines of engineering, basicbiomedical science and clinicalscience. Our graduate educationalprogram is designed to provide abroad education across thesedisciplines as well as knowledgeand in-depth research training ina specialty field. In our rigorouscurriculum, a quantitativeengineering approach is appliedto the study of medically relatedsystems and topics. Ourprogram prepares students forcareers in academia, industry,and government.

The OGI/OHSU Department of BiomedicalEngineering offers students both didacticeducation and nontraditional learning modes.Students can do advanced basic research inleading laboratories and they can doresearch projects that relate directly topatients, working under medical supervisionto develop and apply new technology in theclinics or in laboratories that study patients.

Four degrees are offered:

• Master of Science inBiomedical Engineering


• Master of Science inElectrical Engineering


• Doctor of Philosophy inBiomedical Engineering

• Doctor of Philosophy inElectrical Engineering

ACCREDITATION

The curriculum of the BiomedicalEngineering (BME) program has been

approved by the OHSU Faculty Senate. Fullaccreditation from the Oregon UniversitySystem and the Commission on Colleges ofthe Northwest Association of Schools andColleges is pending and is expected duringthe 2003–2004 academic year. Acceptedapplicants will be initially admitted to theElectrical Engineering program in theDepartment of Biomedical Engineering untilthe BME program is fully accredited, withthe understanding that they will bereassigned to the BME program once fullaccreditation is obtained.

ADMISSIONS REQUIREMENTS

In addition to the general requirements ofOGI, admission to the BME Departmentrequires the following:

• A B.S. degree or M.S. degree in physics,mathematics, engineering or otherquantitative science discipline is required.Highly qualified individuals with degreesin biology may be considered if they havedemonstrated adequate quantitative skills.

• The GRE test is required for both M.S.and Ph.D. applicants unless a waiver isspecifically authorized. Additionally, theTOEFL is required of all applicants whosenative language is not English. However,students who have earned a prior degreein the United States are exempt from thisrequirement. The preferred minimumTOEFL score is 620 paper/250 computer.

Suggested preparatory prerequisites tothe biomedical engineering programinclude: courses in anatomy/physiology,one year of college biology, organicchemistry, calculus through differentialequations and linear algebra, one year ofcalculus-based physics, basicprogramming skills in a higher-levellanguage and some experience withnumerical analysis software.

DEGREE REQUIREMENTS

The basic degree requirements for both theBiomedical Engineering and the ElectricalEngineering programs within the Departmentof Biomedical Engineering are the same. Thetwo programs are differentiated by thechosen electives, research project and/ordissertation topic.

Department ofBiomedical Engineering

www.bme.ogi.edu/

D E P A R T M E N T H E A D Stephen Hanson, Ph.D.

503 748-1435E-mail: [email protected]

A S S O C I AT E D E P A R T M E N T H E A D Wi l l iam Roberts , Ph.D.


D E P A R T M E N T A D M I N I S T R AT O RMelan ie Ersk ine


G E N E R A L I N Q U I R I E S


OGI is home to Oregon’s f i rst BME department ,which exp lores the use of technology to so lvemedica l and hea l thcare prob lems.

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B M E | B I O M E D I C A L E N G I N E E R I N G

During the first year, students will focuson the core courses (listed below)required for both the BiomedicalEngineering program and the ElectricalEngineering program. During the student’sfirst year, a Student Program Committee(SPC) composed of three to five facultymembers, including one from anotherdepartment, will be formed for eachstudent. This committee will work withthe student to advise a course of studyconsistent with both the student’sinterests and the need for broadknowledge in biomedical engineering and knowledge in the student’s chosen specialty.

M A S T E R O F S C I E N C E ( M . S . ) D E G R E E

The M.S. degree requires a total of 61credits, comprised of 28 credits of corecourses, 21 credits from elective coursesand 12 or more research credits on anoriginal research project. A writtensummary of the research project must besubmitted and defended in an oralpresentation. A student’s SPC shouldapprove the selection of elective coursesand research project prior to beginningthe class or project.

The M.S. degree may be earned as a non-thesis or thesis option. The non-thesisoption requires an original researchproject resulting in a written report. Thethesis option requires original thesisresearch resulting in a written thesis andoral defense.

D O C T O R O F P H I L O S O P H Y ( P H . D . ) D E G R E E

The Ph.D. degree requires 28 credits fromthe core courses, 27 credits from electivecourses and a minimum of 36 creditsfrom dissertation research. A Ph.D.student’s SPC committee may petition tohave some of the course requirementswaived if the student demonstratessufficient graduate-level knowledge ofrequired subjects.

A Ph.D. student is required to pass aPh.D. Qualifying Exam. The two-partexamination is normally taken 12 to 24months after initial enrollment. The firstpart tests the student’s knowledge of thebiological sciences, engineering andmathematics as they relate to the fieldof biomedical engineering. The second

part will test knowledge in the student’schosen specialty. After successfulcompletion of the Qualifying Exam, theSPC will work with the student todevelop a research plan and schedulefor the dissertation. The dissertationmust constitute significant, originalresearch resulting in a written document of publishable quality andmust be successfully defended in an oral presentation.

C O R E C U R R I C U L U M ( 2 8 c r e d i t s )

BME 507a Biomedical Engineering Seminar . . . 1 credit/607a (miinimum 3 terms required)CSE 569/669 Scholarship Skills . . . . . . . . . . 3 creditsMINF 515 Ethical, Legal, and Social . . . . . 2 credits

Issues in Medical Informatics

L I F E S C I E N C E S

BME 511/611 Biochemistry for . . . . . . . . . . . . 3 creditsBiolomedical Engineering

NEUS 627 Systems Neuroscience . . . . . . . 5 credits

M AT H E M AT I C S A N D S TAT I S T I C S

MATH 510/610 Multivariate Calculus and . . . . . 3 creditsDifferential Equations

MATH 517/617 Probability and Statistics . . . . . . 3 credits

S I G N A L S A N D S Y S T E M S

BME 513/613 Biomedical Signal Processing I . . 3 creditsBME 514/614 Biomedical Instrumentation . . . 3 credits

– Signals and Sensors

The following specialized tracks are availableto students or they may consult with theirSPC to define a custom program.

B I O M E D I C A L O P T I C S T R A C K ( s u g g e s t e d e l e c t i v e s )

BME 522/622 Biomedical Optics I: . . . . . . . . . 3 creditsTissue Optics

BME 523/623 Biomedical Optics II: . . . . . . . . . 3 creditsLaser-Tissue Interactions

BME 524/624 Biomedical Optics III: . . . . . . . . 3 creditsEngineering Design

BME 525/625 Optical Nondestructive . . . . . . . 4 creditsEvaluation

BME 526/626 Computational Approaches . . . . 3 creditsto Laser Interaction withBiological Tissues

BME 527/627 Computational Approaches . . . . 3 creditsto Light Transport withBiological Tissues

BME 528/628 Physical and Geometrical Optics . . 3 creditsEE 525/625 Introduction to . . . . . . . . . . . . . 4 credits

Electromagnetics forModern Applications

EE 526/626 Electromagnetics for . . . . . . . . . 4 creditsModern Applications II

EE 582/682 Introduction to Digital . . . . . . . . 3 creditsSignal Processing

EE 584/684 Introduction to . . . . . . . . . . . . . 3 creditsImage Processing

Other appropriate Biomedical Optics courses as approved by your SPC

B I O M AT E R I A L S T R A C K ( s u g g e s t e d e l e c t i v e s )

BME 507b Current Topics in . . . . . . . . . . . . 1 credit/607b Tissue EngineeringBME 525/625 Optical Nondestructive . . . . . . . 3 credits

EvaluationBME 541/641 Biomaterials I . . . . . . . . . . . . . . 3 creditsBME 542/642 Biomaterials II . . . . . . . . . . . . . 3 creditsBME 543/643 Advanced Tissue . . . . . . . . . . . . 3 credits

Engineering TechniquesBME 544/644 Advanced Biomaterials . . . . . . . 3 creditsBME 545/645 Biocompatibility — . . . . . . . . . . 3 credits

Host-Implant InteractionsEE 511/611 Analytical Scanning . . . . . . . . . . 3 credits

Electron MicroscopyEE 512/612 Focused Ion Beam Technology . . 3 creditsEE 513/613 Transmission Electron . . . . . . . .3 credits

MicroscopyME 555 (PSU) Finite Element Modeling . . . . . . 4 credits

and Analysis (PortlandState University)

Other appropriate Biomaterials courses as approved byyour SPC

N E U R O E N G I N E E R I N G T R A C K ( s u g g e s t e d e l e c t i v e s )

BME 507c Readings in Neurology . . . . . . . . 1 credit/607c and NeuroscienceBME 561/661 Neuronal Control Systems . . . . . 3 creditsBME 562/662 Motor Control . . . . . . . . . . . . . 3 creditsBME 563/663 Mathematical and . . . . . . . . . .3 credits

Computational Modeling ofNeuronal Systems

BME 564/664 Methods in Neuromedicine . . . . 3 creditsBME 565/665 Introduction to . . . . . . . . . . . . . 3 credits

Computational NeurophysiologyBME 566/666 Biomedical Signal Processing II . . 3 creditsBME 567/667 Visual Sensory Systems . . . . . . 3 creditsBME 568/668 Auditory and Visual Processing . 3 credits

by Human and MachineEE 582/682 Introduction to Digital . . . . . . . . 3 credits

Signal Processing EE 584/684 Introduction to Image . . . . . . . 3 credits

ProcessingNEUS 623 Introduction to Neuroanatomy . . 3 creditsNEUS 624 Cellular Neurophysiology . . . . . . 4 creditsOther appropriate Neuroengineering courses as approved by your SPC

S P E E C H A N D L A N G U A G E E N G I N E E R I N G T R A C K

T R A C K C O R E (select 9 credits from the following)BME 568/668 Auditory and Visual Processing . . 3 credits

by Human and Machine BME 572/672 Speech Synthesis . . . . . . . . . . . 3 creditsCSE 551/651 Structure of Spoken Language . . 3 creditsCSE 552/652 Hidden Markov Models for . . . . . 3 credits

Speech Recognition

T R A C K E L E C T I V E S

(select 12 credits for M.S. and 18 credits for Ph.D.)BME 571/671 Speech Systems . . . . . . . . . . . . 3 creditsCSE 540 /640 Neural Network Algorithms . . . . . 3 credits

and ArchitecturesCSE 547/647 Statistical Pattern Recognition . . 3 creditsCSE 550/650 Spoken Language Systems . . . . 3 creditsCSE 561/661 Dialogue . . . . . . . . . . . . . . . . . . 3 creditsCSE 562/662 Natural Language Processing . . . 3 creditsEE 580/680 Linear Systems . . . . . . . . . . . . 3 creditsEE 581/681 Intro to Signals, Systems, . . . . . 3 credits

and Information Processing

B I O M E D I C A L E N G I N E E R I N G | B M E

EE 582/682 Introduction to Digital . . . . . . . . 3 creditsSignal Processing

EE 586/686 Adaptive and Statistical . . . . . . . 3 creditsSignal Processing

MATH 519/619 Engineering Optimization . . . . . . 3 creditsSySc 545 (PSU) Information Theory . . . . . . . . . . 4 credits

(Portland State University)Other appropriate Spoken Language Engineering courses as approved by your SPC

O T H E R E L E C T I V E S – A L L T R A C K S

BME 502/602 Independent StudyBME 504/604 Professional InternshipBME 505/605 Readings in Biomedical . . . . . . . . 1 credit

EngineeringBME 506/606 Special Topics CoursesBME 566/666 Biomedical Signal Processing II . . 3 creditsBME 581/681 Fourier Analysis . . . . . . . . . . . . 3 credits

RESEARCH PROGRAMS

Biomedical Optics Research in biomedical optics is focused on thedevelopment of uses for lasers and light inmedicine and biology. Examples of ongoingapplications in this well-established researchprogram include the use of lasers in clinicaldiagnosis, nondestructive evaluation of tissues,optical imaging of disease, and light-activatedchemotherapy for cancer. Facilities include thosefor both clinical application and basic research.Holmes, Jacques, Kirkpatrick, Prahl, Song

Cardiovascular Bioengineering Cardiovascular bioengineering (CBE) is a growingarea of interest at OHSU. The CBE program willencompass major areas of interest using engineer-ing tools for investigation. These areas will includecardiac and vessel mechanics, computational fluiddynamics, electrocardiography and electrical signalprocessing, 4-D embryo modeling, functionalmagnetic resonance imaging, ultrasound tech-nology, cellular mechano-transduction and geneexpression, blood-material interactions, thromb-osis, laser thrombolysis, and hemostasis. Baptista,Chugh, Ellenby, Faber, Goldstein, Gregory, Hanson,McNames, Sahn, Thong, Thornburg

Genetic Engineering Genetic engineering is a branch of biology thatinvolves the manipulation and modification of DNA,in particular the introduction of a foreign DNAfragment into a DNA sequence. DNA is theblueprint for the individuality of an organism. Theorganism relies upon the information stored in itsDNA for the management of every biochemicalprocess. The life, growth, and unique features ofthe organism depend on its DNA. Genes are thesegments of DNA that are associated with specificfeatures or functions of an organism. Duvoisin,Frueh, Harrington, Reddy

Imaging Research Imaging technology is now central to the diagnosisand treatment of nearly all diseases and is criticalfor drug development, evaluation of treatmenteffects as basic science on the biology of normaland abnormal tissue function. Core faculty will be

hired in biomedical engineering with research fociin medical imaging. In addition, a wide range offaculty across the OHSU campus use imaging intheir basic and clinical research. Thus, studentswill have an opportunity to implement imagingengineering research in a variety of biomedicalresearch settings. Particular areas ofconcentration at OHSU are Neuroimaging, Cardiac Imaging and Cancer Imaging. Anderson,Bebo, Beer, Buist, Burnell, Cowley, Fletcher,Hitzeman, Janowsky, Lutsep, Neuwelt, Pavel,Quinn, Raber, Rosenbaum, Sahn, Spencer,Szumowski, Wang

Informatics Research Informatics activities at OHSU are wide ranging;currently they include: managing and analyzinggene expression data; programs in medicalinformatics and outcomes research; basic researchin databases; networks and embedded systems; andtechniques for 3-D visualization. The BMEdepartment serves as a focus for developingtechnologies that leverages this expertise, in suchareas as computational bioengineering, medicalvisualization, integration of genomic and medicalinformation, home health networking and hybridinstrumentation. BME will also contribute toexisting curricula in bioinformatics. Baptista,Cohen, Cowan, Delcambre, Dubay, Wu Chang Feng,Wu Chi Feng, Hersh, Hook, Hosom, Jones, Kiebertz,Kramer, Launchbury, Logan, Pentacost, Price,Retzer, Roberts, Searles, Sheard, Walpole

Neuroengineering Research Basic neuroscience research, clinical neurologyand neurosurgery are strong programs withinOHSU. The existence of a department of biomedicalengineering in this center of neuroscience researchand clinical medicine creates rich opportunities forbiomedical engineers. They can work withneuroscientists and clinicians to apply emergingscientific knowledge in the development ofprocesses and devices needed for the diagnosis,assessment and treatment of neurologicaldisorders and diseases. Ongoing researchopportunities range from very basic molecularbiophysics and modeling to systems analysis todrug delivery systems, neuroprosthetics, andneurosurgical devices. Baumann, Burchiel, Cohen,Cordo, Hammerstrom, Hayes, Hermansky, Hinds,Hitzeman, Hosom, Huber, Jabri, Larsson,Macpherson, Neuwelt, Nuttall, Pavel, Peterka,P. Roberts, W. Roberts, Song, Welsh, Westbrook

Point-of-Care Biomedical Engineering Research in this area is focused on thedevelopment of health care delivery systemssuitable for use in homes, assisted-living facilitiesand other residential settings. Application areasinclude processes and technologies for themonitoring, evaluation and treatment of peopledisabled by aging, chronic disease, or disability.Research challenges include the development ofunobtrusive sensors, wireless communication ofmulti-rate signals, processing and fusion of signalsfrom multitudes of noisy sensors, and ubiquitousperceptual interfaces. Fried-Oken, Hammerstrom,Hayes, Hermansky, Horak, Huber, Krohn, Maier,Pavel, Peterka

R e h a b i l i t a t i o n a n d B i o m e c h a n i c s R e s e a r c h Many diseases and disorders of muscle, bone andthe nervous system result in treatment,immobilization, healing and then rehabilitation.Basic and applied research in the Department ofBiomedical Engineering focuses on the normal andabnormal control of movement and musculoskeletalbiology. This research is multidisciplinary andhighly collaborative with both clinical and basicscience departments at OHSU. Currently activeresearch by our faculty has resulted in thedevelopment of novel therapeutic devices andprocedures that are tested on patient groupsprovided by collaborating clinicians. Cordo, Hart,Herzberg, Horak, Jabri, Klein, Macpherson, Nutt,Orwoll, Peterka, P. Roberts, Shea, Welsh

Tissue Engineering and Biomaterials ResearchResearch in tissue engineering and biomaterials isrepresented by a multi-disciplinary group ofmaterials scientists, biomedical and tissueengineers, chemists, physiologists, dentists andphysicians. Faculty projects include the followingresearch: physical biomechanics of dental andorthopedic implants, computational biomechanicsof dental implants, dental restorations, dissolutionand volatilization from dental alloys; non-invasiveand non-destructive evaluation of engineeredtissues; laser welding of tissues; natural, protein-based biomaterials; polymer mechanics;micromechanics of biocomposites; thermal analysis;tribology; collagen and other biocomposites; skinscaffolds; bone healing; blood vessel substitutes,vascular grafts, and endovascular stents.Descriptions of specific projects are linked to thetopics listed below. Dawson, Ferracane, Gregory,Hanson, Herzberg, Hinds, Kirkpatrick, McCarthy,Sakaguchi, Shea, Winn

FACILIT IESThe Department of Biomedical Engineeringoccupies approximately 25,000 square feet on thethird floor of the Bronson Creek building, a modernbuilding on the OHSU/OGI West Campus, andadditional space in the Murdock and Vollumbuildings and the Oregon National PrimateResearch Center on that campus. The department’sspace accommodates “wet” labs with biosafetyhoods as well as other lab space. The departmentis equipped with a modern computer networksystem, serviced by OGI’s and OHSU’s InformationTechnology Groups. Most student work stations areequipped with high-speed network connections.Special facilities, such as a simulated residentialhealth care facility are also available. Videoteleconferencing facilities are available to allowstudents and faculty to interact with others atseminars and other events on OHSU’s MarquamHill Campus. Some students’ research projects are carried out inlaboratories in other OHSU departments or in localindustries. Available facilities in which studentsmay do research projects include: Oregon MedicalLaser Center, Advanced Imaging Center, OregonHearing Research Center, Neurological SciencesInstitute, and Heart Research Center, as well asthe many labs in the basic science departmentsand institutes of OHSU.

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S T E P H E N H A N S O N

Professor and Department HeadPh.D., Chemical EngineeringUniversity of Washington, [email protected]

R E S E A R C H I N T E R E S T S

Thrombosis and vascular healingresponses are being evaluated inanimal models to identify keyhemostatic mechanisms, bloodcomponent interactions withnatural and synthetic surfaces andthe effects of blood-flowphenomena. Our ultimate goalsare to develop more effective anti-thrombotic and anti-arteriosclerotic drug therapies,and to improve the performance ofprosthetic cardiovascular devices.

R E P R E S E N TAT I V E P U B L I C AT I O N SHanson, S.R., “Blood Coagulation and

Blood-Materials Interactions,” inBiomaterials Science, 2nd Edition(Ratner, B.D., Hoffman, A.S., Schoen,F.J., Lemons, J.E., Eds.), AcademicPress, New York, in press, 2003.

Gruber, A., Cantwell, A., DiCera,E., Hanson, S.R., “The W215A/E217AMutant of Thrombin Shows Safeand Potent Anticoagulant andAntithrombotic Effects in vivo. J BiolChem 277(31), 27581–4, 2002.

Verheye, S., Markou, C.P., Salame,M.Y., Wan, B., King, S.B., Robinson,K.A., Chronos, N.A., Hanson, S.R.,“Reduced Thrombus Formation byHyaluronic Acid Coating ofEndovascular Devices,” ArteriosclerThromb Vasc Biol 20, 1168–1172,2000.

Markou, C.P., Lutostansky, E.M., Ku,D.N., Hanson, S.R., “A Novel Method forEfficient Drug Delivery,” Ann BiomedEng 26, 502–511, 1998.

Hanson, S.R. and Sakariassen, K.S.,“Blood Flow and Antithrombotic DrugEffects,” Am Heart Journal 135,S132–S145, 1998.

W I L L I A M J . R O B E R T S

Assistant Professor andAssociate Department HeadPh.D., PhysiologyUniversity of Minnesota, [email protected]


Neuroengineering. Neuronalmechanisms of pain. Influence ofsympathetic nervous system onsensory functions. Electricalstimulation for pain relief.Motor systems.

R E P R E S E N TAT I V E P U B L I C AT I O N S Bon, K., Wilson, S.G., Mogil, J.S.,

Roberts, W.J., “Genetic Evidence forthe Correlation of Deep Dorsal Hornfos Protein Immunoreactivity withTonic Formalin Pain Behavior Journalof Pain. 3,181–189, 2002.

Gillette, R.G., Kramis, R.C., Roberts,W.J., “Suppression of Activity in SpinalNocireceptive ‘Low Back’ Neuronsby Paravertebral Somatic Stimuliin the Cat,” Neurosci Lett. 1998 Jan23;241(1), 45–8.

Kramis, R.C., Roberts, W.J., Gillette,R.G., “Non-nociceptive Aspects ofPersistent Musculoskeletal Pain,”J Orthop Sports Phys Ther. 1996Oct;24(4), 255–67.

Kramis, R.C., Roberts, W.J., Gillette,R.G., “Post-sympathectomy Neuralgia:Hypotheses on Peripheral and CentralNeuronal Mechanisms,” Pain, 1996Jan;64(1), 1–9.

Fine, P.G., Roberts, W.J., Gillette,R.G., Child, T.R., “Slowly DevelopingPlacebo Responses Confound Tests ofIntravenous Phentolamine to DetermineMechanisms Underlying IdiopathicChronic Low Back Pain,” Pain, 1994Feb;56(2), 235–42.

Gillette, R.G., Kramis, R.C., Roberts,W.J., “Sympathetic Activation of CatSpinal Neurons Responsive to NoxiousStimulation of Deep Tissues in the LowBack,” Pain, 1994 Jan;56(1), 31–42.

TA M A R A H AY E S

Assistant ProfessorPh.D., Behavioral NeuroscienceUniversity of Pittsburgh, [email protected]


Algorithms and technologies forimproving speech and languageprocessing in patient and elderlypopulations (augmentativecommunication). Attentionalprocesses in human languageprocessing. Adaptive computerinterfaces for improving humantask performance (augmentedcognition). Unobtrusive monitoringtechnologies for remote care ofelderly populations (point-of-careengineering).

R E P R E S E N TAT I V E P U B L I C AT I O N SA.M. Adami, T. L. Hayes, and

M. Pavel, “Unobtrusive Monitoringof Sleep Patterns,” 25th AnnualInternational Conference of the IEEEEngineering In Medicine And BiologySociety, Cancun, September 2003.

T.L. Hayes, K. Li, and M. Pavel,“Augmenting Search Performance byImproving Attention Allocation,”Bio-Bionics: DARPA AugmentingCognition Workshop, Kona, Hawaii,January 2003.

T.L. Hayes, “Harness the Internet forTelemedicine Programs,” invitedworkshop at Develop and MaintainProfitable Telemedicine Programs,Conference, Boston, MA, April 1996.

T.L. Hayes and D.A. Lewis,“Anatomical Specialization of theAnterior Motor Speech Area:Hemispheric Differences inMagnopyramidal Neurons,” Brain andLanguage 49, 289–308, 1995.

T.L. Hayes and D.A. Lewis,“Hemispheric Differences in Layer IIIPyramidal Neurons of the AnteriorLanguage Areas,” Archives of Neurology50, 501–505, 1993.

M O N I C A T H A C K E R H I N D S

Assistant Professor Ph.D., Mechanical EngineeringJohns Hopkins University, [email protected]


Relationship between fluiddynamics and extracellular matrixproduction by cells, vasculartissue engineering, role ofmechanical stimulation in tissueengineered constructs, elastinbased biomaterials.

R E P R E S E N TAT I V E P U B L I C AT I O N S M.T. Hinds, D.W. Courtman, T. Goodell,

M. Kwong, H. Brant-Zawadzki, A.Burke, B. Fox, and K.W. Gregory,“Development of a Xenogenic Elastin-based Biomaterial: Calcification andInflammatory Effects of AluminumChloride Treatment,” Journal ofBiomedical Materials Research(accepted), 2003.

S.J. Kirkpatrick, M.T. Hinds, andD.D. Duncan, “Acousto-opticalCharacterization of the ViscoelasticNature of a Nuchal Elastin TissueScaffold,” Tiss. Eng. (accepted), 2003.

M.T. Hinds and S.J. Kirkpatrick,“Material Properties of EngineeredTissues Evaluated with NondestructiveMethods,” Proceedings SPIE4617:275–283, 2002.

M. Kajitani, Y. Wadia, M.T. Hinds,J. Teach, K.R. Swartz, and K.W.Gregory, “Successful Repair ofEsophageal Injury Using an Elastin-based Biomaterial Patch,” Asaio J,47(4), 342–5, 2001.

M.T. Hinds, Y.J. Park, S.A. Jones,D.P. Giddens, and B.R. Alevriadou,“Local Hemodynamics Affect MonocyticCell Adhesion to a Three-DimensionalFlow Model Coated with E-selectin,”Journal of Biomechanical Engineering,34(1), 95-103, 2001.

M. Kajitani, Y. Wadia, H. Xie, M. Hinds,S. Shalaby, K. Schwartz, and K.W.Gregory, “Use of New Elastin Patch andGlue,” ASAIO J, 46(4), 409–414, 2000.

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FACULTY

J O H N - P A U L H O S O M

Assistant ProfessorPh.D., Computer Scienceand Engineering,Oregon Graduate Institute ofScience & Technology, [email protected]


Automatic speech recognition(ASR). Time alignment ofphonemes. Acoustic-phoneticanalysis of speech. Assistivetechnology.

R E P R E S E N TAT I V E P U B L I C AT I O N S J. P. Hosom, “Automatic Speech

Recognition,” in Encyclopedia ofInformation Systems, H. Bidgoli (ed.).,vol. 4, pp. 155-169, Academic Press,San Francisco, 2003 (invited chapter).

J. P. Hosom, A. B. Kain, T. Mishra,J. P. H. van Santen, M. Fried-Okenand J. Staehely, “Intelligibility ofModifications to Dysarthric Speech,”The 2003 International Conferenceon Acoustics, Speech, and SignalProcessing (ICASSP 2003), Hong Kong,April 2003.

J. P. Hosom, “Automatic PhonemeAlignment Based on Acoustic-PhoneticModeling.” The 2002 InternationalConference on Spoken LanguageProcessing (ICSLP 2002), Boulder, Co.,vol. I, pp. 357–360, September 2002.

J.P. Hosom and R.A. Cole, “BurstDetection Based on Measurements ofIntensity Discrimination.” The 2000International Conference on SpokenLanguage Processing (ICSLP 2000),Beijing, vol. IV, pp. 564-567, Oct. 2000.

J.P. Hosom, R.A. Cole and P. Cosi,“Improvements in Neural-NetworkTraining and Search Techniques forContinuous Digit Recognition,”Australian Journal of IntelligentInformation Processing Systems, 5(4),277–284, Summer 1999.

J.P. Hosom and M.Yamaguchi,“Proposal and Evaluation of a Methodfor Accurate Analysis of Glottal SourceParameters,” The Institute ofElectronics, Information andCommunication Engineers (IEICE)Transactions on Information andSystems, E77-D (10), pp. 1130-1141,October 1994.

S TA N L E Y J . H U B E R

Assistant ProfessorM.D., School of MedicineOregon Health &Science University, [email protected]


Blood chemistry by ophthalmicspectroscopy; instrumentation;neuroengineering; point-of-carebiomedical engineering

R E P R E S E N TAT I V E P U B L I C AT I O N S S.J. Huber, “Photic Pulse Stimulator

for ERG Analysis,” Sloan Foundation

S.J. Huber, “BattlefieldManagement of Ocular Injuries,”ICMM, Interlochen, Switzerland

S.J. Huber, “Biological Effects ofSpace Radiation Fields,” ClassifiedReport, USAF MOL Project

S.J. Huber, “Triage andManagement of Ocular Injuries,”CIOMR, Brussels, Belgium

S.J. Huber, “Hazards of MilitaryLasers,” CIOMR, Brussels, Belgium

S.J. Huber, “Radiation Induced EyeInjuries,” CIOMR, Brussels, Belgium

S.J. Huber, “TacStar, A New Conceptin Military Medical Training,” CIOMR,Wurzburg, Germany

M A R W A N J A B R I

Gordon and Betty MooreProfessor of MicroelectronicsPh.D., Electrical EngineeringUniversity of Sydney, [email protected]


Artificial intelligence andintelligent signal processing. Theunderstanding of the principles bywhich humans and/or otherorganisms perceive theenvironment, process sensorysignals, reason, make decisionsand learn. The development andapplication of biologically inspiredinformation engineering. Thedesign of integrated systems forintelligent signal processing.

R E P R E S E N TAT I V E P U B L I C AT I O N S O. J.-M. D. Coenen,.M.P. Arnold,

T.J. Sejnowski and M.A. Jabri, “ParallelFiber Coding in the Cerebellum forLifelong Learning,” Autonomous Robots,11(3), 291–7, Kluwer AcademicPublishers, The Netherlands, 2001.

B. Zhang, R. Coggins, M.A. Jabri, D.D. Dersch, and B. Flower, “MultiresolutionForecasting for Futures Trading UsingWavelet Decompositions,” IEEETransactions on Neural Networks,12(4), 767–775, July 2001.

M.A. Jabri and R. Coggins,“Micro Power Adaptive Circuits forImplantable Devices,” in Low Power-Low Voltage Circuits and System,E. Sanchez-Sinencio and AndreasAndreou, eds., IEEE Press, pp. 500-518, 1999.

R. Coggins and M.A. Jabri, “A LowComplexity Intracardiac ElectrogramCompression Algorithm,” IEEETransactions on Biomedical Engineering,46(1), 82–91, January 1999.

J. Raymond, W. Wang and M.A. Jabri,“A Computational Model of the AuditoryPathway to the Superior Colliculus,” inBrain-like Computation and IntelligentInformation Systems, Shun-ichi Amariand Nikola Kasabov, eds., SpringerVerlag, pp. 81-104, 1998.

X.Q. Li and M.A. Jabri, “MachineLearning-based VLSI Cells ShapeFunction Estimation,” IEEETransactions on CAD for IntegratedCircuits and Systems, 17(7), 613–623,1998.

S T E V E N L . J A C Q U E S

ProfessorPh.D., Biophysics andMedical PhysicsUniversity of California,Berkeley, [email protected]


Biomedical optics and laser-tissueinteractions. Development ofdiagnostic and therapeutic devicesfor medicine and biology usingoptical technologies.

R E P R E S E N TAT I V E P U B L I C AT I O N SS.L. Jacques, J.C. Ramella-Roman and

K. Lee, “Imaging Skin Pathology withPolarized Light,” J. Biomed. Opt., inpress, 2002.

J.A. Viator, G. Au, G. Paltauf,S.L. Jacques, S.A. Prahl, H. Ren,Z. Chen and J.S. Nelson, “ClinicalTesting of a Photoacoustic Probe forPort Wine Stain Depth Determination,”Lasers Surg. Med., 30 (2), 141–8,2002.

S.L. Jacques, N. Ramanujam,G. Vishnoi, R. Choe and B. Chance,“Modeling Photon Transport inTransabdominal Fetal Oximetry,”J. Biomed. Optics, 5, 277–282, 2000.

V.V. Vaidyanathan, S. Rastegar,T.W. Fossum, P. Flores, E.W. van derBreggan, N.G. Egger, S.L. Jacquesand M. Motamedi, “A Study ofAminolevulenic Acid-inducedProtoporphyrin IX FluorescenceKinetics in the Canine Oral Cavity,”Lasers Surg. Med., 26, 405–414, 2000.

S.L. Jacques, J. Roman and K. Lee,“Imaging Superficial Tissues withPolarized Light,” Lasers Surg. Med.,26, 119–129, 2000.

L.V. Wang, and S.L. Jacques, “Sourceof Error in Calculation of OpticalDiffuse Reflectance from Turbid MediaUsing Diffusion Theory,” Comput.Methods Programs Biomed., 61(3),163–70, 2000.

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S E A N J . K I R K P AT R I C K

Associate ProfessorPh.D., BiomechanicsUnversity of Miami, [email protected]


Development and application ofcoherent light techniques toaddress issues in biomaterialsscience and tissue mechanics.Laser speckle techniques are ofparticular interest. Recentinvestigations have focused on theevaluation of the micromechanicalbehavior of vascular,dermatological and skeletal tissuesusing novel laser speckle strainmeasurement methods. Otherinterests include experimentalinvestigations into themicromechanics of syntheticbiomaterials used to replace oraugment damaged or pathologicaltissue.

R E P R E S E N TAT I V E P U B L I C AT I O N S S.J. Kirkpatrick and D.D. Duncan,

“Acousto-optical Assessment of SkinViscoelasticity,” Proc. SPIE, 2003(in press).

S.J. Kirkpatrick, M.T. Hinds, andD.D. Duncan, “Acousto-opticalCharacterization of the ViscoelasticNature of a Nuchal Elastin TissueScaffold,” Tissue Engineering(accepted), 2002.

S.J. Kirkpatrick and D.D. Duncan,“Optical Assessment of TissueMechanics,” in Optical BiomedicalDiagnostics, V.V. Tuchin, ed., SPIEPress, Bellingham, WA, 2002.

S.J. Kirkpatrick, D.A. Baker andD.D. Duncan, “Speckle Tracking ofLow-frequency Surface Acoustic Wavesfor Mechanical Characterization ofTissues,” Proceedings SPIE, p. 461,2002.

S.J. Kirkpatrick, M.T. Hinds andD.D. Duncan, “Laser Speckle Methodfor Measurement of Cell and Cell SheetMechanics,” Proceedings SPIE,p. 4617, 2002.

M.T. Hinds and S.J. Kirkpatrick,“Material Properties of EngineeredTissues Evaluated with NondestructiveMethods,” Proceedings SPIE,p. 4617, 2002.

J A C K M C C A R T H Y

Assistant ProfessorPh.D., Materials Scienceand EngineeringOregon Graduate Institute ofScience & Technology, [email protected]


Ongoing research includesmultibeam electronnanolithography, control ofnanoscale hillocks in sputtered Aumetallizations for use in GaAsdevices and the fabrication anddevelopment of sensor-chiphybrids for monitoring theelectrical activity of the heart,pathogens, organic and inorganicgases in the environment. Thisresearch requires fabrication andcharacterization on the micron,sub-micron and nano-scales. Theprimary fabrication tool in thisresearch is the focused ion beamworkstation (FIB), which permitsseeing, machining andmicroforming on the micron andnanoscales. The characterizationis provided by scanning andtransmission electron microscopy(SEM, TEM) and atomic forcemicroscopy (AFM). FIB fabricationtechniques and SEM, AFM andTEM characterization and in-situexperimentation feedback are usedto accelerate research onnanofabrication, biomimeticsensors, biomaterials andmicroelectronic thin films.

R E P R E S E N TAT I V E P U B L I C AT I O N S S. Gosavi, J.M. McCarthy, J.L. House,

B. Scholte van Mast, G. Janaway andC.N. Berglund, “Stability Improvementat High Emission Densities for GoldThin Film Photocathodes Used inAdvanced Electron BeamLithographies,” 45th InternationalConference on Electron, Ion and PhotonBeam Technology and Nanofabrication,accepted for publication in JVSTB,Nov.-Dec. 2001.

J.M. McCarthy, Z. Pei, M. Becker andD. Atteridge, “FIB MicromachinedSubmicron Thickness Cantilevers forthe Study of Thin Film Properties,”Thin Solid Films 358, 146–151, 2000.

M I S H A P A V E L

ProfessorPh.D., Experimental PsychologyNew York University, [email protected]


Analysis and modeling of complexbehaviors of biological systems,including visual and auditoryprocessing, pattern recognition,information fusion and decision-making. Development ofengineering systems mimickingthese abilities to supportmultimodal communicationbetween humans and machines(speech and video), machinevision, visually guided vehicularcontrol and virtual reality.Applications of these techniques tothe development of futurebiomedical and healthcaresystems, in particular point-ofcare biomedical engineering.

R E P R E S E N TAT I V E P U B L I C AT I O N SAdami, A., Yang, K., Song, X.,

and Pavel M., “Model-Base ImageProcessing and Analysis for FractureClassification,” Proceedings of theSecond Joint Engineering in Medicineand Biology Conference, October 2002,Houston, TX, pp. 2525–2527.

McGee, D.R., Pavel, M. and Cohen,P.R. (2001) “Context Shifts:Extending the Meanings of PhysicalObjects with Language,” HumanComputer Interaction, 16, Context-aware computing.

J. Palmer, P. Verghese and M. Pavel,“The Psychophysics of Visual Search,”Vision Research, 40, 1227–1268, 2000.

T. Arai, M. Pavel, H. Hermanskyand C. Avendano, “SyllableIntelligibility for Temporally FilteredLPC Cepstral Trajectories,” Journal ofthe Acoustical Society of America, 105,2783–2791, 1999.

R.K. Sharma, T.K. Leen and M.Pavel,“Probabilistic Image Sensor Fusion,”in Advances in Neural InformationProcessing Systems 11, M.S. Kearns,S.A. Solla and D.A. Cohn, eds., MITPress, Cambridge, Mass., 1999.

T R A N T H O N G

Assistant ProfessorPh.D., Electrical EngineeringPrinceton University, [email protected]


Cardiovascular engineering in thearea of cardiac tachyarrhythmiaprediction and prevention both inatria and ventricles, heart ratevariability as an indicator ofparasympathetic (vagal) toneduring relaxed states such asmeditation and sleep and as a longterm indicator of health in mind-body exercise programs like yogaand tai-chi, effect ofparasympathetic tone ontachyarrhythmia, in-vivo micro-recording of cardiac celldepolarization.

Biomedical signal processing usingdiscrete time modeling and systemdesign.

R E P R E S E N TAT I V E P U B L I C AT I O N ST. Thong and J. McNames,

“Transforms for Continuous TimeSystem Modeling,” Proceedings 45thIEEE Midwest Symposium on Circuitsand Systems, August 4–7, 2002, Tulsa,Oklahoma, pp. II-408–II-411.

T. Thong and J. McNames, “NonlinearRepresentation of Over-sampledCoarsely Quantized Signals,”Proceedings 45th IEEE MidwestSymposium on Circuits and Systems,August 4–7, 2002, Tulsa, Oklahoma,pp. II-416–II-417.

T. Thong, B. Goldstein, “Predictionof Tachyarrhythmia Episodes,”Proceedings of the Second JointEMBS/BMES Conference, Houston, TX,October 23–26, 2002, pp. 1445–1446.

T. Thong, B. Goldstein, “Prediction ofVentricular Tachyarrhythmia Episodesfrom Heart Rhythm Data by a VagalFatigue Index,” Abstract 435,Circulation, 106(19), II-86.

T. Thong, B. Goldstein, “SustainedVentricular Tachyarrhythmia Predictionfrom Heart Rhythm Data,” Abstract333, PACE, Vol. 26, No. 4, Part II,p. 1012.

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J A N P. H . VA N S A N T E N

Professor and CenterDirector of CSLUPh.D., Mathematical PsychologyUniversity of Michigan, [email protected]


Speech timing, intonation, signalprocessing, statistical analysis oftext and speech corpora, and text-to-speech (TTS) system evaluation.

R E P R E S E N TAT I V E P U B L I C AT I O N S J. van Santen and B. Möbius,

“A Model of Fundamental FrequencyContour Alignment,” in Intonation:Analysis, Modelling and Technology,Cambridge University Press,Cambridge, United Kingdom, 2000.

J. van Santen and C. Shih,“Segmental and Suprasegmental Timingin American English and ManadarinChinese,” Journal of the AcousticalSociety of America, 1012–1026, 2000.

J. van Santen and R. Sproat,“Highaccuracy AutomaticSegmentation,” Proceedings ofEUROSPEECH 99, Budapest,Hungary, 1999.

J. van Santen, “Combinatorial Issuesin Text-to-speech Synthesis,”Proceedings of EUROSPEECH 97,Rhodes, Greece, 1997.

J. van Santen and A.L. Buchsbaum,“Methods for Optimal Text Selection,”in Proceedings Eurospeech 1997,Rhodes, Greece, 1997.

J. van Santen, “Prosodic Modelling inText-to-speech Synthesis,” inProceedings Eurospeech, 1997,Rhodes, Greece, 1997.

J. van Santen, “Segmental Durationand Speech Timing,” in Y. Sagisaka,W.N. Campbell and N., Higuchi, eds.,Computing Prosody, New York,Springer, 1996.

J. van Santen, R.W. Sproat, J. Oliveand J. Hirschberg, eds., Progress inSpeech Synthesis, New York, Springer-Verlag, 1996

JOINT FACULTYT H O M A S B A U M A N NAssociated ProfessorDepartment ofNeurological SurgeryOregon Health & Science University

P H I L C O H E NProfessorDepartment of Computer Science& EngineeringOGI School of Science& Engineering

P A U L C O R D OScientist and DirectorNeurological Sciences InstituteOregon Health & Science University

J A C K F E R R A C A N EProfessor and ChairDepartment of Biomaterials& BiomechanicsOregon Health & Science University

M E L A N I E F R I E D - O K E NAssociate ProfessorDepartment of NeurologyOregon Health & Science University

D A N H A M M E R S T R O MProfessorDepartment of Computer Science& EngineeringOGI School of Science& Engineering

FAY H O R A KSenior ScientistNeurological Sciences InstituteOregon Health & Science University

T O D D L E E NProfessorDepartment of Computer Science& EngineeringOGI School of Science& Engineering

M E L A N I E M I T C H E L LAssociate ProfessorDepartment of Computer Science& EngineeringOGI School of Science &Engineering

G E R M A N N U N E ZVice ProvostOffice of Diversity& Multicultural AffairsOregon Health & Science University

A L F R E D N U T TA LProfessorDepartment of OtolaryngologyOregon Health & Science University

R O B E R T P E T E R K AAssociate ScientistNeurological Sciences InstituteOregon Health & Science University

S C O T T P R A H LAssistant ProfessorOregon Medical Laser Center

P AT R I C K R O B E R T SAssistant ScientistNeurological Sciences InstituteOregon Health & Science University

R O N S A K A G U C H IProfessorDepartment of Biomaterials& BiomechanicsOHSU School of Dentistry

X U B O S O N GAssistant ProfessorDepartment of Computer Science& EngineeringOGI School of Science& Engineering

K E N T T H O R N B U R GProfessorDepartment of Physiologyand PharmacologyOHSU School of Medicine

AFFILIATE FACULTYA N T Ó N I O B A P T I S TAProfessor and HeadDepartment of Environmentaland Biomolecular SystemsOGI School of Science& Engineering

N I N I A N J . B L A C K B U R NProfessorDepartment of Environmentaland Biomolecular SystemsOGI School of Science& Engineering

K I M B U R C H I E LChiefDepartment ofNeurological SurgeryOregon Health & Science University

D A V I D D A W S O NProfessor and ChairDepartment of Physiologyand PharmacologyOHSU School of Medicine

J . J O B FA B E RProfessorDepartment of Physiologyand PharmacologyOHSU School of Medicine

R I C H A R D FA I R L E YAssociate Dean of AcademicAffairs and ProfessorDepartment of Computer Scienceand EngineeringOGI School of Science& Engineering

B R A H M N . G O L D S T E I NProfessorDirector of Medical ServicesDoernbecher Children’s Hospital

J A M E S H O O KProfessor and Department HeadDepartment of Computer Scienceand EngineeringOGI School of Science& Engineering

J E R I J A N O W S K YAssociate ProfessorDepartment of NeurologyOHSU School of Medicine

D A V I D M A I E RProfessorDepartment of Computer Scienceand Engineering OGI School of Science& Engineering

E D W A R D N E W E LTProfessorDepartment of Neurology OHSU School of Medicine

S U S A N P R I C EAssistant ProfessorDepartment of Medical Informaticsand Outcomes ResearchOHSU School of Medicine

P. H E M A C H A N D R A R E D D YAssistant ScientistNeurological Sciences Institute Oregon Health & Science University

D A V I D J . S A H NProfessorDepartments of Pediatrics,Diagnostic Radiology, andObstetrics and Gynecology;Director, Clinical Care Centerfor Congenital Heart Disease;and Director, InterdisciplinaryProgram for Cardiac ImagingOregon Health & Science University

M A R I E S H E AAssistant ProfessorDepartment of Orthopedicsand RehabilitationOHSU School of Medicine

G A R Y W E S T B R O O KSenior Scientist, Vollum InstituteProfessor, Departmentof NeurologyOHSU School of Medicine

F A C U L T Y | B I O M E D I C A L E N G I N E E R I N G | B M E

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THE DEPARTMENT OF COMPUTER

SCIENCE AND ENGINEERING has aninternationally acclaimedresearch program. The breadthand depth of the research isapparent in the research projectsand research centers listed below,and in the educational program.Four degrees are offered: Masterof Science in Computer Scienceand Engineering, Master ofScience in Electrical Engineering,Doctor of Philosophy in ComputerScience and Engineeringand Doctor of Philosophy inElectrical Engineering.

ADMISSION REQUIREMENTS

In addition to the general OGI admissionrequirements, the CSE Department requiresthe general aptitude GRE scores, except inthe case of advanced placement admissionfor M.S. students (see below).

The Test of English as a Foreign Language(TOEFL) is required of all M.S. applicantswhose native language is not English unlessthe applicant earned an undergraduatedegree in the United States. Desirable score is 650. An applicant whose score isbetween 580 and 650 may be admitted ifspecial mitigating factors exist, e.g., excellentGRE scores.

Candidates for the CSE degree programtypically hold a bachelor’s degree incomputer science, mathematics, engineering,one of the biological or physical sciences, or one of the quantitative social sciences.However, candidates from nontraditionalbackgrounds are encouraged to apply as well. All candidates are expected to have completed courses in the followingsubject areas:

• An introduction to programming in ahigh-level language

• Data structures*

• Discrete mathematics*

• Logic design and computer organization

• Calculus or other college-level mathematics

*APC 515, Data Structures and DiscreteMathematics, may be taken to meet this prerequisite

To be considered for admission to an EEdegree program, a candidate must hold abachelor’s degree in physics, applied physics, engineering physics, electricalengineering or equivalent. Candidates withundergraduate degrees in appliedmathematics as well as other branches ofengineering will also be considered.

A D VA N C E D P L A C E M E N T A D M I S S I O N SF O R M . S . S T U D E N T S

Students who have completed at least fourOGI courses may be eligible to apply foradmission under the Advanced Placementoption. Under this option, applicants areexempt from the GRE and TOEFLrequirements and are required to provideonly two letters of recommendation. All otheradmissions requirements remain the same.

For students applying to the M.S. CSE degreeprogram through Advanced Placement, thefour courses must include at least two,preferably three, courses from the M.S. CSECore listed below. The remaining credits mustbe CSE, EE or MATH courses.

M . S . C S E C O R E

CSE 511 Principles of Compiler Design CSE 513 Introduction to Operating Systems CSE 514 Introduction to Database Systems CSE 516 Introduction to Software Engineering CSE 521 Introduction to Computer Architecture CSE 532 Analysis and Design of Algorithms CSE 533 Automata and Formal Languages

For students applying to the M.S. EEprogram through Advanced Placement, thefour courses must include at least twocourses from the Computer Engineering andDesign Concentration Core or the Signals and Systems Concentration Core listed below.The remaining courses must be EE, CSE orMATH courses.

M . S . E E C O M P U T E R E N G I N E E R I N G A N DD E S I G N C O N C E N T R AT I O N C O R E

EE 560 Introduction to Electronicsand Instrumentation

EE 570 Advanced Logic Design EE 571 System On a Chip (SOC) Design with

Programmable Logic EE 572 Advanced Digital Design-Timing Analysis

and Test EE 573 Computer Organization and Design EE 574 CMOS Digital VLSI Design IEE 575 CMOS Digital VLSI Design II

Department ofComputer Science

and Engineering

www.cse.ogi.edu

D E P A R T M E N T H E A D James Hook, Ph.D.


A S S O C I AT E C H A I R F O R E D U C AT I O NI N C O M P U T E R S C I E N C E

Lois De lcambre, Ph.D.


A S S O C I AT E C H A I R F O R E D U C AT I O N I N E L E C T R I C A L E N G I N E E R I N G

Danie l Hammerstrom, Ph.D.


A C A D E M I C C O O R D I N AT O R F O RC O M P U T E R S C I E N C E

Shir ley Kapsch


A C A D E M I C C O O R D I N AT O R F O RE L E C T R I C A L E N G I N E E R I N G

Mel issa Kretz


D E P A R T M E N T S E C R E TA R Y Barbara Mosher


C S E A N D E E G E N E R A L I N Q U I R I E S


CSE professor Ph i l Cohen demonstrates h isinte l l igent map technology, one of manypro jects under deve lopment at the Center forHuman-Computer Communicat ion

C S E | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G

M . S . E E S I G N A L S A N D S Y S T E M SC O N C E N T R AT I O N C O R E

CSE 547 Statistical Pattern Recognition EE 580 Linear Systems EE 581 Introduction to Signals, Systems and

Information ProcessingEE 582 Introduction to Digital Signal Processing MATH 510 Multivariate Calculus and

Differential Equations MATH 517 Probability and Statistics MATH 519 Engineering Optimization

Students must earn an overall grade pointaverage of 3.0 in their course work at OGI anda “B” or better in each M.S. core class to beeligible to apply through Advanced Placement.

DEGREE REQUIREMENTS

For M.S. students in CSE and for Ph.D.students in CSE and EE, a Student Program Committee (SPC) that providesacademic advising is assigned for eachmatriculated student. The SPC approves the application of courses toward thestudent’s degree requirements.

For master’s students in EE, a single facultymember will serve as an advisor.

The program of study for each M.S. studentmay be tailored to meet individual needs bythe SPC or advisor. Students are particularlyencouraged to include special-topic coursesrelevant to their interests.

M.S. CSE PROFESSIONAL INTERNSHIP OPTIONParticipation is limited by available industrialinternships. Students declaring this optionmust complete 45 credits of course work andup to an additional three credits of aprofessional internship (CSE504).

MASTER OF SCIENCE IN COMPUTERSCIENCE AND ENGINEERINGAll M.S. CSE students must complete theM.S. CSE core of 21 credits:

M . S . C S E C O R E C O U R S E S

CSE 511 Principles of Compiler Design . . . . 3 creditsCSE 513 Introduction to Operating Systems . . 3 creditsCSE 514 Introduction to Database Systems . . 3 creditsCSE 516 Introduction to . . . . . . . . . . . . . . . 3 credits

Software Engineering CSE 521 Introduction to . . . . . . . . . . . . . . . 3 credits

Computer ArchitectureCSE 532 Analysis and Design of Algorithms . . 3 creditsCSE 533 Automata and Formal Languages . . 3 credits

M . S . C S E T H E S I S O P T I O N

Students choosing the thesis option must finda faculty member willing to serve as a thesis

advisor. The department does not assignthesis advisors.

• M.S. CSE CORE (listed above)• CSE 503 M.S. THESIS RESEARCH (maximum 12 credits)• ELECTIVES (12 credits), as directed by the thesis

advisor or SPC

Please note: Students may not receive credit for bothCSE 519 and OMSE 533.

M . S . C S E N O N - T H E S I S O P T I O N

Students choosing the non-thesis M.S. CSEoption must complete a minimum of 15courses and a minimum of 45 credits. Up tosix credits of non-thesis research (CSE 501)may be included with the approval of thestudent’s Student Program Committee (SPC).The first three credits of research may becounted as one class; an additional threecredits may be counted as a second classtoward the 15-class requirement.

T R A C K S

Students pursuing the non-thesis option must choose one of the nine tracks definedbelow or consult their SPC to define a custom program.

A D A P T I V E S Y S T E M S T R A C K

• M.S. CSE CORE (listed above)• ADAPTIVE SYSTEMS CORE (12 credits)

Required:CSE 547 Statistical Pattern Recognition . . . . 3 creditsCSE 559 Machine Learning . . . . . . . . . . . . . 3 credits

Choose two:CSE 540 Neural Network Algorithms . . . . . . . 3 credits

and ArchitectureCSE 545 Advanced Neural and . . . . . . . . . . 3 credits

Adaptive AlgorithmsCSE 546 Data and Signal Compression . . . . 3 creditsCSE 550 Spoken Language Systems . . . . . . 3 creditsCSE 558 Evolutionary Computation . . . . . . . 3 creditsCSE 560 Artificial Intelligence . . . . . . . . . . . 3 creditsCSE 562 Natural Language Processing . . . . . 3 creditsCSE 564 Introduction to Human- . . . . . . . . . 3 credits

Computer InteractionCSE 568 Empirical Research Methods . . . . . 3 creditsEE 586 Adaptive and Statistical . . . . . . . . . 3 credits

Signal Processing

• SUGGESTED ELECTIVES (12 credits)

CSE 506 Appropriate special topics course CSE 563 Multiagent Systems . . . . . . . . . . . 3 creditsCSE 569 Scholarship Skills . . . . . . . . . . . . . 3 creditsAny CSE class not already takenPlease note: Students may not receive credit for both CSE519 and OMSE 533.

C O M P U T E R S E C U R I T Y T R A C K

• M.S. CSE CORE (listed above)• COMPUTER SECURITY CORE (15 credits)

Required:CSE 517 Software Engineering Processes . . . . 3 creditsCSE 524 TCP/IP Internetworking Protocols . . 3 credits

CSE 527 Principles and Practices of . . . . . . . 3 creditsSystem Security

CSE 528 Cryptography . . . . . . . . . . . . . . . . 3 creditsCSE 506 Building Secure Systems . . . . . . . . 3 credits


CSE 515 Distributed Computing Systems . . . 3 creditsAny CSE class not already taken.Please note: Students may not receive credit for both CSE519 and OMSE 533.

D ATA - I N T E N S I V E S Y S T E M S T R A C K

• M.S. CSE CORE (listed above)• DATA-INTENSIVE SYSTEMS CORE (12 credits)

Choose four:CSE 506 Special Topics: . . . . . . . . . . . . . . . .3 credits

Web Data ManagementCSE 506 Special Topics: . . . . . . . . . . . . . . . 3 credits

Information IntegrationCSE 506 Special Topics: Informational . . . . . 3 credits

Retrieval and the InternetCSE 506 Any special topics course in the

database areaCSE 515 Distributed Computing Systems . . . . 3 creditsCSE 526 Advanced Topics in . . . . . . . . . . . . 3 credits

Operating SystemsCSE 541 Database Implementation . . . . . . . 3 creditsCSE 542 Object Data Management . . . . . . . 3 creditsOne course from the System Software CoreOne course from the Software Engineering Core or theSoftware Engineering for Industry Professionals Core


Any CSE class not already taken.Please note: Students may not receive credit for both CSE519 and OMSE 533.

H U M A N - C O M P U T E R I N T E R A C T I O N T R A C K

• M.S. CSE CORE (listed above)• HUMAN-COMPUTER INTERACTION CORE (18 credits)

Required:CSE 560 Artificial Intelligence . . . . . . . . . . . 3 creditsCSE 564 Introduction to Human- . . . . . . . . . 3 credits

Computer Interactions

Choose three:CSE 506 Special Topics: 3D Graphics . . . . . 3 creditsCSE 550 Spoken Language Systems . . . . . . 3 creditsCSE 559 Machine Learning . . . . . . . . . . . . . 3 creditsCSE 561 Dialogue . . . . . . . . . . . . . . . . . . . . 3 creditsCSE 562 Natural Language Processing . . . . . 3 creditsCSE 563 Multi-Agent Systems . . . . . . . . . . . 3 creditsCSE 565 Advanced Topics in Human- . . . . . . 3 credits

Computer InteractionCSE 567 Developing User-Oriented Systems . . 3 creditsCSE 568 Empirical Research Methods . . . . . 3 credits


CSE 506 Special Topics: Real-time . . . . . . . 3 creditsRendering using Modern Graphics

CSE 515 Distributed Computing Systems . . . . 3 creditsCSE 540 Neural Network Algorithms . . . . . . . 3 credits

& ArchitectureCSE 547 Statistical Pattern Recognition . . . . 3 creditsCSE 551 Structure of Spoken Language . . . . 3 creditsCSE 552 Hidden Markov Models for . . . . . . . 3 credits

Speech Recognition Architecture

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CSE 569 Scholarship Skills . . . . . . . . . . . . . 3 creditsAny CSE class not already taken.Please note: Students may not receive credit for both CSE519 and OMSE 533.

N E T W O R K I N G T R A C K

• M.S. CSE CORE (listed above)• NETWORKING CORE: (18 credits)

Required:CSE 524 TCP/IP Internetworking Protocols . . 3 creditsCSE 525 Advanced Networking . . . . . . . . . . 3 creditsEE 590 Digital Communication I . . . . . . . . . 3 credits

Three of:CSE 515 Distributed Computing Systems . . . 3 creditsCSE 526 Advanced Topics in . . . . . . . . . . . . 3 credits

Operating SystemsCSE 527 Principles and Practices of . . . . . . . 3 credits

System SecurityEE 582 Introduction to Digital . . . . . . . . . . 3 credits

Signal ProcessingEE 591 Digital Communication II . . . . . . . . 3 creditsEE 592 Digital Communication Systems . . . 3 credits

Special Topics in Systems Software or Networkingor Communication such as:CSE 506 Special Topics: . . . . . . . . . . . . . . . 3 credits

Multi-Media NetworkingCSE 506 Special Topics: . . . . . . . . . . . . . . . 3 credits

Advanced Distributed SystemsCSE 506 Special Topics: . . . . . . . . . . . . . . . 3 credits

Networking Practicum Please note: Students may not receive credit for bothboth CSE 519 and OMSE 533.

S O F T W A R E E N G I N E E R I N G T R A C K

• M.S. CSE CORE (listed above)• SOFTWARE ENGINEERING CORE (15 credits)

Required:CSE 517 Software Engineering Processes . . 3 creditsCSE 519 Object-Oriented Analysis . . . . . . . . 3 credits

and DesignCSE 520 Software Architecture . . . . . . . . . . 3 credits CSE 529 Object-Oriented Programming . . . . . 3 creditsOne of:CSE 564 Introduction to Human- . . . . . . . . . 3 credits

Computer InteractionCSE 567 Developing User-Oriented Systems . . 3 credits


MST 512 Project Management . . . . . . . . . . . 4 creditsAny course in software engineering, data-intensive systems,systems software, systems security or human-computerinterfaces or any CSE course not already taken.Please note: Students may not receive credit for both CSE519 and OMSE 533.

S O F T W A R E E N G I N E E R I N G F O R I N D U S T R YP R O F E S S I O N A L S T R A C K

• M.S. CSE CORE (listed above)• SOFTWARE ENGINEERING FOR INDUSTRY

PROFESSIONALS CORE (15 credits)Required:OMSE 511 Managing Software Development . . 3 creditsOMSE 521 Using Metrics and Models . . . . . . . 3 creditsOMSE 531 Software Requirements . . . . . . . . . 3 credits

EngineeringOMSE 533 Software Design Techniques . . . . . 3 credits

Choose one:CSE 564 Introduction to Human- . . . . . . . . . 3 credits

Computer InteractionCSE 567 Developing User-Oriented Systems . . 3 credits


Any CSE class not already taken.Please note: Students may not receive credit for bothCSE 519 and OMSE 533.

S P O K E N L A N G U A G E S Y S T E M S T R A C K

• M.S. CSE CORE (listed above)• SOFTWARE ENGINEERING CORE (15 credits)

Required:CSE 550 Spoken Language Systems . . . . . . 3 creditsCSE 551 Structure of Spoken Language . . . . 3 creditsCSE 552 Hidden Markov Models for . . . . . . . 3 credits

Speech Recognition

Any two:BME 568 Auditory & Visual Processing by . . . 3 credits

Human & MachineBME 571 Speech Systems . . . . . . . . . . . . . . 3 creditsBME 572 Speech Synthesis . . . . . . . . . . . . . 3 creditsCSE 547 Statistical Pattern Recognition . . . . 3 creditsCSE 559 Machine Learning . . . . . . . . . . . . . 3 creditsCSE 560 Artificial Intelligence . . . . . . . . . . . 3 creditsCSE 561 Dialogue . . . . . . . . . . . . . . . . . . . . 3 creditsCSE 562 Natural Language Processing . . . . . 3 credits CSE 564 Introduction to Human- . . . . . . . . . 3 credits

Computer InteractionEE 581 Introduction to Signals, Systems

and Information Processing . . . . . . 3 creditsEE 582 Introduction to Digital . . . . . . . . . . 3 credits

Signal Processing


Courses in the Spoken Language Systems core Any CSE class not already takenPlease note: Students may not receive credit for both CSE519 and OMSE 533.

S Y S T E M S S O F T W A R E T R A C K

• M.S. CSE CORE (listed above)• SYSTEMS SOFTWARE CORE (12 credits)

Choose four:CSE 515 Distributed Computing Systems . . . 3 creditsCSE 524 TCP/IP Internetworking Protocols . . 3 creditsCSE 525 Advanced Networking . . . . . . . . . . 3 creditsCSE 526 Advanced Topics in . . . . . . . . . . . 3 credits


System SecurityCSE 541 Database Implementation . . . . . . . 3 credits

Special Topics in Systems Software or Networking such as:

CSE 506 Special Topics: Advanced . . . . . . . 3 creditsDistributed Systems

CSE 506 Special Topics: . . . . . . . . . . . . . . . 3 creditsNetworking Practicum

CSE 506 Special Topics: . . . . . . . . . . . . . . . 3 creditsMulti-Media Networking


Any course in the Systems Software area core Any CSE class not already taken.Please note: Students may not receive credit for both CSE519 and OMSE 533.

MASTER OF SC I ENCE INELECTR IAL ENG INEER INGM.S. EE students may pursue either aComputer Engineering and DesignConcentration or Signals and SystemsConcentration.

M . S . E E C O M P U T E R E N G I N E E R I N G A N D D E S I G N( C E ) C O N C E N T R AT I O N

All M.S. EE students pursuing the ComputerEngineering and Design Concentration must complete the CE Concentration Core of 28 credits:

M . S . E E C O M P U T E R E N G I N E E R I N G A N D D E S I G NC O N C E N T R AT I O N C O R E

EE 560 Introduction to Electronics . . . . . . . 4 creditsand Instrumentation

EE 570 Advanced Logic Design . . . . . . . . . 4 creditsEE 571 System On a Chip (SOC) Design . . . 4 credits

with Programmable LogicEE 572 Advanced Digital Design-Timing . . . 4 credits

Analysis and TestEE 573 Computer Organization and Design . . 4 creditsEE 574 CMOS Digital VLSI Design I . . . . . . 4 creditsEE 575 CMOS Digital VLSI Design II . . . . . . 4 credits

M . S . E E T H E S I S O P T I O N I N T H E C O M P U T E RE N G I N E E R I N G A N D D E S I G N C O N C E N T R AT I O N

Students choosing the thesis option must finda faculty member willing to serve as a thesisadvisor. The department does not assignthesis advisors.

• M.S. EE CE CONCENTRATION CORE (listed above)• EE 503 M.S. THESIS RESEARCH (maximum 12 credits)• ELECTIVES (8 credits) from the CE Concentration

electives listed below

M . S . E E N O N - T H E S I S O P T I O N I N T H E C O M P U T E RE N G I N E E R I N G A N D D E S I G N C O N C E N T R AT I O N

All M.S. EE students in the ComputerEngineering and Design Concentration mustcomplete the concentration core of 28 credits(listed above), one of the following trackcores, and remaining elective credits to total48 credits.

C I R C U I T D E S I G N T R A C K

• M.S. EE CE CORE (listed above)• CIRCUIT DESIGN CORE (16 credits):

Required:EE 536 Operation of Semiconductor Devices 4 creditsEE 561 Analog Integrated Circuit Design . . 4 creditsEE 562 Digital Integrated Circuit Design . . . 4 creditsEE 563 Analog CMOS Integrated . . . . . . . . 4 credits

Circuit Design

• SUGGESTED CE ELECTIVES (4 credits - listed below)

C O M P U T E R A R C H I T E C T U R E T R A C K

• M.S. EE CE CORE (listed above)• COMPUTER ARCHITECTURE CORE (6 credits)

C O M P U T E R S C I E N C E A N D E N G I N E E R I N G | C S E

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Required:CSE 521 Introduction to . . . . . . . . . . . . . . . 3 credits

Computer ArchitectureCSE 522 Advanced Computer Architecture . . 3 credits


S I G N A L P R O C E S S I N G T R A C K

• M.S. EE CE CORE (listed above)• SIGNAL PROCESSING CORE (9 credits)

Required:EE 581 Introduction to Signals, Systems, . . 3 credits

& Information ProcessingEE 582 Introduction to Digital . . . . . . . . . . 3 credits

Signal ProcessingEE 584 Introduction to Image Processing . . 3 credits


S U G G E S T E D E L E C T I V E S F O R C O M P U T E R E N G I N E E R I N GA N D D E S I G N C O N C E N T R AT I O N

(to total 48 required credits for M.S. EE degree in the CEConcentration)

BME 513 Biomedical Signal Processing I . . . 3 creditsBME 566 Biomedical Signal Processing II . . . 3 creditsEE 525 Introduction to Electromagnetics . . 4 credits

for Modern ApplicationsEE 526 Electromagnetics for Modern . . . . . 4 credits

Applications IIEE 531 Introduction to Quantum Mechanics . . 4 credits

for Electrical & Computer EngineeringEE 535 MOSFET Modeling for VLSI . . . . . . 4 credits

Circuit DesignEE 560 Introduction to Electronics . . . . . . . 4 credits

& InstrumentationEE 565 Introduction to Wireless . . . . . . . . . 4 credits

Integrated Circuit DesignEE 576 Algorithms for VLSI Design & Test . . 4 creditsEE 583 Digital Signal Processing II . . . . . . 3 creditsEE 590 Digital Communication I . . . . . . . . . 3 creditsEE 591 Digital Communication II . . . . . . . . 3 creditsEE 592 Digital Communication Systems . . . 3 creditsEE 593 Analytical Techniques in . . . . . . . . . 3 credits

Statistical Signal Processing & Communications

Any EE or CSE course not already takenAdditionally, students may consider the following coursesfrom other universities:ECE 527 VLSI System Design (Oregon State University)ECE 570 High Performance Computer Architecture

(Oregon State University)ECE 675 Introduction to Integrated Circuit Test

(Portland State University)ECE 699 Digital Design Using Hardware Description

Languages (Portland State University)

M . S . E E S I G N A L S A N D S Y S T E M S( S A S ) C O N C E N T R AT I O N

All M.S. EE students pursuing the Signal andSystems Concentration must complete theSAS Concentration Core of 21 credits:

M . S . E E S I G N A L S A N D S Y S T E M S C O N C E N T R AT I O N C O R E

CSE 547 Statistical Pattern Recognition . . . . 3 creditsEE 580 Linear Systems . . . . . . . . . . . . . . . 3 credits

EE 581 Introduction to Signals, Systems . . . 3 creditsand Information Processing

EE 582 Introduction to Digital . . . . . . . . . . 3 creditsSignal Processing

MATH 510 Multivariate Calculus and . . . . . . . 3 creditsDifferential Equations

MATH 517 Probability and Statistics . . . . . . . . 3 creditsMATH 519 Engineering Optimization . . . . . . . . 3 credits

M . S . E E T H E S I S O P T I O N I N T H E S I G N A L SA N D S Y S T E M S C O N C E N T R AT I O N

Students choosing the thesis option must finda faculty member willing to serve as a thesisadvisor. The department does not assignthesis advisors.

• M.S. EE SAS CONCENTRATION CORE (listed above)• EE 503 M.S. THESIS RESEARCH (maximum 12 credits)• ELECTIVES (15 credits) from the SAS Concentration

electives listed below

M . S . E E N O N - T H E S I S O P T I O N I N T H E S I G N A L SA N D S Y S T E M S C O N C E N T R AT I O N

All M.S. EE students in the Signals andSystems Concentration must complete theconcentration core of 21 credits (listedabove), one of the following track cores andremaining elective credits to total 45 credits.

S I G N A L A N D I M A G E P R O C E S S I N G T R A C K

• M.S. EE SAS CORE (listed above)• SIGNAL AND IMAGE PROCESSING CORE (12 credits)

Required:BME 568 Auditory & Visual Processing by . . . 3 credits

Human & MachinexEE 584 Introduction to Image Processing . . 3 creditsEE 585 Introduction to Digital . . . . . . . . . . 3 credits

Video ProcessingEE 586 Adaptive & Statistical . . . . . . . . . . 3 credits

Signal Processing

• SUGGESTED SAS ELECTIVES (12 credits – listed below)

M A C H I N E L E A R N I N G T R A C K

• M.S. EE SAS CORE (listed above)• SIGNAL MACHINE LEARNING CORE (12 credits)

Required:CSE 540 Neural Networks Algorithms . . . . . . 3 credits

and ArchitecturesCSE 558 Evolutionary Computation . . . . . . . 3 creditsCSE 559 Machine Learning . . . . . . . . . . . . . 3 creditsEE 586 Adaptive & Statistical . . . . . . . . . . 3 credits

Signal Processing• SUGGESTED SAS ELECTIVES (12 credits - listed below)

S P E E C H P R O C E S S I N G T R A C K

• M.S. EE SAS CORE (listed above)• SPEECH PROCESSING CORE (12 credits)

Required:BME 572 Speech Synthesis . . . . . . . . . . . . . 3 creditsCSE 550 Spoken Language Systems . . . . . . 3 creditsCSE 551 Structure of Spoken Language . . . . 3 creditsCSE 552 Hidden Markov Models for . . . . . . . 3 credits

Speech Recognition• SUGGESTED SAS ELECTIVES (12 credits - listed below)

S U G G E S T E D E L E C T I V E S F O R S I G N A L SA N D S Y S T E M S C O N C E N T R AT I O N

(to total 45 required credits for M.S. EE degree in theSAS Concentration)

BME 513 Biomedical Signal Processing . . . . 3 creditsBME 568 Auditory & Visual Processing by . . . 3 credits

Human & MachineBME 571 Speech Systems . . . . . . . . . . . . . . 3 creditsCSE 506 Special Topics: Real-Time . . . . . . . 3 credits

Rendering using ModernGraphic Architecture

CSE 532 Analysis and Design of Algorithms . . 3 creditsCSE 540 Neural Networks Algorithims . . . . . 3 credits

and ArchitecturesCSE 546 Data and Signal Compression . . . . 3 creditsCSE 552 Hidden Markov Models for . . . . . . . 3 credits

Speech RecognitionCSE 559 Machine Learning . . . . . . . . . . . . . 3 creditsCSE 560 Artificial Intelligence . . . . . . . . . . . 3 creditsCSE 562 Natural Language Processing . . . . . 3 creditsEE 584 Introduction to Image Processing . . 3 creditsAny EE or CSE course not already takenAdditionally, students may consider the following coursesfrom other universities:SySc 545 Information Theory (Portland State University)

COOPERATIVE COMPUTERSCIENCE PROGRAMSThe OGI School has establishedundergraduate/graduate cooperativeprograms with Lewis & Clark College, PacificUniversity, Reed College and WillametteUniversity. These programs allow selectedundergraduate students to enter the master’sprogram in computer science and engineeringat the beginning of their senior year. In twoyears of residence at OGI, the student cansimultaneously fulfill requirements for thebachelor’s degree at the undergraduateinstitution and the master’s degree at OGI.

COMPUTER SCIENCE ANDENGINEERING PH.D. PROGRAM

In addition to the general OGI requirementsfor a Ph.D., candidacy in CSE is satisfied inthree parts:

FOUNDATION REQUIREMENTS: Students arerequired to take six foundation courses.Particularly well-prepared students canwaive some of these courses by passing anexamination on the course material.

AREA REQUIREMENTS: Students choosethree courses within one area and threecourses out of that area, as outlined below.

RESEARCH SKILLS ASSESSMENT:Students are required to take CSE 669,Scholarship Skills, and to pass the research

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proficiency examination (RPE), whichrequires a written and oral presentation ofa research paper. The RPE usually takesplace in the spring quarter of the secondyear of residence.

Ph.D. students must obtain a grade of “B”or better in each required course. Thedoctoral dissertation will document asignificant, original research contributionand must be of publishable quality in bothcontent and presentation.

The faculty strongly recommends thatstudents prepare a formal thesis proposalbetween 9 and 18 months before the Ph.D.defense. The proposal is not a candidatescreening tool, but instead a means toensure an acceptable level of intellectualvigor and maturity. Starting in the secondyear, the faculty strongly recommends thatstudents deliver yearly research talks. TheRPE, presentation at the student researchsymposium, the thesis proposal and talksat refereed conferences satisfy thisrequirement. Practice talks for conferencepapers should be open for commentary.

The program of study for each Ph.D.student is tailored to meet individual needsand interests. Each student’s StudentProgram Committee provides academicadvising and is in direct control of thestudent’s program of study. The SPC willwork with the student to set and reviewgoals on a twice-yearly basis. Studentsmust write a progress report for all SPCmeetings except the first one. The entirefaculty reviews each Ph.D. student’sacademic progress annually.

F O U N D AT I O N R E Q U I R E M E N T S ( 1 8 c r e d i t s )

Required: CSE 613 Introduction to Operating Systems . . 3 creditsCSE 621 Introduction to Computer . . . . . . . . 3 credits

ArchitectureCSE 632 Analysis and Design of Algorithms . . 3 creditsCSE 633 Automata and Formal Languages . . 3 credits

Choose one programming language course:CSE 629 Object-Oriented Programming . . . . . 3 creditsCSE 631 Foundations of Semantics . . . . . . . 3 creditsCSE 636 Functional Programming . . . . . . . . 3 credits

Choose one interactive and adaptive systems course:CSE 640 Neural Network Algorithms

and Architectures . . . . . . . . . . . . .3 creditsCSE 659 Machine Learning . . . . . . . . . . . . . 3 creditsCSE 660 Artificial Intelligence . . . . . . . . . . . 3 creditsCSE 664 Introduction to Human- . . . . . . . . . 3 credits

Computer Interaction

R E S E A R C H S K I L L S R E Q U I R E M E N T ( 3 c r e d i t s )

CSE 669 Scholarship Skills . . . . . . . . . . . . . . . . 3 credits

A R E A R E Q U I R E M E N T S ( 1 8 c r e d i t s )

Three courses from one of the following fiveareas, and three other courses not from thatarea and not already taken:

ADAPTIVE SYSTEMS AND APPLICATIONSBME 668 Auditory and Visual Processing . . . 3 credits

by Human and MachineCSE 606 Special topics in Cognitive ScienceCSE 640 Neural Network Algorithms . . . . . . . 3 credits

and ArchitecturesCSE 645 Advanced Neural and . . . . . . . . . . 3 credits

Adaptive AlgorithmsCSE 646 Data and Signal Compression . . . . 3 creditsCSE 647 Statistical Pattern Recognition . . . . 3 creditsCSE 658 Evolutionary Computation . . . . . . . 3 creditsCSE 659 Machine Learning . . . . . . . . . . . . . 3 creditsCSE 668 Empirical Research Methods . . . . . 3 creditsEE 686 Adaptive and Statistical . . . . . . . . . 3 credits

Signal Processing

HUMAN-COMPUTER INTERACTIVE SYSTEMSBME 668 Auditory and Visual Processing . . . 3 credits

by Human and MachineCSE 606 Special Topics: . . . . . . . . . . . . . . . 3 credits

Computer GraphicsCSE 606 Special Topics: . . . . . . . . . . . . . . . 3 credits

Scientific VisualizationCSE 606 Special Topics: Real-time . . . . . . . . 3 credits

Rendering using ModernGraphics Architecture

CSE 650 Spoken Language Systems . . . . . . 3 creditsCSE 651 Structure of Spoken Language . . . . 3 creditsCSE 652 Hidden Markov Models for . . . . . . . 3 credits

Speech RecognitionCSE 660 Artificial Intelligence . . . . . . . . . . . 3 creditsCSE 661 Dialogue . . . . . . . . . . . . . . . . . . . . 3 creditsCSE 663 Multiagent Systems . . . . . . . . . . . 3 creditsCSE 664 Introduction to Human- . . . . . . . . . 3 credits

Computer InteractionCSE 665 Advanced Topics in Human- . . . . . . 3 credits

Computer InteractionCSE 667 Developing User-Oriented Systems . . 3 creditsCSE 668 Empirical Research Methods . . . . . 3 credits

PROGRAMMING LANGUAGES AND SOFTWARE ENGINEERINGCSE 606 Special Topics: High Assurance . . . 3 credits

Software EngineeringCSE 606 Special Topics: Model Checking . . . 3 credits

for Bug DiscoveryCSE 606 Special Topics: Domain . . . . . . . . . 3 credits

Specific LanguagesCSE 611 Principles of Compiler Design . . . . 3 creditsCSE 612 Compiling Functional Languages . . 3 creditsCSE 616 Introduction to . . . . . . . . . . . . . . . 3 credits

Software EngineeringCSE 617 Software Engineering Processes . . 3 creditsCSE 618 Software Design and Development . . 3 creditsCSE 619 Object-Oriented Analysis . . . . . . . . 3 credits

and DesignCSE 620 Software Architecture . . . . . . . . . . 3 creditsCSE 629 Object-Oriented Programming . . . . . 3 creditsCSE 630 Introduction to Mathematical Logic . . 3 credits

CSE 631 Foundations of Semantics . . . . . . . 3 creditsCSE 636 Functional Programming . . . . . . . . 3 credits

SYSTEMS SOFTWARECSE 606 Special Topics: Building . . . . . . . . . 3 credits

Secure SystemsCSE 606 Special Topics: . . . . . . . . . . . . . . . 3 credits

Web Distribution ArchitectureCSE 606 Special Topics: Security Protocols . . 3 creditsCSE 614 Introduction to Database Systems . . 3 creditsCSE 615 Distributed Computing Systems . . . 3 creditsCSE 622 Advanced Computer Architecture . . 3 creditsCSE 624 TCP/IP Internetworking Protocols . . 3 creditsCSE 625 Advanced Networking . . . . . . . . . . 3 creditsCSE 626 Advanced Topics in . . . . . . . . . . . . 3 credits


System SecurityCSE 628 Cryptography . . . . . . . . . . . . . . . . 3 creditsCSE 629 Object-Oriented Programming . . . . . 3 creditsCSE 641 Database Implementation . . . . . . . 3 creditsCSE 642 Object Data Management . . . . . . . 3 credits

THEORYCSE 606 Special Topics: Principles of . . . . . 3 credits

Database Systems

CSE 628 Cryptography . . . . . . . . . . . . . . . . 3 creditsCSE 630 Introduction to Mathematical Logic . . 3 creditsCSE 631 Foundations of Semantics . . . . . . . 3 creditsCSE 634 Computability and Intractability . . . 3 creditsCSE 635 Categories in Computer Science . . 3 credits

ELECTRICAL ENGINEERINGPH.D. PROGRAM

A Ph.D. program in Electrical Engineeringwith emphasis in Computer Engineering andDesign or Signals and Systems is offeredthrough the Department of Computer Scienceand Engineering. Upon entry into theprogram a Student Program Committee (SPC)of three faculty members is formed. Thestudent discusses feasible research areasand eventual research directions with thecommittee and together they chart anindividualized course of study to prepare thestudent for the qualifying exam.

The qualifying exam may be written or oral orboth, at the discretion of the SPC, and mayadditionally involve a formal researchproposal. It is usually taken within 12 monthsof enrolling in the program, and may bescheduled at any time of year. The amount ofcourse work to be completed before takingthe qualifying exam depends on theindividual’s level of preparation at entry. Atminimum, three graded ElectricalEngineering courses from OGI must becompleted before taking the exam.

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After passing the qualifying exam, the studentworks with the SPC to develop a researchplan specifically for the dissertation. Ph.D.students are required to make annual reportsto the SPC on the status of their research,and may be called upon to deliver timelyresearch presentations as the workprogresses. The dissertation itself mustconstitute a significant research contributionand must be of publishable quality. The Ph.D.degree is granted following the presentationof an acceptable dissertation and successfuloral defense.

RESEARCH PROGRAMS

The specific research projects under way atany given time depend upon current interestsand obligations of faculty, students andresearch sponsors.

RESEARCH PROGRAMS

Adaptive Systems

Our work on adaptive systems includes theoretical,algorithmic, scientific and practical aspects.Research on theory and algorithms for machinelearning includes supervised, unsupervised andreinforcement learning; neural networks; geneticalgorithms; generalization theory (model selectionand pruning, invariant learning and theoreticalcharacterization); stochastic optimization; localand mixture models; time series; control; andcontext-sensitive learning. Research on biologicaland cognitive modeling includes the effect of noiseon learning in neural circuits, cognitive models ofvisual pattern recognition and analogy-making, andmodeling of evolutionary systems. Practicalapplications of our research in these areas includespeech and image processing, medical screeningtechnology, environmental forecasting andobservation systems, anomaly detection foraeronautics, aircraft control, sensor fusion andoptimization, and automatic programming.Hammerstrom, Hayes, Leen, Mitchell, Pavel, Song, Wan

Agent-Based Systems

This project is designing a new agentcommunication language (AGENTTALK) andmultiagent architecture. Unlike DARPA’s currentlanguage (KQML), the language offers a truesemantics, and provably correct dialogue protocols,based on joint intention theory. The Adaptive AgentArchitecture, a successor to our earlier OpenAgent Architecture, offers platform and applicationinteroperability, facilitated communication, properconcurrent operation, dynamic reconfigurability offacilitators and separation of data and control.Quickset has been reimplemented to use this

architecture, gaining a more robust capability forsupporting human-human collaboration,multimedia and dynamic adaptation to processingenvironments. Cohen

Digital Government

DOT is collaborating with the U.S. Forest Service,Bureau of Land Management, Fish and WildlifeService and other government agencies to build aforest information portal for the AdaptiveManagement Area (AMA) program. The AMAsdevelop and test innovative approaches to forestmanagement. We are developing an informationmodel called Metadata++ to locate documents anddocument fragments along several dimensions andto search for documents based on “similaritysearch” between locations. The forest project alsoincludes participants from the MST and ESEdepartments at OGI, from Portland StateUniversity, the University of Nevada, Las Vegasand from the private sector.Delcambre and Maier (CSE), Toccalino (ESE),Phillips, Steckler, and Koch (MST), Tolle (ForestService), Landis (consultant), Palmer (UNLV),and Shapiro (PSU)

Efficient Intrusion Detection and Response Systems(Intel and ETIC)

This project is focused on studying the perfor-mance of full-packet classification algorithms andpacket classification caching algorithms. Byunderstanding emerging network traffic patternsand leveraging hardware support provided bythe IXP network processor platform, we plan onsystematically studying alternative architecturesfor providing high-speed classifiers.Wu-chang Feng

Environmental Observation and Forecasting Systems(EOFS)

The goal of this research is to develop softwaretechnology to enable EOFS to evolve efficiently andto deliver quantifiably reliable information aboutthe environment. Our focus is on EOFS forestuarine and coastal regions. The project includesdeveloping quality-scalable information processing,storage and access; developing machine learningtechnology to improve sensor reliability, tocategorize and detect different estuarine dynamics,and to fuse sensor data with numerical models;improving data product generation andmanagement; applying parallelism to simulationand data manipulation, improving sensornetworking technology; and developing newvisualization techniques.Baptista, Feng, Feng, Leen, Maier, Silva, Walpole

Forensix: Large-scale Tamper-Resistant ComputerForensic Systems (NSF)

The goal of the Forensix (“4N6”) Project is to allowa system to be monitored so that, in the event of asecurity compromise, it is easy to track thecompromise back to its source. To facilitate this,

the system requires two machines: a potentiallyinsecure “front-line” machine, and a known secureback-end. Information about system calls is storedin a MySQL database on the back-end. 4N6 is builton top of SNARE. Feng, Feng, Walpole, Maier

Infopipes

The Infopipes project is building tools to aid in thedevelopment of timing-sensitive distributedapplications, such as streaming video and real-time sensor networks.

The goal of most existing communicationsmiddleware is Communication Transparency:communication is hidden behind a conventionalinvocation interface and, as far as possible, theprogrammer is unaware that communication istaking place. The property that makes this possibleis Blocking Transparency: the idea that aninvocation that performs some computation andimmediately returns can be transparently replacedby an invocation that blocks for an arbitrary time.In effect, Blocking Transparency disconnects“application time” from “real time.” Hence, neitherCommunication Transparency nor BlockingTransparency is appropriate for distributedstreaming applications that require control overtiming. In addition, streaming applications mayrequire control over other aspects ofcommunication, such as bandwidth, reliability,ordering and topology.

Infopipes are a powerful communicationsabstraction that have been designed to meet theneeds of streaming applications. Current workincludes creating appropriate Middleware librariesfor Infopipes, and developing a domain-specificlanguage to describe Infopipe components andInfopiplines at a high enough level of abstractionthat tools can automatically check the properties ofproposed Infopipelines before they are constructed,and then generate the code that manages many ofthe low-level details such as thread management,synchronization, deadlock avoidance and threadlatency. Black, Walpole, Pu

Image, Video Processing and Analysis

Both low-level processing and high-level analysisare studied. Special emphasis is on the interfaceof machine learning and computer vision, whereinsights from probability theory, stochastic systemsand information theory are used to produce newalgorithms that are robust, accurate and efficient.Current projects include information fusion, theincorporation of context for image recognition,model-based image segmentation, enhancementand 3-D reconstruction, and motion analysis forautonomous navigation. Song, Pavel

Model-Relative Control of Autonomous Vehicles

This multidisciplinary project is exploring thedesign and implementation of nonlinearreconfigurable controllers that exploit the coupleddynamics between a model of a flight vehicle,such as a helicopter, and adaptive models of the

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environment. New model-predictive techniques aredeveloped to perform on-line optimization ofvehicle control trajectories under dynamic andsituational constraints. This resultingenvironmentally informed control approach willenable aircraft operations under all-weatherconditions, as well as increased automation formodeless control and extreme maneuvers atlevels not realizable with conventional controlapproaches. Kieburtz, Wan, Baptista

Multimodal Systems

Multimodal interfaces enable more natural andefficient interaction between humans and machinesby supporting multiple coordinated channelsthrough which input and output can pass. TheCenter for Human-Computer Communication isengaged in empirical investigation of multimodalinteraction. This informs our research anddevelopment of architectures for multimodallanguage processing, work which draws on a rangeof fields such as cognitive science, naturallanguage processing, multimedia, user interfacedesign, speech recognition, gesture recognition andvisual parsing. The Quickset system developed atCHCC supports multimodal pen/voice interactionwith complex visual/spatial displays, such as maps.The Rasa system allows users to engagemultimodally with tangible tools, such as paper andPost-it notes. Finally, work is ongoing to developtechniques for 3-D multimodal interaction inaugmented and virtual reality environments.Cohen, Oviatt

Natural Language Dialogue

The performance of speech recognition systemsimproves significantly when the spoken languageunderstanding system can predict the nextutterance. Accordingly, we are performingperceptual studies of dialogue and building modelsof human and human-computer dialogue in order to develop computational models of conversationthat can be used to track and predict spokenlanguage. This work is based on speech-act theory, multiagent architectures and models ofspontaneous speech. Cohen, Heeman, Oviatt

Net Data Management

We believe that data management systems of thefuture must stress data movement over datastorage. NIAGARA is an initial effort, conductedwith the University of Wisconsin, to move beyonddisk-centric data management to net-centricsystems. Current work includes algebras andspecial operators for XML, exploiting streamsemantics for efficient processing, data-queryhybrids for distributed query evaluation, andpeer-to-peer catalog management.Maier, DeWitt, Naughton

Neurobiological Modeling

The brain handles a continuous temporal flow ofsensory information. At the microscopic level of the

synapses, the relevant signals are the smallvariable electrophysiological events called synapticpotentials. When learning occurs, there is a changein the relative weighted value of these synapticpotentials. At the macroscopic level of a functionalregion of the brain, the relevant variables aresystems properties of the response to largenumbers of cellular inputs. The system needs tooptimize the trade-off between accuracy, whichmay take some time to establish, and adaptability,which often requires rapid adjustment to changesin the sensory environment. This collaborativeproject combines statistical adaptive systemapproaches with tools from computational biologyand experimental neurophysiology. The presentfocus is on modeling adaptation in a sensory-motorsystem in weakly electric mormyrid fish. Themodeling forms a bridge between microscopicdynamics and macroscopic system behavior. Thisproject involves a novel aspect of modelingemphasizing statistical properties of then-synapticadaptation in the presence of noise, and makingtestable predictions about how noise can affect theaccuracy of the fish’s stored signal memories.Leen, Roberts

Operating Systems

Our operating systems-related research focusesprimarily on adaptive systems software and itsapplication in distributed, mobile and multimediacomputing environments. Several large projectsare currently under way in the areas of quality ofservice control, defining abstractions that supportadaptive resource management and dynamicspecialization for enhanced performance ofstreaming applications. Black, Walpole

Perspectives

The Perspectives project aims to producefoundational results and practical tools forrepresenting and manipulating software frommultiple viewpoints. Our ability to build complexsoftware systems relies on composition techniquesand programming language mechanisms thatenable us to construct complete programs fromsmaller pieces. A particular decomposition imposesa structure that makes it possible to manage thecomplexity of a large system, provided that eachcomponent can be developed and maintained withsome degree of independence, and that eachfeature can be localized in one or two components.Unfortunately, the same decomposition makes itharder to add or change features that cut acrossthat structure.

We believe that the design, evolution, maintenanceand comprehension of software can be bettersupported by tools that allow programmers toexamine and work with multiple perspectives on aprogram instead of constraining them to a singledecomposition. That is, programmers should beempowered to think of programs not as linear textsbut as equivalence classes of concrete views, eachof which is useful for certain tasks, but none ofwhich is more definitive than any other.

These are the problems that we are tackling in thePerspectives project at OGI. Our work to date hasbeen focused in three areas.

• The search for new, high-level representationsof program source code - which we refer to asan “abstract program structure” or APS - that isable to capture program semantics fully whilesimultaneously abstracting away from specificdetails of syntax and physical structure. Instead,common representations of a program - such asthe one- or two-dimensional syntax of a linearsource text, the underlying abstract syntaxtrees, or the class diagrams that describe itsarchitecture — should be obtained as differentviews on a rich APS.

• The design and implementation of a practicaltool called Sweet that permits considerablymore flexible decomposition and construction ofJava programs than do conventional Javacompilers. In the input to Sweet, a programmerblends definitions of parts of the programstructure, for example, packages, classhierarchies, or methods, with descriptions of the executable content that should be placedwithin that structure.

• The integration and experimentation with theseideas in the context of a practical, interactivedevelopment system. This work is based on theEclipse IDE and is sponsored by ObjectTechnology International. Black, Jones

Programatica

“Programming as if properties mattered.” We aredeveloping a new kind of program developmentenvironment that actively supports and encouragesits users in thinking about, stating and validatingcorrectness properties of software as an integralpart of the programming process. TheProgramatica framework allows programmers toassert precise properties of program elements aspart of their source code. Assertions can then beannotated with one or more “certificates” thatprovide evidence of their validity. The certificateinterface is generic; certificate servers can rangefrom “pencil and paper” proofs, randomized testsuites, all the way to formal proofs checked by atheorem prover. Changes to the original programare tracked by the framework, requiring only thosecertificates that depend on the changed code to bereverified. Property-oriented developmentenvironments such as Programatica are a keytechnology in helping developers build more robustand secure software systems.Hook, Jones, Kieburtz, Matthews

Project Timber

Project Timber (“Time as a basis for embeddedreal-time systems”) is exploring new techniques forbuilding more reliable software for embeddedsystems. One of the project’s goals is to investigatethe role that advanced programming languages canplay in this area. We have designed a newprogramming language, also called Timber, that we

29


are using, as a proof-of-concept demonstration, todevelop control algorithms for a small roboticvehicle called Timbot. The language offers a high-level, declarative approach to key aspects ofembedded systems development such as real-timecontrol, event handling, and concurrency. Anothergoal is to develop techniques for building systemsthat adapt dynamically to changes in theirenvironment or in the way that they are beingused. One of our motivating examples in this areais a video pipeline that relays live video across awireless network from a camera on Timbot to aremote viewer. When other tasks leave Timbotwithout the CPU power or network bandwidth thatit needs to send a full quality video signal, thesoftware adapts automatically and according touser preferences, for example by sending fewerframes or less detailed images, to maximize qualityof service. Jones, Black, Kieburtz, Walpole

Query Optimization

Our work on query optimization and evaluationdeals with both general frameworks and specifictechniques for different data model and querylanguage features. Columbia is a C++-based, top-down framework for construction of cost-basedquery optimizers. We are currently examiningpruning techniques for searching, transforms forcollection-valued attributes and nested queries,and “multiplex” query optimization for efficientlyoptimizing groups of queries. Columbia is a jointproject with Portland State University.Maier, Shapiro

Speech Recognition

The goal of Large Vocabulary Continuous SpeechRecognition research is to enable normal humanspeech as an input device in next-generationcomputers alongside today’s keyboard and mouseinput. This technology can be used by itself fordictation and command control applications.It can also form part of a powerful informationprocessing system when used together withinformation retrieval and natural languageunderstanding systems. The research focusesinclude accurate acoustic modeling, speakeradaptation, confidence measure and rejection,and modeling spontaneous speech.

The goal for language and speaker recognition is toidentify which language is being used in aconversation and who is talking by using signalprocessing, pattern recognition and computerscience technology. The technology can be used toincrease security and customer services. Ourresearch in this area includes how to analyze,identify and capture these nuances and how tomodel these specific acoustics landmarks andphonotactic constraints contained in the targetedlanguage and speakers. Yan, Heeman

Spoken Language Engineering

Speech is the most natural and efficient means bywhich individuals may access a wide variety ofinformation, and the need for speech-based

interfaces is growing as computing graduallymoves off of the desktop and into mobile devices.Spoken language engineering is an interdisciplinaryfield that draws elements from digital signalprocessing, computer science, linguistics, machinelearning, and human perception. The Center forSpoken Language Understanding (CSLU) hasunique breadth and depth of experience in allcomponents of spoken language engineering,including text-to-speech synthesis, speechrecognition, dialogue modeling, and signalprocessing. Research efforts at CSLU includeassistive technology, speech as an informationsource for medical diagnosis, universal access tocomputers, small-footprint speech recognition andtext-to-speech synthesis, and basic research on allaspects of spoken-language processing.Heeman, Hosom, van Santen, Wan

Spoken Language Systems

Spoken language systems make it possible forpeople to interact with computers using speech,the most natural mode of communication. A spokenlanguage system combines speech recognition,natural language understanding and humaninterface technology. It functions by recognizing theperson’s words, interpreting the words in terms ofthe context and goals of the task, and providing anappropriate response to the user. We are involvedin the analysis and development of variouscomponents of such systems, ranging fromempirical studies of human dialogues through theconstruction of interactive systems to thedevelopment of abstract models of behavior. Cohen, Oviatt, Heeman, van Santen

Superimposed Information and SuperimposedApplications

We are interested in providing typical databasesystem capabilities in an environment where we donot own or manage the underlying, baseinformation. We seek to develop a superimposedlayer of information that can reference selectedinformation from the base layer and can also addnew information to highlight, interconnect,elaborate or annotate the selected information. Wehave defined an architecture for buildingsuperimposed applications and have implementedour first tool: SLIMPad, a scratchpad applicationthat allows users to easily create “scraps” thatreference selected items from the base layer andorganize scraps into bundles. The tendency to usescraps and bundles to organize our thoughts iscommon practice, as confirmed by ourobservational research team that is studying howclinicians seek and use information in a hospitalintensive-care unit. Observational team (OHSUDivison of Medical Informatics and OutcomesResearch): Gorman, Ash, Lavelle; computer scienceteam: Delcambre, Maier

VLSI Architecture for Intelligent Computing

Moore’s law is pushing VLSI design down to themolecular scale where devices are more stochastic

in operation and quantum effects become the rulerather than the exception. It is unlikely thatexisting computational models will be an optimalmapping to these new devices and technologies.One source of inspiration for new kinds ofcomputing structures is coming fromComputational Neuroscience. Biology uses looselycoupled, relatively slow, globally asynchronous,distributed computing with unreliable (andoccasionally failing) components. Furthermore,even simple biological systems perform highlysophisticated pattern recognition and control.Biological systems are self-organizing, tolerant ofmanufacturing defects, and they adapt, rather thanbeing programmed, to their environments. Theproblems they solve are important, involving theinteraction of an organism/system with the realworld. An important aspect of this is the efficientrepresentation of knowledge or contextualinformation. In this project a variety of highlyparallel algorithms are being studied, includingneuromorphic structures, with the intent ofenhancing the representation and manipulation ofknowledge in silicon. Borrowing fromComputational Neuroscience is very difficult, but itdoes promise a new way to look at computationand insight into new solutions to importantproblems. These models will be massively paralleland require massively parallel silicon architecturesfor efficient execution. Hammerstrom, Jabri

RESEARCH CENTERS

CENTER FOR HUMAN-COMPUTER COMMUNICATION

D E B B I E D E S H A I S , F i n a n c i a l / B u s i n e s s M a n a g e r

Phone: 503 748-1248E-mail: [email protected]

The Center for Human-Computer Communication isdedicated to realizing a vision of transparentinformation and service access. Research projectsare broadly interdisciplinary, and includecollaborations with numerous universities, federalresearch laboratories, and the Data-IntensiveSystems Center at the OGI School of Science &Engineering. Research activities focus on:

• Multimodal human-computer interaction thatallows people to state their needs using speech,writing and gestures, and that providesmultimedia output.

• User-centered design of next-generationinterface technology, including spoken languageand multimodal interfaces, and interfaces formobile and multimedia technology.

• Intelligent agent technologies-software systemsthat help users accomplish tasks and can reasonabout how and where to carry out users’requests in a worldwide distributed informationenvironment.

• Collaboration technologies to support human-human communication, and collaborativedecision making among groups of people.

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CHCC organizes an annual Distinguished LectureSeries on the Future of Human-ComputerInteraction. World-class researchers are invited toshare current topics.

Dr. Philip Cohen and Dr. Sharon Oviatt are co-directors of the center. Other center faculty includeDr. Peter Heeman and Dr. Misha Pavel. For moreinformation, visit CHCC’s Web pages atwww.cse.ogi.edu/CHCC/. 39

P A C I F I C S O F T W A R E R E S E A R C H C E N T E R

K E L LY AT K I N S O N , C e n t e r A d m i n i s t r a t o r


S H E R I D H U Y V E T T E R , C e n t e r A d m i n i s t r a t o r


The Pacific Software Research Center (PacSoft) isa team of faculty, students and professionalresearch staff who study mathematically basedtechniques for the specification, development andvalidation of complex computer software. Our goalsare to explore and test new techniques that cansupport the development of software products inwhich clients can have high confidence.

PacSoft’s approach to software specification anddevelopment is grounded in functional program-ming, type theory, meta-programming, formalmethods, and programming language semantics.Our research methods extend from theoreticalinvestigation, through prototype software tooldevelopment, to experimental validation.

Much of our work during the past decade hasfocused on techniques for the design andimplementation of domain-specific languages.A domain-specific language is able to express theabstractions and operations used in a particularengineering domain in terms familiar to domainexperts. This allows non-programmers, who aredomain experts, to create significant softwareartifacts that meet their own needs. Constructionof domain specific languages requires experts inboth the domain and language design. Domains inwhich this work has demonstrated considerablesuccess are the design of complex microarchi-tectures for high performance microprocessors,the construction of encryption algorithms, andlanguages where time plays a central role.

Dr. Tim Sheard is the director of the Center.Dr. Richard Kieburtz is the founding director. Otherfaculty members of PacSoft are Dr. Andrew Black,Dr. James Hook, Dr. Mark Jones, Dr. JohnLaunchbury, and Dr. John Matthews of the OGISchool of Science & Engineering, and Dr. AndrewTolmach of Portland State University. The Centeremploys six postdoctoral researchers and hasnumerous visitors each year. Research by PacSoftscientists is supported by grants and contractsfrom the National Science Foundation, DARPA,DOD, Intel Corp. and OTI. For additionalinformation, visit the PacSoft Web site,http://www.cse.ogi.edu/PacSoft/.

D ATA B A S E A N D O B J E C TT E C H N O L O G Y L A B O R AT O R Y

J O A N N B I N K E R D , C e n t e r A d m i n i s t r a t o r


The Database and Object Technology Lab (DOT)conducts theoretical and applied research related todatabase management and object-oriented systems.Query processing is a long-term focus, particularlyquery optimization frameworks as well as queryprocessing over Internet data sources, particularlythose containing XML. DOT research also considersand develops conceptual models, including modelsfor superimposed information and datatransformation. DOT has a history of involvementwith database support for scientific applications,including forest canopy research, and morerecently, data product management for scientificobservation and simulation. Web data managementis another area of research carried out at DOT,particularly management of semi-structured dataand XML, Web information integration andubiquitous access to Web data and services. Dr.David Maier of the OGI School of Science &Engineering is the director of DOT. Additional DOT-affiliated faculty members are Dr. Lois Delcambreand Dr. Juliana Freire, all with OGI, and Dr.Leonard Shapiro of Portland State University.

S Y S T E M S S O F T W A R E L A B O R AT O R Y

C Y N T H I A P FA LT Z G R A F F, C e n t e r A d m i n i s t r a t o r


The Systems Software Lab (SySL) is a center forresearch spanning the areas of distributed andmobile computing, operating systems, networkingand wide-area-network-based informationmanagement systems. SySL focuses on thedevelopment of adaptive systems that utilizetechniques such as feedback control, specialization,domain-specific languages, and quality of servicemanagement to enable them to operate effectivelyin today’s rapidly evolving and widelyheterogeneous distributed environments. Weemphasize the real-world applicability of ourresearch results and we continue to builddistributed and scalable prototype systems forapplication areas such as multimedia computingand communications, active networks, Internet-based information management and survivabledistributed systems. We collaborate closely withindustry sponsors such as Intel and IBM, and havestrong federal funding from DARPA and NSF. Dr.Jonathan Walpole is the director of SySL.Additional SySL-affiliated faculty are Drs. Wu-chiFeng, Wu-chang Feng, and Andrew Black of OGI,and Dr. Molly Shor of Oregon State University.

FACILIT IESThe Department of Computer Science andEngineering provides a state-of-the-art computingenvironment designed to support the needs ofresearch and education. The computing facilitiesstaff has a wide range of skills that allow thecomputing environment at CSE to be flexibleand responsive in meeting the department’schanging needs.

Support for central services such as mail, dial-upaccess, video conferencing, database access andfile- and printer-sharing, as well as access toInternet and Internet2 services, is distributedacross a group of Sun computers and a NetworkAppliance file server that make up the coresupport environment.

Although Sun computers are highly visible at CSE,both Intel- and Alpha-based machines runningWindows or Linux are mainstays of our researchactivities. The generous support of our industryand government research partners allows CSE tomaintain a high-quality computing infrastructurecapable of supporting a high degree ofheterogeneity as required for high-quality research.

The department also has facilities for research andteaching in computer hardware design andelectrical engineering. Mentor Graphics IC DesignStation is used for VLSI design. Chips arefabricated at the Mosis foundry and can be testedon our IMS XL60 chip tester. Mentor and AlteraCAD tools are provided for FPGA programmablelogic design. The computer design lab is equippedwith PC workstations, Tektronix digitaloscilloscopes, FPGA development boards and TIDSP boards. We have test equipment and facilitiesfor analog and mixed signal design along withsimulation support with Cadence PSpice. A digitaltelevision lab is available for video signalprocessing projects.

In all, a facilities staff of eight supports almost400 computer systems, X terminals andperipheral devices spanning multiple networksusing a variety of automated techniques, manydeveloped internally, to cope with the highdegree of complexity inherent in such aheterogeneous environment.

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C S E | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G | F A C U L T Y

J A M E S H O O K

Associate Professorand Department HeadPh.D., Computer ScienceCornell University, [email protected]


Domain-specific languages, formalmethods and functionalprogramming.

R E P R E S E N TAT I V E P U B L I C AT I O N SW. Harrison, T. Sheard and J. Hook,

“Fine Control of Demand in Haskell,”Proceedings of the Sixth InternationalConference on the Mathematics ofProgram Construction, Dagstuh,Germany, July 2002.

J. Hook, E. Meijer and D. Leijen,“Client-side Web Scripting inHaskell,” in proceedings of PracticalApplications of Declarative Languages,January 1999.

J. Hook, E. Meijer and D. Leijen,“Haskell as an Automation Controller,”in Advanced Functional Programming,Swierstra, Henriques and Oliveira, eds.,Springer Verlag, LNCS, Vol.1608.

T. Widen and J. Hook, “SoftwareDesign Automation: Language Designin the Context of Domain Engineering,”Sere 98, June 1998.

J. Bell, F. Bellegarde and J. Hook,“Type-driven Defunctionalization,” ICFP 97, June 1997.

R. Kieburtz, F. Bellegarde et al.,“Calculating Software Generators fromSolution Specifications,” TAPSOFT 95,Springer-Verlag, LNCS, May 1995.

F. Bellegarde and J. Hook,“Substitution: A Formal Methods Case Study using Monads andTransformations,” Science of ComputerProgramming, 22 (2-3), 287, 1994.

J. Bell, J. Hook et al., “SoftwareDesign for Reliability and Reuse:A Proof-of-Concept Demonstration,”TRI-Ada 94 Proceedings, ACM Press,November 1994.

A N D R E W P. B L A C K

ProfessorD. Phil. University of Oxford(Balliol College), [email protected]


Programming languages;distributed systems; streaminginfrastructure for wide-areanetworks; object-orientedlanguages and systems;programming environments; andthe ways in which all of theseareas interrelate.

R E P R E S E N TAT I V E P U B L I C AT I O N SNathanael Schärli, Stéphane Ducasse,

Oscar Nierstrasz and Andrew Black,“Traits: Composable Units of Behavior,”European Conference on Object-OrintedProgramming, Springer Lecture Notesin Computer Science, July 2003.

A.P. Black, J. Huang, R. Koster,J. Walpole, and C. Pu, “Infopipes: anAbstraction for Multimedia Streaming,”Multimedia Systems (special issue onMultimedia Middleware) 8(5), 406-419,2002.

Johan Nordlander, Mark P. Jones,Magnus Carlsson, Richard B. Kieburtzand Andrew Black, “Reactive Objects,”5th IEEE International Symposium onObject-oriented Real-time DistributedComputing, Crystal City, Virginia, USA,April 2002.

C. Pu, T. Autrey, A.P. Black, C. Consel,C. Cowan, J. Inouye, L. Kethana, J.Walpole and K. Zhang, “OptimisticIncremental Specialization:Streamlining in a CommercialOperating System,” Proceedings of the15th ACM Symposium on OperatingSystems Principles, December 1995.

R.K. Raj, E.D. Tempero, H.M. Levy,A.P. Black, N.C. Hutchinson and E. Jul,“Emerald, A General PurposeProgramming Language,” SoftwarePractice & Experience, 21 (1), 91,January 1991.

A.P. Black and Y. Artsy, DigitalEquipment Corp., “ImplementingLocation Independent Invocation,” IEEETrans. on Parallel and DistributedSystems, B 1(1), 107, January 1990.

N I R U P A M A B U L U S U

Assistant ProfessorPh.D., Computer ScienceUniversity of California atLos Angeles, 2002


Embedded Networked Sensing(ENS) systems; computernetworks; mobile and wirelessnetworks; network applicationsand security; large-scaledistributed systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SN. Bulusu, J. Heidemann, D. Estrin

and T. Tran, “Self-configuringLocalization Systems: Design andExperimental Evaluation,” ACMTransactions on Embedded ComputingSystems (TECS), Special Issue onNetworked Embedded Systems. May2003. To appear.

N. Bulusu, J. Heidemann and D.Estrin, “Adaptive Beacon Placement,”in Proceedings of 21st InternationalConference on Distributed ComputingSystems (ICDCS-21), Phoenix, Arizona,April 2001.

N. Bulusu, J. Heidemann and D.Estrin, “GPS-less Low Cost OutdoorLocalization for Very Small Devices,”IEEE Personal Communications, 7(5),28-34, October 2000.

P H I L C O H E N

Professor, Co-Director Center forHuman-Computer CommunicationPh.D., Computer ScienceUniversity of Toronto, [email protected]


Multimodal interfaces; human-computer interaction; naturallanguage processing; dialogue;delegation technology; cooperatingagents; communicative action;applications to mobile computing;information management; networkmanagement; manufacturing.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Kumar, P. Cohen and H. Levesque,

“The Adaptive Agent Architecture:Achieving Fault-Tolerance UsingPersistent Broker Teams,” in theFourth International Conference onMultiagent Systems (ICMAS 2000),Boston, July 2000.

S. Kumar and P. Cohen, “Towardsa Fault-Tolerant Multiagent SystemArchitecture,” in the FourthInternational Conference onAutonomous Agents (Agents 2000),Barcelona, June 2000.

D. McGee, P. Cohen and L. Wu,“Something from Nothing: Augmentinga Paper-based Work Practice withMultimodal Interaction,” Proceedingsof the Designing Augmented RealityEnvironments Conference, ACM Press,71-80, Copenhagen, April 2000.

S. Oviatt and P. Cohen, “MultimodalInterfaces That Process What ComesNaturally,” Communications of theACM, 43( 3), 45-53, March 2000.

L. Wu, S.L. Oviatt and P. Cohen,“Multimodal Integration — AStatistical View,” IEEE Transactionson Multimedia, 1( 4), 334-341,December 1999.

P. Cohen, D. McGee, S.L. Oviatt,L. Wu, J. Clow, R. King, S. Julier andL. Rosenblum, “Multimodal Interactionsfor 2-D and 3-D Environments,” IEEEComputer Graphics and Applications,pp.10-13, July-August 1999.

FACULTY

32

C R I S P I N C O W A N

Assistant Research ProfessorPh.D., Computer ScienceUniversity of Western Ontario,[email protected]


System security and survivability;operating systems; distributedsystems; computer architecture;optimism; programming languages.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. Wright, C. Cowan, S. Smalley,

J. Morris and G. Kroah-Hartman,“Linux Security Modules: GeneralSecurity Support for the LinuxKernel,” Eleventh USENIX SecurityConference, 2002.

C. Cowan, S. Beattie, C. Wrightand G. Kroah-Hartman, “RaceGuard:Automatic Adaptive Detection andPrevention of Buffer-Overflow Attacks,” Tenth USENIX SecurityConference, 2001.

C. Cowan, M. Barringer, S. Beattie,G. Kroah-Hartman, M. Frantzen andJ. Lokier, “FormatGuard: AutomaticAdaptive Detection and Prevention ofBuffer-Overflow Attacks,” Tenth USENIXSecurity Conference, 2001.

D. McNamee, J. Walpole, C. Cowan,C. Pu, C. Krasic, P. Wagle, C. Consel,G. Muller and R. Marlet, “SpecializationTools and Techniques for SystematicOptimization of Systems Software,”ACM Transactions on ComputerSystems, 19(2), May 2001.

C. Cowan, C. Pu, D. Maier, H. Hinton,J. Walpole, P. Bakke, S. Beattie,A. Grier, P. Wagle and Q. Zhang,“Stackguard: Automatic AdaptiveDetection and Prevention of Buffer-Overflow Attacks,” Seventh USENIXSecurity Conference, 1998.

C. Cowan and H. Lutfiyya, “AWait-Free Algorithm for OptimisticProgramming: HOPE Realized,” 16thInternational Conference on DistributedComputing Systems (ICDCS’96),Hong Kong, 1996.

C. Cowan, T. Autrey, C. Krasic, C. Puand J. Walpole, “Fast ConcurrentDynamic Linking for an AdaptiveOperating System,” in the InternationalConference on Configurable DistributedSystems (ICCDS’96), Annapolis, 1996.

L O I S D E L C A M B R E

ProfessorPh.D., Computer ScienceUniversity of SouthwesternLouisiana, [email protected]


Superimposed information;database system data models;scientific data management.

R E P R E S E N TAT I V E P U B L I C AT I O N SM. Weaver, L. Delcambre and

D. Maier, “A SuperimposedArchitecture for Enhanced Metadata,”DELOS Workshop on Interoperabilityin Digital Libraries, held in conjunctionwith European Conference on DigitalLibraries (ECDL 2001), Darmstadt,Germany, September 2001.

S. Bowers and L. Delcambre, “AGeneric Representation for ExploitingModel-Based Information,” ETAIJournal, Linköping Electronic Articlesin Computer and Information Science,ISSN 1401-9841, Vol. 6, nr 006, 2001,www.ep.liu.se/ea/cis/2001/006/.

L. Delcambre, D. Maier, S. Bowers,L. Deng, M. Weaver, P. Gorman,J. Ash, M. Lavelle and J. Lyman,“Bundles in Captivity: An Applicationof Superimposed Information,”Proceedings of the IEEE InternationalConference on Data Engineering,Heidelberg, Germany, April 2001.

S. Bowers and L. Delcambre.“Representing and TransformingModelbased Information,” inProceedings of the InternationalWorkshop on the Semantic Web, inconjunction with ECDL 2000, Lisbon,September 2000.

P. Gorman, J. Ash, M. Lavelle,J. Lyman, L. Delcambre, D. Maier,S. Bowers and M. Weaver, “Bundlesin the Wild: Tools for ManagingInformation to Solve Problems andMaintain Situation Awareness,”Library Trends 49 (2), Fall 2000.

D. Maier and L. Delcambre,“Superimposed Information for theInternet,” in Proc. of the ACM SIGMODWorkshop on the Web and Databases(WebDB ‘99), pp. 1-9, June 1999.

L. Delcambre and D. Maier, “Modelsfor Superimposed Information,” inAdvances in Conceptual Modeling(ER ‘99), Vol. 1727, Lecture Notesin Computer Science, pp. 264-280,November 1999.

R I C H A R D E . ( D I C K ) FA I R L E Y

Professor and Associate Deanfor Academic AffairsPh.D., Computer ScienceUCLA, [email protected]


All aspects of softwareengineering, including but notlimited to systems engineering ofsoftware-intensive systems;software process modeling andprocess improvement; softwarerequirements engineering;software design; software qualityengineering; software metrics;software project management;software cost and scheduleestimation; software riskmanagement; and softwareengineering policies, procedures,standards and guidelines.

R E P R E S E N TAT I V E P U B L I C AT I O N S“Software Project Management,”

Encyclopedia of Computer Science,Groves Dictionaries, 2001.

“Software Estimation Risk,”Encyclopedia of Software Engineering,Vol. 2, John Wiley and Sons, 2000.

R. Fairley, “A Process-OrientedApproach to Software ProductImprovement,” PROFES’99 ConferenceProceedings, Oulu, Finland, June 1999.

R. Fairley, “The Concept ofOperations – The Bridge fromOperational Requirements to TechnicalSpecifications,” Annals of SoftwareEngineering, Vol. 3, Amsterdam,September 1997.

R. Fairley, “Standard for Conceptof Operations Documents,” IEEEStandard, Vol. 1362, IEEE ComputerSociety, 1997.

R. Fairley, “Standard for SoftwareProject Management Plans,” IEEEStandard, Vol. 1058, IEEE ComputerSociety, 1997.

R. Fairley, “Risk-Based CostEstimation,” Proceedings of the 11thCOCOMO Users Group, Los Angeles,November 1996.

R. Fairley, “Some Hard Questionsfor Software Engineering Educators,”keynote presentation, CSEE 95Proceedings, ACM Conference onSoftware Engineering Education,New Orleans, March 1995.

W U - C H A N G F E N G

Assistant ProfessorPh.D., Computer ScienceUniversity of Michigan, [email protected]


Scalable Internet systems;Internet congestion control andqueue management; wirelessnetworking; programmablenetwork infrastructure.

R E P R E S E N TAT I V E P U B L I C AT I O N SW. Feng, F. Chang, W. Feng and

J. Walpole, “Provisioning On-lineGames: A Traffic Analysis of aBusy Counter-Strike Server,”Internet Measurement Workshop,November 2002.

W. Feng, D. Kandlur, D. Saha andK. Shin, “Adaptive Packet Marking forMaintaining End-to-End Throughputin a Differentiated Services Internet,”IEEE/ACM Transactions on Networking,7(5), October 2001.

W. Feng, D. Kandlur, D. Saha andK. Shin, “Blue: An Alternative Approachto Active Queue Management,”NOSSDAV 2001, June 2001.

W. Feng, D. Kandlur, D. Saha andK. Shin, “Stochastic Fair Blue: A QueueManagement Algorithm for EnforcingFairness,” INFOCOM 2001, April 2001.

W. Feng, D. Kandlur, D. Saha andK. Shin, “A Self-Configuring REDGateway,” INFOCOM 1999, May 1999.

W. Feng, D. Kandlur, D. Saha andK. Shin, “Understanding and ImprovingTCP Performance over Networks withMinimum Rate Guarantees,” IEEE/ACMTransactions on Networking, 7(2),173-187, April 1999.

F A C U L T Y | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G | C S E

33


W U - C H I F E N G

Associate ProfessorPh.D., Computer ScienceUniversity of Michigan, [email protected]


Networking; multimediasystems; multimedia networking;video coding; middlewareservices; and massively scalablestreaming infrastructures.

R E P R E S E N TAT I V E P U B L I C AT I O N SA.S. Tosun and W. Feng, “On Error

Preserving Video Encryption Algorithmsfor Wireless Transmission,” inProceedings of the ACM Multimedia2001, October 2001.

W. Feng and M. Liu, “ExtendingCritical Bandwidth AllocationTechniques for Stored VideoDelivery Across Best-EffortNetworks,” International Journalof Communication Systems, 14,925-940, September 2001.

A.S. Tosun and W. Feng, “LightweightSecurity Mechanisms for Wireless VideoTransmission,” in Proceedings of theIEEE International Conference onInformation Technology: Coding andComputing 2001, Las Vegas, April 2001.

A.S. Tosun and W. Feng, “OnImproving Quality of Video for H.263over Wireless CDMA Networks,” inProceedings of the IEEE WirelessCommunications and NetworkingConference, Chicago, September 2000.

A. Agarwal, W. Feng and C. Wolfe,“A Multi-Differential Video CodingAlgorithm for Robust VideoConferencing,” in Proceedings ofthe SPIE Voice, Video and DataCommunications Conference, Boston,November 2000.

A.S. Tosun, A. Agarwal and W. Feng,“Providing Efficient Support forLossless Video Transmission andPlayback,” in 10th InternationalWorkshop on Network and OperatingSystems Support for Digital Audio andVideo, Chapel Hill, North Carolina,June 2000.

J U L I A N A F R E I R E

Assistant ProfessorPh.D., Computer ScienceState University of New Yorkat Stony Brook, [email protected]


Databases and knowledge-basesystems; information integration;management of semi-stuctureddata; Web information systems andInternet applications.

R E P R E S E N TAT I V E P U B L I C AT I O N SM. Benedikt, C-Y. Chan, W. Fan,

J. Freire, and R. Rastogi. “Capturingboth Types and Constraints inData Integration,” ACM SIGMODInternational Conference onManagement of Data, 2003.

P. Bohannon, J. Freire, J.R. Haritsa,M. Ramanath, P. Roy and J. Siméon,“Bridging the XML-Relational Dividewith LegoDB: A Demonstration,” IEEEInternational Conference on DataEngineering (ICDE), 2003.

J. Freire, J.R. Haritsa, M. Ramanath,P. Roy and J. Siméon, “StatiX:Making XML Count,” ACM SIGMODInternational Conference onManagement of Data, pp. 181-192,2002.

J. Freire and J. Simeon, “AdaptiveXML Shredding: Architecture,Implementation, and Challenges,”Efficiency and Effectiveness of XMLTools, and Techniques (EEXTT),pp. 104-116, 2002.

P. Bohannon, J. Freire, J.R. Haritsa,M. Ramanath, P. Roy and J. Siméon,“LegoDB: Customizing RelationalStorage for XML Documents,” VeryLarge Databases Conference (VLDB),pp. 1091-1094, 2002.

M. Benedikt, J. Freire andP. Godefroid, “VeriWeb: AutomaticallyTesting Dynamic Web Sites,”International World Wide WebConference (WWW), 2002.

P. Bohannon, J. Freire, P. Roy andJ. Siméon, “From XML Schema toRelations: A Cost-based Approach toXML Storage,” IEEE InternationalConference on Data Engineering(ICDE), pp. 64-75, 2002.

J. Freire, D.F. Lieuwen andJ.J. Ordille, “Integrating NetworkDevices in a Metadirectory: TheMetaComm experience,” InformationSystems 27(3), 193-217, 2002.

D A N H A M M E R S T R O MDoug Strain ProfessorPh.D., Electrical EngineeringUniversity of Illinois, [email protected]


Biologically inspired computation;VLSI chip design for imageprocessing, digital video,signal processing and intelligentsignal processing; molecularand nanoscale architecture;technology transfer.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.R. Kerr, C. H. Luk, D. Hammerstrom,

M. Pavel, “Advanced IntegratedEnhanced Vision Systems,” ProceedingsSPIE, April 2003.

C. Gao, D. Hammerstrom, S. Zhu,M. Butts, “FPGA Implementation OfVery Large Associative Memories –Scaling Issues,” chapter submitted forbook, FPGA Implementations of NeuralNetworks, Amos Omondi (ed.), KluwerAcademic Publishers, Boston, 2003.

C. Gao and D. Hammerstrom,“Platform Performance Comparisonof PALM Network on Pentium 4 andFPGA,” IJCNN 03, July 2003.

S. Zhu and D. Hammerstrom,“Reinforcement Learning in AssociativeMemory,” Proceedings of the IJCNN,July 2003.

G. Zeng and D. Hammerstrom,“Distributed Associative NeuralNetwork Model Approximates BayesianInference,” Proceedings of ANNIE 2003,St. Louis Mo., December 2002.

S. Zhu and D. Hammerstrom,“Simulation of Associative NeuralNetworks,” Proceedings of theInternational Conference on NeuralInformation Processing, Singapore,November 2002.

D. Hammerstrom, “Digital VLSI forNeural Networks,” in The Handbookof Brain Theory and Neural Networks,2nd Ed., Michael Arbib (ed.), MITPress, 2003.

D. Hammerstrom and D. Lulich,“Image Processing Using One-Dimensional Processor Arrays,”The Proceedings of the IEEE, 84(7),27-43, July 1996.

P E T E R A . H E E M A N

Assistant ProfessorPh.D., Computer ScienceUniversity of Rochester, [email protected]


Spontaneous speech recognition;modeling disfluencies andintonation; dialoguemanagement; collaboration;spoken dialogue systems;natural language processing.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Strayer and P. Heeman, “Dialogue

Structure and Mixed Initiative,’’ secondworkshop of the Special Interest Groupon Dialogue, Aalborg, Denmark,September 2001.

P. Heeman and J. Allen, “ImprovingRobustness by Modeling SpontaneousSpeech Events,” in Robustness inLanguage and Speech Technology,J. Junqua and G. van Noord, eds.,Kluwer Academic Publishers, 2000.

K. Ward and P. Heeman,“Acknowledgments in Human-ComputerInteraction,” in Proceedings of the1st Conference of the North AmericanChapter of the Association forComputational Linguistics, Seattle,May 2000.

P. Heeman, “Modeling Speech Repairsand Intonational Phrasing to ImproveSpeech Recognition,” in IEEE Workshopon Automatic Speech Recognition andUnderstanding, Keystone, Colorado,December 1999.

P. Heeman and J. Allen, “SpeechRepairs, Intonational Phrases andDiscourse Markers: ModelingSpeakers’ Utterances in SpokenDialog,” Computational Linguistics,Vol. 25-4, 1999.

P. Heeman, “POS Tags and DecisionTrees for Language Modeling,” inProceedings of the Joint SIGDATConference on Empirical Methods inNatural Language Processing and VeryLarge Corpora, College Park, Maryland,June 1999.

P. Heeman, M. Johnston, J. Denneyand E. Kaiser, “Beyond StructuredDialogues: Factoring Out Grounding,”in Proceedings of the InternationalConference on Spoken LanguageProcessing ICSLP-98, Sydney,December 1998.

34

M A R K P. J O N E S

Associate ProfessorD.Phil., ComputationUniversity of Oxford, [email protected]


Programming language design andimplementation; programmingparadigms; module and componentsystems; type theory; semantics;program transformation andanalysis.

R E P R E S E N TAT I V E P U B L I C AT I O N SMark P. Jones, “Type Classes with

Functional Dependencies,” inProceedings of the 9th EuropeanSymposium on Programming, ESOP2000, Berlin, Germany, Springer-VerlagLNCS 1782, March 2000.

M.P. Jones, “First-class Polymorphismwith Type Inference,” in Proceedingsof the 24th Annual ACM SIGPLAN-SIGACT Symposium on Principles ofProgramming Languages, Paris,January 1997.

M.P. Jones, “Using ParameterizedSignatures to Express ModularStructure,” in Proceedings of the23rd Annual ACM SIGPLAN-SIGACTSymposium on Principles ofProgramming Languages, St.Petersburg Beach, Fla., January 1996.

M.P. Jones, “Simplifying andImproving Qualified Types,” inProceedings of FPCA ‘95: Conferenceon Functional Programming Languagesand Computer Architecture, La Jolla,Calif., June 1995.

M.P. Jones, “A System of ConstructorClasses: Overloading and ImplicitHigher-order Polymorphism,” Journalof Functional Programming, 5(1),Cambridge University Press, January1995.

S. Liang, P. Hudak and M.P. Jones,“Monad Transformers and ModularInterpreters,” in Conference Record ofPOPL’95: 22nd ACM SIGPLANSIGACTSymposium on Principles ofProgramming Languages, SanFrancisco, January 1995.

M.P. Jones, Qualified Types: Theoryand Practice, Cambridge UniversityPress, November 1994.

R I C H A R D B . K I E B U R T Z

ProfessorPh.D., Electrical EngineeringUniversity of Washington, [email protected]


Functional programming; programtransformation; domain-specificlanguages; program verification;high-confidence software.

R E P R E S E N TAT I V E P U B L I C AT I O N SR.B. Kieburtz, “Real-time Reactive

Programming for EmbeddedControllers,” QAPL 2001,September 2001.

R.B. Kieburtz, “A Logic for RewritingStrategies,” Strategies ‘01, June 2001.

R.B. Kieburtz, “Defining andImplementing Closed Domain-SpecificLanguages,” SAIG ‘00, September 2000.

R.B. Kieburtz, “Taming Effectswith Monadic Typing,” in Proc. 3rdInternational Conf. on FunctionalProgramming, ACM Press, April 1998.

R.B. Kieburtz, “Reactive FunctionalProgramming,” in PROCOMET’98,pp. 263-284, Chapman and Hall,June 1998.

R.B. Kieburtz, L. McKinney, J. Bell,J. Hook, A. Kotov, J. Lewis, D. Oliva,T. Sheard, I. Smith and L.Walton, “ASoftware Engineering Experiment inSoftware Component Generation,” inProceedings of the 18th InternationalConference on Software Engineering,Berlin, March 1996.

R.B. Kieburtz, F. Bellegarde, J. Bell, J. Hook, J. Lewis, D. Oliva, T. Sheard,L. Walton and T. Zhou, “CalculatingSoftware Generators from SolutionSpecifications,” TAPSOFT ‘95, Springer-Verlag, series LNCS, 915, 546, 1995.

R.B. Kieburtz, “Programming withAlgebras,” in Advanced FunctionalProgramming, E. Meijer and J.Jeuring,eds., Springer-Verlag, Series LNCS,Vol. 925, 1995.

R.B. Kieburtz, “Results of the SDRRValidation Experiment,” PacificSoftware Research Center SoftwareDesign for Reliability and Reuse:Phase I Final Scientific and TechnicalReport, Vol. VI, CDRL No. 0002.11,February 1995

J O H N L A U N C H B U R Y

ProfessorPh.D., Computing ScienceUniversity of Glasgow, [email protected]


Functional programminglanguages; semantics-basedprogram analysis; programtransformation and partialevaluation.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Lewis, M. Shields, E. Maijer and

J. Launchbury, “Implicit Parameters,”Implicit Parameters, ACM Principles ofProgramming Languages, 2000.

J. Matthews and J. Launchbury,“Elementary MicroarchitectureAlgebra,” Computer AidedVerification, 1999.

J. Launchbury, J. Lewis and B. Cook.“On Embedding a MicroarchitectureDesign Language within Haskell,”International Conference on FunctionalProgramming, ACM, 1999.

J. Launchbury and A. Sabry,“Axiomatization and Type Safetyof Monadic State,” Proc. ACMInternational Conference on FunctionalProgramming, 1997.

J. Launchbury and R. Paterson,“Parametricity and Unboxing withUnpointed Types,” Proc. EuropeanSymposium on Programming,Linkoping, 1996.

J. Launchbury and S.P. Jones, “Statein Haskell,” J. of Lisp and SymbolicComputation, December 1995.

J. Launchbury and S.P. Jones, “LazyFunctional State Threads,” in Proc.SIGPLAN Programming LanguagesDesign and Implementation, Orlando,Fla., 1994.

A. Gill, J. Launchbury and S.P. Jones,“A Short Cut to Deforestation,” inProc. SIGPLAN/SIGARCH FunctionalProgramming and ComputerArchitecture, Copenhagen, 1993.

J. Launchbury, “A Natural Semanticsfor Lazy Evaluation,” in Proc. SIGPLANPrinciples of Programming Languages,Charleston, S.C., 1993.

J. Hughes and J. Launchbury,“Projections for PolymorphicFirst- Order Strictness Analysis,” inMathematical Structures in ComputerScience, 2, 301, C.U.P., 1992.

T O D D K . L E E N

ProfessorPh.D., PhysicsUniversity of Wisconsin, [email protected]


Machine learning, local andmixture models, invariance,stochastic learning, withapplications to anomaly detection,environmental systems monitoring,and data coding. Modelingneurobiological systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SR. Sharma, T.K. Leen and M. Pavel,

“Bayesian Image Sensor Fusion UsingLocal Linear Generative Models,”Optical Engineering, 40, 1364, 2001.

C. Archer and T.K. Leen, “The CodingOptimal Transform,” in Proceedings ofthe Data Compression Conference2001, IEEE Computer Press, 2001.

C. Archer and T.K. Leen, “FromMixtures of Mixtures to AdaptiveTransform Coding,” in Advances inNeural Information Processing Systems,T. Leen, T. Dietterich, V. Tresp, eds.,13, MIT Press, 2001.

W. Wei, T.K. Leen and E. Barnard, “AFast Histogram-Based Postprocessorthat Improves Posterior ProbabilityEstimates,” Neural Computation, 11,1235, 1999.

T.K. Leen, B. Schottky and D. Saad,“Optimal Symptotic Learning:Macroscopic Versus MicroscopicDynamics,” Physical Review E, 59,985, 1999.

T.K. Leen and J.E. Moody, “StochasticManhattan Learning: Time-EvolutionOperator for the Ensemble Dynamics,”Physical Review E, 56, 1262, 1997.

N. Kambhatla and T.K. Leen,“Dimension Reduction by LocalPrincipal Component Analysis,”Neural Computation, 9, 1493, 1997.

T.K. Leen, “From Data Distribution toRegularization in Invariant Learning,”Neural Computation, 7, 974, 1995.

T.K. Leen, “A Coordinate-IndependentCenter Manifold Reduction,” PhysicsLetters, A 174, 89, 1993.

FACULTY


35


D A V I D M A I E R

ProfessorPh.D., Electrical Engineeringand Computer SciencePrinceton University, [email protected]


Database systems (includingobject-oriented databasemanagement systems, queryprocessing, scientific informationmanagement, superimposedinformation and net datamanagement); object-oriented andlogic programming languages;algorithms; bioinformatics andhealth information technology.

R E P R E S E N TAT I V E P U B L I C AT I O N SP. Tucker, D. Maier, T. Sheard and

L. Fegaras. “Exploiting PunctuationSemantics in Continuous DataStreams,” IEEE Transactions onKnowledge and Data Engineering,15(3), May/June 2003.

V. Papadimos, D. Maier and K. Tufte.“Distributed Query Processing andCatalogs for Peer-to-Peer Systems,”Proceedings CIDR 2003: First BiennialConference on Database SystemsResearch, Asilomar, CA, January 2003.

L. Shapiro, D. Maier, P. Benninghoff,K. Billings, Y. Fan, K. Hatawal, B.Vanceand Q.Wang, “Exploiting Upper andLower Bounds in Top-down QueryOptimization,” Proceedings of IDEAS2001, Grenoble, France, July 2001.

J. Shanmugasundaram, K. Tufte,D. DeWitt, J. Naughton and D. Maier.“Architecting a Network Query Enginefor Producing Partial Results,” in TheWorld Wide Web and Databases (ThirdInternational Workshop WebDB 2000),Lecture Notes in Computer Science,Vol. 1997, Springer-Verlag, 2001.

L. Delcambre, D. Maier, S. Bowers,L. Deng, M. Weaver, P. Gorman, J. Ash,M. Lavelle and J. Lyman, “Bundles in Captivity: An Application ofSuperimposed Information,”Proceedings of the IEEE InternationalConference on Data Engineering,Heidelberg, Germany, April 2001.

L. Fegaras and D. Maier, “Optimizing Object Queries Using an Effective Calculus,” ACMTransactions on Database Systems25 (4), December 2000.

J O H N M AT T H E W S

Assistant ProfessorPh.D., Computer ScienceOregon Graduate Institute, [email protected]


Formal verification; theoremproving; model checking;specification languages; functionaland constraint logic programminglanguages.

R E P R E S E N TAT I V E P U B L I C AT I O N SL. Lamport, J. Matthews, M. Tuttle

and Y. Yu, “Specifying and VerifyingSystems With TLA+,” Tenth ACMSIGOPS European Workshop: Can wereally depend on an OS?, Saint-Emilion,France, September 2002 (to appear).

S. Krstic and J. Matthews, “VerifyingBDD Algorithms through MonadicInterpretation,” Proceedings of theThird International Workshop onVerification, Model Checking andAbstract Interpretation, Venice, Italy,January 2002.

J. Matthews, “Recursive FunctionDefinition over Coinductive Types,”Proceedings of the 12th InternationalConference on Theorem Proving inHigher Order Logics, Nice, France,LNCS Vol. 1690, September 1999.

J. Matthews and J. Launchbury,“Elementary MicroarchitectureAlgebra,” Proceedings of the 11thInternational Conference on ComputerAided Verification, Trento, Italy, LNCSVol. 1633, July, 1999.

B. Cook, J. Launchbury and J.Matthews, “Specifying SuperscalarMicroprocessors in Hawk,” Workshopon Formal Techniques for Hardwareand Hardware-like Systems, Marstrand,Sweden, June 1998.

J. Matthews, J. Launchbury and B.Cook, “Microprocessor Specification inHawk,” Proceedings of the IEEEInternational Conference on ComputerLanguages 1998, Chicago, May 1998.

M E L A N I E M I T C H E L L

Associate ProfessorPh.D., Computer ScienceUniversity of Michigan, [email protected]


Artificial intelligence; machinelearning; cognitive science andcomplex systems;. computermodeling of perception andanalogy-making; theory andapplications of evolutionarycomputation; collectivecomputation in spatially extendedsystems such as cellular automataand neural models; history ofscience and technology.

R E P R E S E N TAT I V E P U B L I C AT I O N SL. Pagie and M. Mitchell, “A

Comparison of Evolutionary andCoevolutionary Search,” to appear inInternational Journal of ComputationalIntelligence and Applications, in press.

M. Mitchell, “Analogy-making as aComplex Adaptive System,” in DesignPrinciples for the Immune System andOther Distributed Autonomous Systems,L. Segel and I. Cohen, eds., OxfordUniversity Press, 2001.

M. Mitchell, “Can Evolution ExplainHow the Mind Works? A Review of theEvolutionary Psychology Debates,”Complexity, 3 (3), 17-24, 1999.

E. van Nimwegen, J.P. Crutchfield andM. Mitchell, “Statistical Dynamics ofthe Royal Road Genetic Algorithm,”Theoretical Computer Science, 229 (1),41-102, 1999.

M. Mitchell, “A Complex-SystemsPerspective on the ‘Computation vs.Dynamics’ Debate in CognitiveScience,” in M. A. Gernsbacher andS. J. Derry, eds., Proceedings of the20th Annual Conference of theCognitive Science Society-Cogsci98,pp. 710-715, 1998.

J.P. Crutchfield and M. Mitchell, “TheEvolution of Emergent Computation,”Proceedings of the National Academy ofSciences, USA, 92 (23), 10742, 1995.

M. Mitchell, J.P. Crutchfield and P.T.Hraber, “Dynamics, Computation, andthe ‘Edge of Chaos’: A Re-examination,”in Complexity: Metaphors, Models, andReality, G. Cowan, D. Pines and D.Melzner, eds., Addison-Wesley, 1994.

S H A R O N L . O V I AT T

ProfessorCo-Director for Center forHuman Computer CommunicationPh.D., Experimental PsychologyUniversity of Toronto, [email protected]


Multimodal and spoken languageinterfaces; conversationalinterfaces; ubiquitous andperceptive interfaces; modalityeffects in communication andcommunication models; tele-communication and technology-mediated communication;mobile and interactive interfaces;human-computer interaction;empirically based design andevaluation of human-computerinterfaces; cognitive science andresearch methodology.

R E P R E S E N TAT I V E P U B L I C AT I O N SS.L. Oviatt, “Breaking the Robustness

Barrier: Recent Progress on the Designof Robust Multimodal Systems,”Advances in Computers (ed. byM. Zelkowitz) Academic Press, 2002,vol. 56, pp. 305-341.

S.L. Oviatt, “Multimodal Interfaces,”in J. Jacko and A. Sears, eds., Handbookof Human-Computer Interaction,Lawrence Erlbaum Assoc., Mahwah,N.J., 2002, ch. 14, pp. 286-304.

S.L. Oviatt, P.R. Cohen, L. Wu,J. Vergo, L. Duncan, B. Suhm, J. Bers,T. Holzman, T. Winograd, J. Landay, J. Larson and D. Ferro. “Designing the User Interface for MultimodalSpeech and Gesture Applications:State-of-theart Systems and ResearchDirections,” Human ComputerInteraction, 15 (4), 263-322, 2000. Reprinted in J. Carroll, ed.,Human-Computer Interaction in theNew Millennium, Addison-WesleyPress, 2001.

S.L. Oviatt, “Multimodal SystemProcessing in Mobile Environments,”Proceedings of the 13th Annual ACMSymposium on User Interface SoftwareTechnology UIST’2000, pp. 21-30, 2000.

S.L. Oviatt, “Taming RecognitionErrors with a Multimodal Architecture,” Communications of the ACM, 43 (9), 45-51, (special issue on “Conversational Interfaces”),September 2000.

36

C A LT O N P U

ProfessorPh.D., Computer ScienceUniversity of Washington, [email protected]


Transaction processing,distributed databases, scientificdatabases, parallel anddistributed operating systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SL. Liu and C. Pu, “An Adaptive Object-

Oriented Approach to Integration andAccess of Heterogeneous InformationSources,” International Journal onDistributed and Parallel Databases,5 (2), April 1997.

K.L. Wu, P.S. Yu and C. Pu,“Divergence Control for Epsilon-Serializability,” IEEE Transactions onKnowledge and Data Engineering, 9(2), March-April 1997.

J. Biggs, C. Pu, A. Groeninger andP.E. Bourne, “pdbtool: An InteractiveBrowser and Geometry Checker forProtein Structures,” Journal of AppliedCrystallography, 29 (4), 1996.

L. Liu, C. Pu, R. Barga and T. Zhou,“Differential Evaluation of ContinualQueries,” Proceedings of the 16thInternational Conference on DistributedComputing Systems, Hong Kong, May1996.

K. Ramamrithan and C. Pu, “A FormalCharacterization of EpsilonSerializability,” IEEE Transactions onKnowledge and Data Engineering, 7 (6),December 1995.

C. Pu, T. Autrey, A.P. Black, C. Consel,C. Cowan, J. Inouye, L. Kethana, J.Walpole and K. Zhang, “OptimisticIncremental Specialization:Streamlining a Commercial OperatingSystem,” Proceedings of the 15thSymposium on Operating SystemsPrinciples, December 1995.

R. Barga and C. Pu, “A Practical andModular Implementation Technique ofExtended Transaction Models,”Proceedings of the 21st InternationalConference on Very Large Data Bases,Zurich, September 1995.

K. Ramamrithan and C. Pu, “A FormalCharacterization of EpsilonSerializability,” IEEE Transactions onKnowledge and Data Engineering, 7 (3),June 1995.

T I M S H E A R D

Associate Professor,Director Pacific SoftwareResearch CenterPh.D., Computerand Information ScienceUniversity of Massachusettsat Amherst, [email protected]


Functional programming; softwarespecification; program generation;meta-programming and staging.

R E P R E S E N TAT I V E P U B L I C AT I O N ST. Sheard, “Accomplishments and

Research Challenges in Meta-Programming,” Second InternationalWorkshop on Semantics, Applicationsand Implementation of ProgramGeneration (SAIG 2001), LNCS 2196,Florence, Italy, September 2001.

T. Sheard, “Generic Unification viaTwo-Level Types and ParameterizedModules,” Sixth ACM SIGPLANInternational Conference on FunctionalProgramming (ICFP’01), ACM Press,Florence, Italy, September 2001.

T. Sheard, Z. Benaissa and E. Pasalic,“DSL Implementation Using Staging andMonads,” Usenix, Second Conference onDomain Specific Languages. Austin,Texas. October 1999.

W. Taha, Z. Benaissa and T. Sheard,“Multi-Stage Programming:Axiomatization and Type Safety,” 25thInternational Colloquium on Automata,Languages and Programming, July 1998.

M. Shields, T. Sheard and S. PeytonJones, “Dynamic Typing as Staged TypeInference,” ACM-SIGPLAN-SIGACTSymposium on Principles ofProgramming Languages (POPL ‘98),San Diego, January 1998.

T. Sheard, “A Type-Directed, On-Line,Partial Evaluator for a PolymorphicLanguage,” ACM-SIGPLAN Conferenceon Partial Evaluation and Semantics-Based Program Manipulation,Amsterdam, June 1997.

W. Taha and T. Sheard, “Multi-StageProgramming with ExplicitAnnotations,” ACM-SIGPLANConference on Partial Evaluation andSemantics-Based ProgramManipulation, Amsterdam, June 1997.

C L Á U D I O T. S I LVA

Associate ProfessorPh.D., Computer ScienceState University of New Yorkat Stony Brook, [email protected]


Computer graphics; scientificvisualization; appliedcomputational geometry; highperformance computing.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Fleishman, M. Alexa, D. Cohen-Or

and C. Silva, “Progressive Point SetSurfaces,” ACM Transactions onGraphics (to appear).

W. Corrêa, J. Klosowski and C. Silva,“Out-Of-Core Sort-First ParallelRendering for Cluster-Based TiledDisplays,” Parallel Computing, 29,325-338, 2003.

M. Alexa, J. Behr, D. Cohen-Or,S. Fleishman, C. Silva and D. Levin,“Computing and Rendering Point SetSurfaces,” IEEE Transactions onVisualization and Computer Graphics,9(1), 3-15, 2003.

R. Farias and C. Silva, “Out-Of-CoreRendering of Large UnstructuredGrids,” IEEE Computer Graphics andApplications, 21(4), 42-50, 2001.

P. Lindstrom and C. Silva, “A MemoryInsensitive Technique for Large ModelSimplification,” IEEE Visualization2001, pp. 121-126.

J. El-Sana, N. Sokolovsky and C. Silva,“Integrating Occlusion Culling withView-Dependent Rendering,” IEEEVisualization 2001, pp. 371-378.

J. Klosowski and C. Silva, “ThePrioritized-Layered ProjectionAlgorithm for Visible Set Estimation,”IEEE Transactions on Visualization andComputer Graphics, 6(2), 108-123,2000.

B. Wei, C. Silva, E. Koutsofios,S. Krishnan and S. North. “VisualizationResearch with Large Displays,” IEEEComputer Graphics and Applications,20(4), 50-54, 2000.

F. Bernardini, J. Mittleman, H.Rushmeier, C. Silva and G. Taubin, “TheBall-Pivoting Algorithm for SurfaceReconstruction,” IEEE Transactions onVisualization and Computer Graphics,5(4), 349-359, 1999.

X U B O S O N G

Assistant ProfessorPh.D. Electrical EngineeringCalifornia Institute of Technology,[email protected]


Digital image and videoprocessing; statistical patternrecognition; machine learning;sensor fusion; computer vision;information theory; biomedicalengineering.

R E P R E S E N TAT I V E P U B L I C AT I O N SG. Wang, M. Pavel, X. Song, “Robust

Recognition Based on Combination ofWeak Classifiers,” International JointConference of Neural Networks, July 2003.

X. Song, Y.S. Abu-Mostafa, J. Sill, H.L. Kasdan and M. Pavel, “ImageRecognition by Fusion of ContextualInformation,” Information FusionJournal 3, 277-287, 2002.

A. Adami, K. Yang, X. Song, M. Paveland D. Dirschl, “Model-based ImageProcessing and Analysis for FractureClassification,” The Second JointMeeting of the IEEE Engineering inMedicine and Biology Society (EMBS)and the Biomedical Engineering Society(BMES), 2002.

X. Song, Y. Abu-Mostafa, J. Sill andH. Kasdan, “Image Recognition inContext: Application to MicroscopicUrinalysis,” in Advances in NeuralInformation Processing Systems, S.A.Solla, T.K. Leen, and K.R. Muller (eds.),MIT Press, pp. 963-969, 2000.

X. Song, Y. Abu-Mostafa, J. Sill and H. Kasdan, “Incorporating ContextualInformation into White Blood Cell ImageRecognition,” in Advances in NeuralInformation Processing Systems, M.I. Jordan, M.J. Kearns, and S.A. Solla(eds.), MIT Press, pp. 950-956, 1998.

Y. Abu-Mostafa, and X. Song, “BinModel for Neural Networks,” inProceedings of the InternationalConference on Neural InformationProcessing, S. Amari, L. Xu, L. Chan, I. King, and K. Leung (eds.), Springer,pp. 169-173, 1996.


37


J O N AT H A N W A L P O L E

ProfessorPh.D., Computer ScienceUniversity of Lancaster, [email protected]


Adaptive systems softwareand its application in distributed,mobile and multimediacomputing environments andenvironmental observation andforecasting systems; quality ofservice specification, adaptiveresource management anddynamic specialization forenhanced performance,survivability and evolvabilityof large software systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SA. Goel, B. Krasic, K. Li and

J. Walpole, “Supporting Low-LatencyTCP-Based Media Streams,” inProceedings International Workshop on Quality of Service (IWQoS), 2002.

A. Black, R. Koster, J. Huang,J. Walpole and C. Pu, “Infopipes: AnAbstraction for Multimedia Streaming,”to appear in ACM / Springer-VerlagMultimedia Systems Journal, 2002.

K. Li, C. Krasic, J. Walpole, M. Shorand C. Pu, “The Minimal BufferingRequirements of Congestion-ControlledInteractive Multimedia Applications,”in Proceedings of the 8th International

Workshop on Interactive DistributedMultimedia Systems - iDMS 2001,Lancaster, UK, September 2001. Alsopublished in Springer-Verlag’s LectureNotes in Computer Science SeriesLNCS 2158, pp. 181-192.

R. Koster, A. Black, J. Huang, J. Walpole and C. Pu, “ThreadTransparency in Information FlowMiddleware,” in ProceedingsMiddleware 2001-IFIP/ACMInternational Conference onzDistributed Systems Platforms,Heidelberg, Germany, November 2001.Also appears as OGI Technical ReportCSE-01-004.

D. McNamee, J. Walpole, C. Cowan, C. Pu, C. Krasic, P. Wagle, C. Consel, G. Muller and R. Marlet, “SpecializationTools and Techniques for SystematicOptimization of Systems Software,”ACM Transactions on ComputerSystems, 19(2), 217-251, May 2001.

E R I C A . W A N

Associate ProfessorPh.D., Electrical EngineeringStanford University, [email protected]


Learning algorithms andarchitectures for neuralnetworks and adaptive signalprocessing; applications totime-series prediction, speechenhancement, adaptive controland telecommunications.

R E P R E S E N TAT I V E P U B L I C AT I O N SE.A. Wan, A.A. Bogdanov, R. Kieburtz,

A. Baptista, M. Carlsson, Y. Zhang andM. Zulauf, “Model Predictive NeuralControl for Aggressive HelicopterManeuvers,” IEEE volume on Software-Enabled Control, T. Samad and G. Balas(eds.), 2003.

E.A. Wan and R. van der Merwe,“The Unscented Kalman Filter,” inKalman Filtering and NeuralNetworks, S. Haykin (ed.), John Wiley& Sons, 2001.

E. Wan, and A. Nelson, “Networks for Speech Enhancement,” inHandbook of Neural Networks forSpeech Processing, S. Katagiri (ed.),Artech House, Boston, 1999.

E. Wan and F. Beaufays,“Diagrammatic Methods for Derivingand Relating Temporal Neural NetworksAlgorithms,” in Adaptive Processingof Sequences and Data Structures,”Lecture Notes in Artificial Intelligence,M. Gori, and C.L. Giles (eds.), SpringerVerlag, 1998.

E. Wan, and A. Nelson, “NeuralDual Extended Kalman Filtering:Applications in Speech Enhancementand Monaural Blind Signal Separation,”IEEE Workshop on Neural Networksand Signal Processing, 1997.

E. Wan, “Adjoint LMS: An Alternativeto Filtered-X LMS and Multiple ErrorLMS,” ICASSP96, 3, 1842-1845, 1996.

E. Wan, “Time Series Prediction Usinga Neural Network with EmbeddedTapped Delay-Lines,” in Predicting theFuture and Understanding the Past,A. Weigend, and N. Gershenfeld (eds.),SFI Studies in the Science of Complexity,Proc., 17, Addison-Wesley, 1993.

E. Wan, “Discrete Time NeuralNetworks,” Journal of AppliedIntelligence, 3(1), 91-105, 1993.

Y O N G H O N G YA N

Associate Professor Ph.D., Computer Science& Engineering,Oregon Graduate Institute, 1995. [email protected]


Human computer interface design;spoken language systems; largevocabulary speech recognition;computer vision; real-timeembedded system and speechsignal processing.

R E P R E S E N TAT I V E P U B L I C AT I O N SX. Wu, and Y. Yan, “Linear Regression

Under Maximum a Posteriori Criterionwith Markov Random Field Prior,”in Proceedings IEEE ICASSP2000,June, 2000.

C. Liu, and Y. Yan, “Speaker ChangeDetection Using Minimum MessageLength Criterion,” in Proceedings 6thInternational Conference on SpokenLanguage Processing, October, 2000.

C. Zheng, and Y. Yan, “EfficientlyUsing Speaker Adaptation Data,” inProceedings 6th InternationalConference on Spoken LanguageProcessing, October, 2000

Y. Yan, “Speech Recognition UsingCorrelation Generated Neural NetworkTarget,” IEEE Trans. on Speech andAudio Processing, May 1999.

E. Barnard, and Y. Yan, “Toward NewLanguage Adaptation for LanguageIdentification,” Speech Communication,21(4), 245-254, May 1997.

Y. Yan, E. Barnard, R.A. Cole,“Development of an Approach toAutomatic Language Identificationbased on Phone Recognition,” inComputer, Speech Language, 10(1),37-54, January, 1996.

38

INSTRUCTORSR O B E R T J A F F E , P H . D .(electrical and computerengineering),

Portland State University, 1988.Signals and applied systems;applied mathematics;mathematical systems theory;linear systems; robust control.

S A VA K R S T I C , P H . D .(mathematics)

Belgrade University, 1986. Theoretical computer science;hardware and softwareverification; cryptography;group theory.

J O H N D . LY N C H , B . S .(electrical engineering),

University of Utah, 1979.System-on-Chip design;electronic design automation;self-timed logic design; logicsynthesis and timing analysis.Has 23-year industry careerin designing digital systems.

JOINT FACULTYD R . A N T Ó N I O B A P T I S TAEnvironmental &Biomolecular SystemsOGI School of Science& Engineering

D R . F R A N C O I S E B E L L E G A R D EUniversity of FrancheComte, France

D R . TA M A R A H AY E SBiomedical EngineeringOGI School of Science& Engineering

D R . S H A N N O N K . M C W E E N E YPublic Health andPreventive MedicineOregon Health &Science University

D R . M I S H A P A V E LBiomedical EngineeringOGI School of Science& Engineering

D R . L E O N A R D S H A P I R ODepartment of Computer SciencePortland State University

D R . A N D R E W T O L M A C HDepartment of Computer SciencePortland State University

PART-TIME FACULTYD R . C H A R L E S C O N S E LUniversity of Bordeaux

D R . D A V I D G . N O V I C KUniversity of Texas, El Paso

ADJUNCT FACULTYM R . M A R K A N D E R S Intel Corporation

M R . C H E D L E Y A O R I R I Consultant

M R . R O B E R T B A U E RRational Software Corp.

D R . C . M I C B O W M A NIntel Corporation

M R . S H E K H A R B O R K A R Intel Corporation

M R . B R E N T C A P P SOregon Master ofSoftware Engineering

D R . C H R I S T O P H E R D U B AYOregon Health &Science University

D R . A N R E W G I L LGalois

M R . R O Y H A L LCrisis in Perspective

D R . D A V I D H A N S E NGeorge Fox University

M R . R O Y K R A V I T Z RadiSys Corporation

D R . J A M E S L A R S O NIntel Corporation

D R . W AY N E M U S I CLattice Semiconductor

D R . G I L N E I G E RIntel Corporation

M R . S A N J E E V Q A Z IIntel Corporation

D R . R I C H A R D S P R O ATAT&T Labs, New Jersey

M S . E L I S A B E T H S U L L I VA NTruSec Solutions

M R . J A M E S T S C H A N Z Intel Corporation

M R . S T E W A R T TAY L O R Maxim

D R . P A U L T H A D I K A R A N Intel Corporation

M R . P E R R Y W A G L EComputer Science and EngineeringOGI School of Science& Engineering

M S . R E B E C C A W I R F S - B R O C KConsultant

D R . M A Z I N Y O U S I FIntel Corporation


39

The academic and researchprograms in Electrical andComputer Engineering (ECE) havebeen realigned within theComputer Science andEngineering (CSE) and BiomedicalEngineering (BME) departments.OGI will continue to offer M.S.and Ph.D. degrees in electricalengineering with programemphasis in computerengineering; signals and systemsprocessing; and biomedicalengineering, as well as pursuingresearch in these three areas.Students interested in theseareas should refer to the CSEand/or BME departments foradditional information.

The academic program in semiconductor-related topics is being phased out. OGI is nolonger accepting M.S. and Ph.D. applicants inthis area of emphasis. During the academicyear 2003 - 2004, the Electrical EngineeringProgram in Semiconductor Engineering(EESE) will offer as many semiconductor-related courses as possible for studentsinterested in a curriculum concentration inthis area while assisting matriculatedstudents to complete their degree programs.

The research activities of the EESE Programcreate a number of opportunities for studentsto participate, via M.S. and Ph.D. thesisresearch or non-thesis student projects, inthe research of the EESE faculty. Studentsmay become involved in relativelyfundamental investigations such assemiconductor materials characterizationand processing. In all cases, the emphasis ison scientific and engineering investigationshaving well-defined goals and real utility inan atmosphere resembling that of a workingresearch development laboratory. The EESEProgram has close ties to local industry,particularly Intel. The academic program,while rigorous, is innovative and individuallyplanned to meet each student’s needs. Thelimited number of students in residenceassures close attention to each student and

progress at a rate determined by thestudent’s ability and effort.

The major fields of research activity in theEESE Program are:

• Atmospheric Optics

• Display Technology including Thin FilmTransistors and Phosphors

• Electro-Optic Systems

• Micro-Electrical-Mechanical Analysis(MEMS)

• Processing for Ultra Shallow DeviceTechnology

• Semiconductor Electronic Devices

• Semiconductor Materials, Characterizationand Processing

• Sensors

• Systems Dynamics

• Thermal Processing

• Nanotechnology applications forelectronics

Program Seminars

The EESE Program and other localeducational and corporate organizations mayhost invited talks and seminars on topics ofinterest in the field of semiconductorengineering. Although not required forgraduate credit, we recommend that allEESE students attend these informativemeetings. Seminar schedules are generallyposted in the program each quarter. Theseseminars are free of charge and offer anopportunity to meet leading local andnationally recognized EE professionals andlearn about the latest technical advance-ments in the high-technology industry.

DEGREE REQUIREMENTS

M A S T E R O F S C I E N C E ( M . S . ) A N D P H . D . P R O G R A M S

Those students admitted into the Electricaland Computer Engineering Department (ECE)prior to July 1, 2003 for a matriculated EEdegree should follow the degree requirementsas stated in the OGI catalog effective theiryear of matriculations.

Independent Study credits may be taken onlyduring a student’s final quarter of graduateprogram for a maximum of 3 credits. Refer tothe 2002/2003 OGI catalog (page 58) foradditional details.

Electrical EngineeringProgram in

Semiconductor Engineering

www.ece.ogi.edu

P R O G R A M D I R E C T O R Don Johansen


A D M I N I S T R AT I V E C O O R D I N AT O RJoan S ims


E E S E G E N E R A L I N Q U I R I E S


Er ic Thompson, a Ph.D. student , stud ies thee lectron work funct ion of var ious photocathodemater ia ls . OGI of fers numerous ways forstudents to pursue M.S. and Ph.D. degrees ine lectr ica l eng ineer ing .

42

E E S E | E L E C T R I C A L E N G I N E E R I N G P R O G R A M I N S E M I C O N D U C TO R E N G I N E E R I N G

CURRICULUM FOCUS AREA

Students should refer to EESE Program’s12-month Curriculum Planner to learn whatcourses may be offered in the 2003-2004academic year. The following arerecommended core courses and tracks forthe semiconductor focus areas.

S E M I C O N D U C T O R D E V I C E S , M AT E R I A L S ,A N D P R O C E S S I N G

EESE offers a broad spectrum of courses insemiconductor synthesis, processing, devicephysics and integrated circuits. Courses aredesigned to prepare the student for growthareas in semiconductor-based technology.Specific groups of courses are designed toprovide a strong, cohesive, and marketablebody of knowledge in device processing,device physics and design, and integratedcircuit design. Students may tailor courseselections to create unique specializations inpreparation for careers in this importanttechnology field.

R E C O M M E N D E D C O R E C L A S S E S

1. EE 528/628 Introduction to Electronic Materials2. EE 547/647 Statistical Process Control and DOE3. Choose one device class from: EE 529/629 Fundamentals of Semiconductor

Device StructuresEE 533/633 Advanced MOSFET Analysis I: DC Models

The following course tracks are recom-mended for anyone who wishes to specializein a particular area of microelectronics.

S E M I C O N D U C T O R D E V I C E S / C I R C U I T S

EE 529/629 Fundamentals of SemiconductorDevice Structures

EE 530/630 Advanced Semiconductor DeviceStructures and Materials

EE 533/633 Advanced MOSFET Analysis I: DC ModelsEE 534/634 Advanced MOSFET Analysis II:

Dynamic ModelsEE 535/635 MOSFET Modeling for VLSI Circuit DesignEE 561/661 Analog Integrated Circuit DesignEE 562/662 Digital Integrated Circuit DesignEE 574/674 CMOS Digital VLSI Design IEE 575/675 CMOS Digital VLSI Design II

S E M I C O N D U C T O R P R O C E S S I N G A N D M AT E R I A L S

EE 514/614 Failure and Reliability in MicroelectronicsEE 537/637 Thin Film Deposition and Applications

in Semiconductor FabricationEE 540/640 Microelectronic Device Fabrication IEE 541/641 Microelectronic Device Fabrication IIEE 542/642 Microelectronic Device Fabrication IIIEE 543/643 Plasma Processing of SemiconductorsEE 553/653 Modern Photolithographic Engineering

EE 554/654 Reliability and Failure of ElectronicDevices, Packages, and Assemblies

EE 555/655 Simulation & Modeling of VLSI InterconnectEE 557/657 Technology of Photoresists

S E M I C O N D U C T O R M AT E R I A L S A N DD E V I C E C H A R A C T E R I Z AT I O N

EE 511/611 Analytical Scanning Electron MicroscopyEE 512/612 Focused Ion Beam TechnologyEE 513/613 Transmission Electron MicroscopyEE 514/614 Failure and Reliability in MicroelectronicsEE 545/645 Electronic Materials and

Device Characterization

M E M S A N D S E N S O R S

EE 548/648 Fundamentals of Sensors andMEMS Fabrication

EE 550/650 Introduction to Sensor MicrofabricationEE 552/652 Micro-electro-mechanical SystemsEE 556/656 Semiconductor Sensors

The following classes are required for Ph.D.students and are electives for M.S. students.However, these are recommended for M.S.students planning to continue with our Ph.D. program.

EE 525/625 Introduction to Electromagnetics forModern Applications

EE 526/626 Electromagnetics for Modern Applications IIEE 527/627 Electromagnetics for Modern Applications IIIEE 531/631 Introduction to Quantum Mechanics for

Electrical and Computer EngineersEE 532/632 Advanced Quantum Mechanics for

Electrical and Computer Engineers

RESEARCH PROGRAMS

Atmospheric Optics

The use of laser systems to transmit signalsthrough the atmosphere for purposes ofcommunication, radar, recognition, and designationis severely limited by scattering due to turbulenceand particulates such as water droplets or dust.Turbulence, which causes shimmer on a hot dayand makes stars seem to twinkle, results in therandom steering, spreading and breaking-up(scintillation) of a laser beam. Particulatescattering that severely attenuates the receivedsignal also causes depolarization and multiple patheffects such as pulse stretching and scrambling ofthe signal. Experimental studies, in conjunctionwith concurrent theoretical work, are contributingsignificantly to fundamental understanding of theeffects of atmospheric turbulence on laser beam,speckle propagation and its application to opticalremote sensing. Holmes

Nanoelectronics

The current microelectronics revolution has beendriven by miniaturization of the sillicon transistor.This trend is fast approaching fundamental limitsthat will create barriers to further downscaling.

A possible solution for overcoming this barrier is to make devices with nanoscale structures that can take advantage of quantum mechanical effects.The objective of this research is to addressfundamental problems related to integration ofnanowires and nanotubes for development ofnanoelectronic devices. Freeouf, Hammerstrom,Rananavare, Solanki

Electronic Materials and Devices

An active research program in electronic materialsgrowth and characterization focused on demands ofthe ever-shrinking microelectronic devices. Themain materials growth technique investigated isatomic layer deposition, which allows growth ofhighly conformal thin films, one atomic layer at atime. Materials investigated using this approachinclude thin gate dielectrics, includingnanolaminates and metallic films which includecopper seed layers and barrier metals. Anotherarea of research involves electrodeposition ofcopper films for microelectronic deviceinterconnect applications. The focus of thisinvestigation is to determine the correlationbetween the bath chemistry to the physicalproperties of the films and their electromigrationlifetimes. Freeouf, Solanki

Optical Remote Sensing

Analytical and experimental studies are exploringthe use of the interaction of electromagneticradiation and turbulence to measure winds andturbulence. Recent efforts include analytical,numerical and experimental work on a CO2, opticalheterodyne system for remote measurement ofatmospheric cross winds and strength ofturbulence. Holmes

RESEARCH FACILIT IESThe EESE program has access to a completecomplement of electronic measuring, recording,amplifying, signal generating, data processing, andservicing gear with associated power supplies andcomponent stocks. Additional facilities andequipment include:

C O M P U T I N G R E S O U R C E S

• Windows 2000 computer lab with workstations and server

• Sun Enterprise 3500 departmental computer server

• Unix lab with Solaris workstations and X-terminals

• 8 Node Beowulf Computer Cluster

C I R C U I T D E S I G N

• Computer design lab with eight stations, each consisting of a PC workstation an Altera UP1 board, Altera Niosdevelopment board, TI DSP development board

• VLSI and FPGA circuit design software

• Digital television lab

M AT E R I A L S A N D E L E C T R O N I C C H A R A C T E R I Z AT I O N

• Far-infrared Fourier spectrometer

• Parallel field-vibrating sample magnetometer

• X-ray diffraction generator and cameras

• Facility for electronic transport and luminescencemeasurements as a function of temperature

• Visible, ultraviolet, and infrared gas, solid state and dye lasers

• C-V, I-V measurement facilities

• Electrical characterization (Hall)

• Recombination Lifetime system suitable for bulk and thin film studies

• Two spectroscopic ellipsometry systems: 250-750 nmand 140-300 nm

• Process and device two-dimensional simulators, three-dimensional simulators, Monte Carlo simulators

• Work function and high intensity photo-current stabilitymeasurement equipment

• Atomic force microscope

• Deep-UV spectroscopic ellipsometer

M I C R O S C O P Y

• Inverted and upright optical photomicroscopes

• Field electron and ion micro–copes

• Focused Ion Beam micromachining and microforming capabilities

• Analytical scanning electron microscope –Heating, straining specimen stage

• Analytical scanning/transmission electron microscopes —Heating specimen stage

• High-resolution electron and ion microprobes

• Scanning Auger microprobe microscopy

• Scanning confocal microscopy

• Ion mill, chemical jet-milling, sample preparationfacilities, microtome

• Complete JCPDF x-ray and electron powder diffraction database

• Electron diffraction and image simulation program

• Digital video capture for in-situ microscopy experiments

S E M I C O N D U C T O R A N D L C D FA B R I C AT I O N T E C H N O L O G Y

• Photolithography mask generation and exposure systems

• Semiconductor metallization

• Sputter etching

• Wet etching facilities

• Sputter deposition systems

• Pulsed UV-laser processing system

• Atomic layer epitaxy deposition system

• Liquid crystal display lab with pre-tilt, rubbing and single-cell electro-optic characterization facilities

• Electrochemical deposition

• Process simulators

E L E C T R I C A L E N G I N E E R I N G P R O G R A M I N S E M I C O N D U C TO R E N G I N E E R I N G | E E S E

43

E E S E | E L E C T R I C A L E N G I N E E R I N G P R O G R A M I N S E M I C O N D U C TO R E N G I N E E R I N G | F A C U L T Y

44

FACULTY

J . F R E D H O L M E S

Professor EmeritusPh.D., Electrical EngineeringUniversity of Washington, [email protected]


Speckle propagation throughturbulence, optical remotesensing of wind and turbulence,electro-optic systems, instru-mentation signal processingand biomedical optics.

R E P R E S E N TAT I V E P U B L I C AT I O N SHolmes, J.F., Jacques, S.L., and

Hunt, J.M., “Adapting AtmosphericLidar Techniques to ImagingBiological Tissue,” SPIE, Bios 2000Conference, San Jose, California,January 22-28, 2000.

Becker, M., Holmes, J.F., andMeekisho, L., “InterdisciplinaryCurriculum Development in ElectronicsPackaging Using Course Segmentation,”ASEE 1998 Frontiers in EducationConference, Tempe, Arizona, November4-7, 1998.

Homes, J.F., and Rask, B.J.,“Range Resolved, 3-D Optical RemoteSensing of Atmospheric WindsUsing a CW Lidar,” Advances inAtmospheric Remote Sensing withLidar, A. Amsmann, R. Neuber,P. Rairoux, and U. Wandinger, eds.,Springer-Verlag, Berlin, 1997.

Holmes, J.F., and Zhou, C.,“Path Resolved, Optical RemoteSensing of the Strength of TurbulenceUsing a Pseudo Random CodeModulated CW Lidar and CoherentOptical Processing,” 9th Conferenceon Coherent Laser Radar, Linkoping,Sweden, June, 1997.

Holmes, J.F., and Rask, B.J.,“The Effect of Aerosol Speckle PhaseDecorrelation on the Allowable SignalAveraging Time for Coherent OpticalReceivers,” SPIE Annual Meeting,August 1996.

Holmes, J.F., and Rask, B.J.,“Range Resolved, 3-D, Optical RemoteSensing of Atmospheric Winds Using aCW Lidar,” 18th International LaserRadar Conference, Berlin, Germany,July 1996.

Holmes, J.F., and & B.J. Rask,“Optimum, Optical Local OscillatorLevels for Coherent Detection UsingPhotodiodes,” Appl. Opt., 34,February 1995.

R A J S O L A N K I

ProfessorPh.D., PhysicsColorado State University, [email protected]


Atomic layer deposition ofnanoscale films, copper electro-deposition and electropolishingfor multilevel interconnects,high-k gate dielectrics, polysiliconthin film transistors (TFTs),silicon nanowires.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Huo, J. McAndrew, and R. Solanki,

“Electropolishing of Copper forMicroelectronics Applications,”J. Surface Engineering 19, 1 2003.

R. Solanki, J. Huo, J. F. Freeouf, andB. Miner, “Atomic layer Deposition ofZnSe/CdSe Superlattice Nanowires,”Appl. Phys. Lett., 81, 3864, 2002.

J. Huo, R. Solanki, and J. McAndrew,“Characteristics of Copper FilmsProduced via Atomic Layer Deposition,”J. Mat. Research. 17, 2394 2002.

A. Y. Kang, P. M. Lenahan,J. F. Conley, and R. Solanki, “AnElectron Spin Resonance Study ofInterface Defects in ALCVD HafniumOxide on Si,” Appl. Phys. Lett. 81,1128 2002.

J. F. Conley, Y. Ono, W, Zhuang,D. J. Tweet, S. K. Mohammed, andR.Solanki, “Atomic Layer Deposition ofHafnium Oxide Using AnhydrousHafnium Nitrate,” Electrochem. andSolid-State Lett., 5 , C57 2002.

A.T. Voutsas, H. Kisdarjono, andR.Solanki, “Numerical Simulation ofNon-Equilibrium, Ultra-Rapid Heatingof Si Thin Films by Nanosecond PulsedExcimer Lasers,” Simulation ofSemiconductor Processes and Devices,D. Tsoukalas and C. Tsamis, eds.,Spinger Wien, New York, 2001.

H. Zhang and R. Solanki,“Atomic Layer Deposition of HighDielectric Constant Nanolaminates,”J. Electrochem. Soc., 148, 63 2001.

(Invited) B. Pathangey and R. Solanki,“Atomic Layer Deposition for NanoscaleThin Films,” Vacuum Technology andCoatings, 1, 32 2000.

R. Engelmann, J. Ferguson, and R.Solanki, “Quantum Well ActivatedPhosphors — A New Concept forElectroluminescent Displays, Appl.Phys. Lett. 70, 411 1997.

JOINT FACULTYY O N G H O N G YA N Associate Professor,Department of Computer Science& EngineeringPh.D., Computer Science& EngineeringOregon Graduate Institute, 1995

ADJUNCT FACULTY A N T H O N Y B E L LConsultant

S T E V E B R A I N E R DMaxim Integrated Products

Y O U S S E F A . E L - M A N S YIntel Corp.

R E I N H A R T E N G L E M A N NConsultant

D A V I D E VA N SSharp MicroelectronicsTechnology Inc.

W AY N E K . F O R DIntel Corp.

J O H N F R E E O U FInterface Studies, Inc.

J O D Y H O U S EiSense Corp.

H A R I S H M U T H A L IIntel Corp.

S H A N K A R R A N A N A VA R EPortland State University

K A R T I K R A O LIntel Corp.

E D W A R D F. R I T Z , J R .Consultant

M I LT O N S C H O L LConsultant

T H O M A S T H O M A SIntel Corp.

The mission of the DEPARTMENT OF

ENVIRONMENTAL AND BIOMOLECULAR

SYSTEMS is to study physical,chemical and biological processesthat occur naturally or resultfrom the interaction of humanswith the environment,emphasizing approaches that arepossible through novel advancesin biomolecular, genetic,computational and informationsciences and technology.

Three over-arching goals characterize ourresearch and education programs:

• Fundamental understanding of processesat molecular, cellular and particle levels

• Integrative, process-based understandingof ecosystems and other complexenvironmental and biological systems

• Effective integration of science in society’sapproaches to ecosystem health, humanhealth, and economic development

Prospective students are asked to carefullyexamine faculty research interests anddepartmental research programs todetermine whether their specific professionalgoals can be fulfilled at OGI in theDepartment of Environmental andBiomolecular Systems. Communication withindividual faculty members is encouragedbefore applying or enrolling.

DEGREES OFFERED

For students entering during the 2003-2004academic year, the department offers thefollowing degrees:

Master of Science in Environmental Scienceand Engineering

Doctor of Philosophy in EnvironmentalScience and Engineering

Master of Science in Biochemistry andMolecular Biology

Doctor of Philosophy in Biochemistry andMolecular Biology

Special tracks in Environmental InformationTechnology and Environmental HealthSystems are available in the EnvironmentalScience & Engineering degree programs.

M.S. degrees are available in the thesis ornon-thesis options. The thesis optiongenerally requires up to eight academicquarters, and the non-thesis option can becompleted in four academic quarters.

For students entering during the 2004-2005academic year, the department expects tooffer the following degrees only:

Master of Science in Environmental andBiomolecular Systems

Doctor of Philosophy in Environmental andBiomolecular Systems

Special tracks in Environmental Science and Engineering, Environmental InformationTechnology, Environmental Health Systems,and Biochemistry and Molecular Biologywill be available.

M . S . A N D P H . D . , E N V I R O N M E N TA L S C I E N C EA N D E N G I N E E R I N G

The ESE program balances practicalapplications with fundamental investigationsof the physical, chemical and biologicalprocesses underlying environmentalphenomena. The M.S. in EnvironmentalScience and Engineering prepares studentsfor careers in environmental management,practice, or research. The curriculum ishighly interdisciplinary and is built on a solidfoundation of fundamental science andengineering. For more information, seewww.ese.ogi.edu/curriculum.html.

• Environmental Information Technology Track – EIT (M.S. and Ph.D.)

The EIT track combines the expertise andcourse work found in EBS and in theDepartment of Computer Science andEngineering (CSE). The goal of the EITtrack is to combine a deep understandingof environmental processes with masteryof sensing, modeling and informationtechnology. Requirements for the EITtrack are the same as for the M.S. thesisand non-thesis options described above,except that students in the EIT trackcomplete approximately 20 percent oftheir course work in the CSE department.The EIT curriculum includes fundamentalcourses, science courses, technologycourses, electives and capstoneintegrative courses. For more informationon the EIT track and its curriculum, seehttp://www.ese.ogi.edu/eit/.

Department ofEnvironmental and

Biomolecular Systems

www.ebs.ogi.edu

D E P A R T M E N T H E A D Antón ia M. Bapt ista , Ph.D.


A S S O C I AT E D E P A R T M E N T H E A D F O R E D U C AT I O N James J . Huntz icker, Ph.D.


A C A D E M I C A D M I N I S T R AT O RTherese Young


E B S G E N E R A L I N Q U I R I E S


Coasta l research in EBS department .

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E B S | E N V I R O N M E N TA L A N D B I O M O L E C U L A R S YS T E M S

• Environmental Health Systems Track – EHS(M.S. only)

The EHS track focuses on how environ-mental factors combine with genetics toaffect the well-being of humans, otherspecies and ecosystems, as well as themethods used to manage environmentalhealth in its broadest sense — with equalemphasis on human and ecological riskassessments, recognizing the complexinterdependencies. The EHS track willprepare students to take on leadership,management and research roles in the broad domain of environmental health systems.

M . S . A N D P H . D . , B I O C H E M I S T R Y A N DM O L E C U L A R B I O L O G Y

The BMB program offers studentsimmediate participation in research uponentering. This early exposure to researchallows each student to become familiar withthe variety of activities represented in thedepartment and aids the student in thesisresearch selection.

ADMISSION REQUIREMENTS

In addition to the general OGI admissionsrequirements, the EBS Department requiresthe following:

M . S . A N D P H . D . I N E N V I R O N M E N TA L S C I E N C EA N D E N G I N E E R I N G

GRE general scores are required. GREsubject scores are not required. TOEFLminimum score is 600 for the paper-basedtest or 250 for the computer-based test.

M . S . I N B I O C H E M I S T R YA N D M O L E C U L A R B I O L O G Y

GRE scores are not required. TOEFLminimum score is 550 for the paper-basedtest or 213 for the computer-based test.

P H . D . I N B I O C H E M I S T R YA N D M O L E C U L A R B I O L O G Y

GRE general scores and GRE subjectscores for one of the following tests: (a)biology, (b) chemistry or (c) biochemistry,cell and molecular biology are required.TOEFL minimum score is 550 for thepaper-based test or 213 for the computer-based test.

APPLICATION DEADLINES

Applications for fall quarter received by March 1 receive priority review foradmission and financial support. M.S.applications are accepted year-round,and applicants are encouraged tocomplete the application process by July 31 for fall quarter admission. Ph.D. applications for admission inquarters other than fall are consideredon the basis of available space andfinancial assistance.

CREDITS FROM OTHEROHSU DEPARTMENTS

Up to eight credits from courses takenin other OHSU departments may beapplied to an EBS program. The student’sprogram committee (SPC) must firstapprove the appropriateness of creditsfrom other OHSU departments.

DEPOSIT

Upon acceptance, applicants to the M.S.program are reequired to pay a non-refundable deposit of $100 to guaranteetheir places in the program. For thosestudents who receive less than a fulltuition scholarship, this fee will beapplied to the tuition payment for thefirst quarter of residence.

TUIT ION

Tuition for full-time students in theDepartment of Environmental andBiomolecular Systems department ischarged on an annual (four-quarter) basisfor the first academic year and quarterlythereafter. Completing the program inless than four quarters still incurs theannual tuition charge ($21,420 for 2003-2004, exclusive of any scholarshipaward). Transferring credits from anotherinstitution can reduce the time to complete a degree but does not reduce the annual first year tuition charged. The first year tuition can be paid inquarterly installments corresponding to the academic quarters.

DEGREE REQUIREMENTS

E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G

Students may pursue the Ph.D. programor M.S. program (non-thesis or thesisoptions) in ESE, EIT or EHS. EIT andEHS are educational tracks within theESE program. Students who complete theEIT or EHS tracks receive their degree inEnvironmental Science and Engineering.

M . S . I N E N V I R O N M E N TA L S C I E N C EA N D E N G I N E E R I N G

M . S . N O N - T H E S I S O P T I O N

Students pursuing the M.S. non-thesis option must complete at least 45 credithours. These credits include the distributionrequirements as outlined below andadditional courses selected with the approvalof the SPC. Up to eight credit hours may begranted for approved participation in non-thesis research or approved work as anintern with a local company or governmentagency. Comprehensive examinations are not required.

M . S . T H E S I S O P T I O N

Students pursuing the M.S. thesis optionmust complete at least 45 credits. Thesecredits include the distribution requirementsoutlined below, additional courses selectedwith the approval of the SPC, and researchcredits. M.S. thesis research (EBS 503) isusually no more than nine credits. A writtenM.S. dissertation with an oral defense isrequired. Comprehensive examinations arenot required.

P H . D . I N E N V I R O N M E N TA L S C I E N C EA N D E N G I N E E R I N G

Ph.D. students must complete at least 52credit hours of coursework. These creditsinclude the distribution requirementsoutlined below and additional coursesselected with the approval of the SPC. Ph.D. candidates must pass a two-partcomprehensive examination. The first part isa written examination covering four subjectareas selected by the department. Thesecond part is the preparation and oraldefense of a proposal that defines thestudent’s Ph.D. dissertation research. A written Ph.D. dissertation with an oraldefense is required.

M . S . A N D P H . D . I N E N V I R O N M E N TA L S C I E N C EA N D E N G I N E E R I N G D I S T R I B U T I O N R E Q U I R E M E N T S

To achieve the necessary breadth in training,M.S. and Ph.D. students take courses thatcover a range of scientific disciplines andenviron-mental media. Five courses must betaken that satisfy the following distributionrequirements. No course can satisfy morethan one requirement.

At least one course must be taken from threeof the following four discipline groups:

1. Applied Mathematics - EBS 545/645; EBS547/547; EBS 550/650; EBS 555/655

2. Chemistry - EBS 510/610; EBS 535/635;EBS 537/637

3. Fluid Dynamics - EBS 560/660; EBS575/675; EBS 578/678

4. Biology - EBS 590/690; EBS 593/693

At least one course must be taken from eachof the following environmental media groups:

1. Surface Waters - EBS 560/660; EBS575/675; EBS 578/678

2. Groundwater - EBS 570/670; EBS571/671; EBS 572/672; EBS 573/673

Students in the EIT and EHS tracks havecustomized requirements defined by the SPC.

M.S. and Ph.D. students in the ESE programare required to take the EBS DepartmentSeminar (EBS 507A/607A) each academicquarter, except summer. This course does notcount toward degree credit requirements.

B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y

Students may pursue the Ph.D. program orM.S. program (non-thesis or thesis options)in BMB.

M.S . IN B IOCHEMISTRY AND MOLECULAR B IOLOGY

M . S . N O N - T H E S I S O P T I O N

Students pursuing the M.S. non-thesisoption must satisfactorily complete aminimum of 44 credits, 28 in gradedcourses and 16 derived from anexperimental research project (EBS 501),as well as a written report on the research.Graded courses include 12 credits in EBS512, 513, 514, and 16 or more credits inadvanced courses (EBS 525 - 598), StudentSeminars (EBS 507B or 507C), and SpecialTopics (EBS 506). Research for the M.S.non-thesis option is typically a specific

contribution to a larger project, providingthe student with extensive hands-onexperience in biochemical and molecularbiological techniques.

M . S . T H E S I S O P T I O N

The M.S. thesis option is a research degreethat requires satisfactory completion of 44credits, 20 of which are in graded courses(12 credits in EBS 512, 513 and 514, pluseight or more credits in advanced courses),and a written thesis based on independentresearch (EBS 503).

M.S. students in the BMB program areencouraged to take the EBS DepartmentSeminar (EBS 507A). This course does notcount toward degree credit requirements.

P H . D . I N B I O C H E M I S T R YA N D M O L E C U L A R B I O L O G Y

Ph.D. students are required to take the EBS612, 613, 614 biochemistry sequence andthree of the following core courses:

EBS 625 Bioenergetics and . . . . . . . . . . . 4 creditsMembrane Transport

EBS 628 Enzyme Structure, Functionand Mechanisms . . . . . . . . . . . 4 credits

EBS 640 Instrumental Methodsin Biophysics . . . . . . . . . . . . . . I-4 credits

EBS 685 Advanced Molecular Biology . . . . 4 credits EBS 687 Molecular Cell Biology . . . . . . . . 4 credits Courses in other departments and schools within OHSUmay be substituted for the core course requirements withpermission of the SPC. The SPC may also advise additionalcourses based upon the particular research interests andneeds of the student.

Ph.D. Students must register for 12 creditsper quarter. These credits typically includeStudent Seminars (EBS 607B or 607C),Department Seminar (EBS 607A; requiredeach quarter, except summer), andResearch (EBS 601 or 603). The qualifyingexamination for the Ph.D. is acomprehensive examination in biochemistry.It must be completed within two years ofentering the school. An oral defense of thePh.D. dissertation is required.

RESEARCH PROGRAMS(alphabetically by faculty name)

CORIE: A Multipurpose Coastal Observatory

Operating since 1996, CORIE is a multipurposecoastal observatory for the Columbia River(http://www.ccalmr.ogi.edu/ CORIE). The motivationof this research program is twofold. First, the

Columbia River and its near-shore plume are a dominant oceanographic feature of thenortheastern Pacific Ocean and the focus ofcontroversial ecosystem management issues.CORIE represents a novel, promising and much-needed infrastructure for physical andecological research in this system. Second, weenvision that multipurpose observation andforecasting systems will become central to themanagement of coasts and estuaries worldwide.The Columbia River estuary is a challengingnatural laboratory to test concepts and tools, andCORIE is a pilot system developed to anchor ourenvironmental information technology and ourcoastal observation and prediction research.Baptista, Chawla, Zhang, Zulauf

Quality-Scalable Information Flow Systems forEnvironmental Observation and Forecasting

Recent advances in computer power andconnectivity have fueled the development of real-time Environmental Observation and ForecastingSystems (EOFS). These systems will revolutionizethe way scientists share information about theenvironment and represent an unprecedentedopportunity to break traditional informationbarriers separating scientists from society at large.Incipient forms of EOFS are already in use in areasof strong social relevance, but they tend to besmall-scale, application- and domain specific,stand-alone systems. There is a need to evolvetoward multipurpose, shared systems designed toadapt flexibly to evolving needs of informationconsumers. To meet this need, we have assembledan interdisciplinary team, including computerscience and environmental science researchersand a heterogeneous base of pilot users. Our goalsinclude (a) developing missing integration conceptsand technologies for EOFS, (b) closing the loopbetween environmental models and sensors, (c)using, evaluating and refining the CORIE coastalobservatory (www.ccalmr.ogi.edu /CORIE) as apilot EOFS and (d) developing pilot multileveleducational programs (http://www.ese.ogi.edu/eit/).Baptista, Walpole, Maier, Leen, Feng and Feng

Ocean Survival of Salmonids Relative to MigrationalTiming, Fish Health and Oceanographic Conditions.

Interannual variation in ocean recruitment ofsalmon is high and thought to be associated withvariation in nearshore ocean conditions. Thenearshore ocean environment, particularly thatassociated with the Columbia River plume, is acritical habitat to outmigrating juvenile salmon.Several investigators have suggested that survivalduring the first year of ocean life is a key toestablishing year-class strength. In the case ofsalmonids originating in the Columbia River Basin,survival success hinges on the complex interactionof smolt quality and the abiotic and biotic oceanconditions at the time of entry and during theirfirst year of ocean existence. This researchhypothesizes that variation in the physical andbiological conditions of the nearshore environment,

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particularly that associated with the ColumbiaRiver plume, affects overall survival of ColumbiaRiver stocks. Further, the research hypothesizesthat primary factors driving the variation in thenearshore environment include (a) food availabilityand habits, (b) time of entry, smolt quality andgrowth and bioenergetic status at the time of entryand during the first growing season in the oceanand (c) predation (a companion study on predationon juvenile salmon is ongoing). This project, willcharacterize, over a 10-year period, the physicaland biological features of the nearshore oceanenvironment with real-time and modelingprojections of the Columbia River plume as itinteracts with the coastal circulation regime, andwill relate these features, both spatially andtemporally, to variation in salmon health, conditionand survival. Baptista, Jay, and multi-institutionalcollaborators (PI: E. Casillas, NOAA Fisheries)

Estuarine Habitat and Juvenile Salmon —Current and Historic Linkages in the LowerColumbia River and Estuary

Estuaries are considered important to rearing ofjuvenile salmon and represent an integralcomponent of the continuum of habitats thatsalmon occupy for significant periods of time.There is, however, a general lack of science-basedinformation concerning attributes of these tidalfreshwater and oligohaline transition zones neededto support juvenile salmon, particularly in theColumbia River estuary. Further, recent evidencesupports the concern that flow in the ColumbiaRiver significantly affects the availability ofestuarine habitats, that flow is much reducedcompared to historic levels, and that seasonal flowpatterns are much different now than a centuryago. The long history of wetland loss in theColumbia River estuary coupled with change inflow patterns suggests that restoration of thehabitats may benefit recovery of depressed salmonstocks. The need to develop effective restorationstrategies led us to propose empirically identifyingthe benefit of these habitats to juvenile salmon byevaluating habitat-salmon linkages in the lowerColumbia River and estuary. We are conducting amonitoring approach to identify associationsbetween salmon and habitat in the lower ColumbiaRiver and estuary. Baptista, Jay, and multi-institutional collaborators (PI: D. Bottom, NOAAFisheries)

Chemistry of Copper-Containing Enzymes

Increasing numbers of important enzymes areknown to contain copper at their active sites. Ofparticular interest are enzymes involved inneurotransmitter biosynthesis and metabolism(including important neuroactive amines such asnor-adrenaline and amphetamine); enzymesprotecting against oxidative cellular damagecaused by reactive oxygen metabolites; andenzymes catalyzing the biosynthesis ofneuropeptide hormones. A major goal is tounderstand the catalytic role of copper and the

molecular mechanism of oxygen binding andutilization by these oxidase and oxygenaseenzymes. In our laboratory we overexpress wild-type and mutant proteins in mammalian cellculture using large-scale hollow fiber bioreactors,purified them to homogeneity and study them usinga variety of physical and kinetic methods whichinclude high pressure liquid chromatography(HPLC), mass spectrometry (MS), electronparamagnetic resonance (EPR), Fourier transform-infrared (FT-IR) and X-ray absorption spectroscopy(XAS). The XAS technique is performed at theStanford Synchrotron Radiation Laboratoryhttp://www-ssrl.slac.stanford.edu/, which is anational user facility. Funded by grant R01NS27583 (Chemistry and Spectroscopy ofCopper Monooxygenases) from the NationalInstitutes of Neurological Disorders and Strokehttp://crisp.cit.nih.gov/ Blackburn

Cellular Transport and Regulation of Metal Ions

Metal ions such as iron and copper play anessential role in many cellular processes includingenergy production, biosynthesis and antioxidation.The key to their usefulness as enzyme cofactorslies in their ability to catalyze redox reactions, butthis very chemistry introduces the need to tightlyregulate the speciation, concentration andtransport of cellular metal ions, since the free ionsare themselves cytotoxic. Our lab is involved indeducing the molecular mechanism of metal iontransport. Copper enters the cell through thetransporter CTR1 and is then partitioned between anumber of small molecule metallochaperonemolecules (CCS, COX17, SCO1, HAH1) whichselectively metallate target copper enzymes (e.g.,SOD1, cytochrome c oxidase), or P-type ATPases(MNK, WND) which provide further transportmachinery for metallation of secreted proteins.Through application of advanced spectroscopictechniques such as X-ray absorption and massspectrometry we are studying the mode of copperbinding and transport within a number of thesechaperone-target systems. Part of this researchinvolves developing semisynthetic methods forincorporation of Se as selenocysteine into themetallochaperones which will provide us with aunique probe of metal coordination via Se- andCu-K absorption edge spectroscopy. These studieswill lead to a better understanding of the molecularmechanisms of metal-ion homeostasis and will aidin combating diseases (Menkes, Wilson, ALS)believed to be associated with aberrant metalion regulation. Funded by a Program Projectgrant from the National Institute of GeneralMedical Studies (Mechanisms of Metal IonRegulation in Human Cells), P01GM067166%www.crisp.cit.nih.gov/) Blackburn

Cascadia Subduction Zone Tsunamis

Large tsunamis are believed to be locallygenerated in the Cascadia Subduction Zone (CSZ)every 200 to 600 years, based on geologicalrecords. The last large tsunami dates back about

300 years, raising concerns about the protection of coastal communities in Oregon, Washington,California and British Columbia. The coastal impactof potential CSZ tsunamis is being investigatedthrough numerical modeling. The need to usegeological evidence on paleotsunamis as the sole,loose reference for model validation makes this anunusually interesting and challenging problem. TheOregon Department of Geology and MineralIndustry (DOGAMI) has incorporated our jointresearch results into the development of tsunamiinundation maps for the Oregon coast.Chawla, Baptista, external collaborators

Collaborative Research: Productivity, BiogeochemicalTransformations and Cross-Margin Transport in anEastern Boundary Buoyant Plume Region (A.K.A. RISE-River Influences on Shelf Ecosystems)

River plumes significantly alter nutrient supply,plankton growth rates and standing stocks as wellas enhance material export from productivecoastal areas across the continental margin.Because the typical (upwelling-favorable) windstress and ambient currents act to move plumesaway from the coast during high productionperiods, cross margin export is extremely effectiveon eastern boundaries. In this proposal we focuson a highly productive Eastern Boundary riverplume, the Columbia — a plume sufficiently largeto be of regional importance, yet small enough toallow determination of dominant processesaffecting river plumes, and to facilitate ratecomparisons with regions outside the plume.Available data suggest that the Columbia affectsregional productivity from phytoplankton up thefood chain to juvenile fish (e.g., salmon). Priormeasurements provide a framework for a newcollaborative study that uses the Columbia toexamine plume effects on a productive easternmargin. This study will integrate results from anearby wind-driven CoOP study as well as salmon-related regional studies to provide definitive newinformation on alteration of rates ofbiogeochemical processes by the uniquestratification, turbidity, mixing environment andnutrients of a river plume. Because the ColumbiaRiver provides no significant terrigenous nitrate tothe plume in the growing season, our study allowsplume-endemic processes to be isolated and henceprocess results can be directly applied to otherplumes. Results can also be contrasted withcontrasted with more eutrophic, buoyancyinfluenced coasts.

Our study is designed to address the followingthree hypotheses:

• During upwelling the growth rate ofphytoplankton within the plume exceeds that innearby areas outside the plume being fueled bythe same upwelling macronutrients.

• The plume enhances cross-margin transport ofplankton and nutrients.

• Plume-specific nutrients (iron and silicate) alterand enhance productivity on nearby shelves.

Jay, Baptista, and multi-institutional collaborators(PI: B. Hickey, University of Washington)

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Remediation of Explosives in Groundwater UsingPassive In Situ Permeable Reactive Barriers

Groundwater contamination associated with theuse of explosives (e.g., TNT) is widespread at manyDepartment of Defense sites. Research in ourlaboratories has shown that explosives can berapidly destroyed in situ using zero-valent iron(ZVI). When ZVI is placed in the subsurface as partof a permeable reactive barrier, it can prevent themigration of explosives in groundwater for decadesin a manner that is completely passive.Johnson and Tratnyek

Simulation of Subsurface Processes Using VeryLarge Scale Experimental Aquifers

Many important chemical, physical and biologicalprocesses are difficult to study in the laboratorybecause of problems of scaling. Many of theseprocesses are also difficult to characterize in thefield, because of the complex and uncontrollednature of environmental systems. For thesereasons, OGI has established the LargeExperimental Aquifer Program (OGI/LEAP). Atpresent, the facility consists of five large aquifersused to examine the movements of organic solventsand petroleum compounds in the unsaturated andsaturated porous media. Future LEAP aquifers willexamine inorganic geochemistry and theinteractions between chemical, biological andphysical processes in contaminated aquifers.Johnson and other faculty

Gas-Phase Transport in Unsaturated Porous Media

Gas-phase transport is important in controllingmany subsurface processes, including respiration,pesticide behavior and contaminant volatilizationand movement. Laboratory experiments have beenconducted to determine diffusion rates of a varietyof organic compounds in porous media and thekinetics of adsorption and desorption for a varietyof soil types and a range of water contents.Johnson

Watershed Hydrology and Transport Modeling

Water and chemical movement through watershedshas an important impact on surface- and ground-water quality. The processes that control thatmovement are, in turn, impacted by a range of landuse and water use issues. These complex systemsare frequently difficult to model because of theirlarge scales and the level of detailed understandingnecessary to represent the important processes.We have developed new mathematical tools foraddressing these problems and providing near-real-time modeling of flow and transport inwatersheds. Johnson

Gas-Phase Transport in Unsaturated Porous Media

Gas-phase transport is important in controllingmany subsurface processes, including respiration,pesticide behavior and contaminant volatilizationand movement. Laboratory experiments have been

conducted to determine diffusion rates of a varietyof organic compounds in porous media and thekinetics of adsorption and desorption for a varietyof soil types and a range of water contents.Johnson

Multiphase Monitoring of Gasoline MovementUsing a Very Large Physical Model (OGI/LEAP)

Leaks from underground storage tanks (UST)represent a major ongoing source of groundwatercontamination. The rapid detection of leaks is,therefore, a major goal of UST legislation. TheOGI/LEAP facility is used to study the movement ofgasoline components in the vapor, aqueous andpure-product phases. This work will help establishwhich of a variety of leak-detection technologies isbest suited to detect leaks under a range ofenvironmental conditions. Johnson

Statistical Pattern Recognition in EnvironmentalObservation and Forecasting Systems

Environmental observation and forecasting systems(EOFS) are emerging new technologies withunparalleled potential to impact sustainabledevelopment. EOFS are expected to foster andsupport new paradigms for generation, transferand social application of knowledge in domains thatrange from the global earth to its regional andlocal subsystems. At the core of EOFS is the timelyand customized acquisition, generation, processingand delivery of reliable, relevant information tomany and very diverse audiences. Multiplechallenges need to be met to implement thisconcept. A critical challenge is the development ofautomated procedures to verify the quality of thehuge amounts of observational and simulation datathat are generated by EOFS both in real time andoff-line. Processing based strategies for qualitycontrol of scientific data, while effective formoderate-sized archival data, are too labor-intensive to map well into EOFS-scale data sets.Strategies based on pattern recognition andmachine learning hold significant promise as analternative or complement. Under the proposedproject, we are developing approaches based onstatistical pattern recognition and signalprocessing, on-line adaptive systems, data miningand advanced search to address critical qualitycontrol issues including: 1) Detecting sensorcorruption in non-stationary, spatial-temporalsystems, 2) Estimating true signals from corruptedsensor data, and 3) Detecting and characterizingregimes where model anomalies are likely. Thesequality control techniques will be developed andexercised on CORIE, a pilot coastal observatory forthe Columbia River estuary and adjacent coastalwaters (www.ccalmr.ogi.edu/CORIE/).Leen and Baptista

Vibrational Spectroscopy of Metalloprotein Active Sites

We are interested in the structural and functionalproperties of metal ions in enzymes and proteins,and we use electronic, vibrational (especially rR)and EPR spectroscopy to characterize metal-ion

active sites. Our laboratory has a sensitive, state-of-the-art Raman instrument: a fast spectrographwith a liquid N2-cooled CCD detector. We also use a combined FT-IR/FT-Raman instrument for proteinand model compound studies. Our research focuseson heme (iron porphyrin), nonheme-iron andcopper enzymes and the roles of their metal ions in enzymatic catalysis. Of particular interest is thebiochemistry of O2. Metalloproteins are involved inO2 binding (e.g., hemoglobin or hemocyanin) and in oxidative chemistry whereby O2 is reduced and substrates are oxygenated or oxidized. Theinvestigation of trapped reaction intermediates and model compounds helps us to unravel thesecomplex processes and to define reactionmechanisms. The availability of site-directedmutants permits the alterations in structures andreactivities to be studied. Loehr

Heme Oxygenase

Heme oxygenase is a fascinating system that usesthe O2-binding affinity of its heme substrate in thecellular degradation of heme to open-chainbiliverdin. These studies are carried out with PaulR. Ortiz de Montellano’s group at U.C. SanFrancisco. The resting heme-heme oxygenaseenzyme substrate complex is much like myoglobin:The heme is linked to the enzyme by anironhistidine bond and the iron exists mainly in asix-coordinate, high-spin state with an additionalwater ligand. The Fe-NHis bond was identified fromits resonance Raman vibration at 216 cm-1 in theFe(II)-heme complex. The absence of thisfingerprint frequency in the H25A mutant clearlyidentified His25 as the axial ligand. Remarkably,when imidazole was added to the inactive H25Apreparation, activity was fully restored. Ourcurrent efforts, in collaboration with Angela Wilksat University of Maryland, examine the structureand activity of several bacterial heme oxygenases.Loehr and Moënne-Loccoz

Oxygen Activation by Iron Proteins

Several diiron enzymes react with molecularoxygen to form powerful oxidizing agents importantin biology. Examples include (i) ribonucleotidereductase protein R2, which oxidizes tyrosine 122to its catalytically important neutral radical form;(ii) methane monooxygenase, whose hydroxylasecomponent oxidizes hydrocarbons to alcohols; (iii)plant desaturases, which oxidize fatty acids toolefins, e.g., stearoyl to oleoyl; and (iv) ferroxidasereactions, in which Fe2+ is oxidized to Fe3+ . Acommon feature of these enzymes appears to bethe formation of an initial peroxo intermediateupon exposure of the reduced enzyme to O2. In therespiratory protein, hemerythrin, O2 binding isaccomplished by reduction to peroxide, and thisreaction is readily reversible. However, inribonucleotide reductase, peroxide is similarlyformed but decomposes irreversibly to a ferrylintermediate that is capable of carrying outoxidative chemistry. This dichotomy of behavior isreminiscent of the respiratory vs. peroxidase

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functions of different heme-containing proteins. We are interested in determining commonprinciples that influence the pathways of oxygenutilization. This problem is being approached bystructural elucidation of the iron sites in theproteins themselves and in model complexes,as well as by studying mechanisms of theirreactions with oxygen-containing substrates.Loehr and Moënne-Loccoz

Anaerobiosis of Bacillus subtilis

A gram-positive soil bacterium, B. subtilis, ishighly amenable to genetic analysis and has beenused as a model system to study fundamentalmicrobiological research. In addition, B. subtilis ismedically and industrially important since itproduces a variety of antibiotics and extracellularenzymes. Although the organism has been widelyused, it has been mistakenly referred to as a strictaerobe until recently. Our studies, together withothers, have shown that B. subtilis is able to growunder anaerobic conditions by utilizing nitrate ornitrite as an alternative electron acceptor. In theabsence of terminal electron acceptors, itundergoes fermentative growth. Our research aimsinclude elucidation of the regulatory mechanismsthrough which the cells adapt to oxygen limitation.Molecular genetic and biochemical approaches areapplied. Nakano

ResD-ResE Two-Component Signal Transduction System

Bacteria often encounter sudden environmentalchanges. Cells cope with such changes by anelaborate network of adaptive responses. The two-component signal transduction system senses andthen processes information derived fromenvironmental changes so that the cell can choosethe appropriate adaptive response. This simplesignal transduction system is widespread inbacteria and also found in plants and lowereukaryotes. ResE is a histidine kinase and ResD isa response regulator of this large protein family.We have shown that ResD and ResE areindispensable for anaerobic respiration in B.subtilis. A specific signal derived by oxygenlimitation is recognized by the N-terminal inputdomain of the ResE kinase leading toautophosphorylation of a conserved histidineresidue in the C-terminal transmitter domain. Thisphosphoryl group is then transferred to aspartatein the conserved N-terminal domain of ResD,altering the activity of its C-terminal domain as atranscriptional activator. The ResD-ResE signaltransduction system is activated by oxygenlimitation or by addition of nitric oxide generators.The objectives of our studies are to determine howResE senses oxygen limitation or nitric oxide andhow anaerobically induced genes are activated by ResD. Nakano

Flavohemoglobin (Hmp)

Flavohemoglobin is a ubiquitous protein present inorganisms ranging from Escherichia coli toSaccharomyces cerevisiae. The N-terminal part of

the protein has similarity to hemoglobin and the C-terminus is homologous to reductase with aflavin-binding domain. Recent studies showed thatflavohemoglobin is involved in detoxification ofnitric oxide. B. subtilis hmp was identified amonggenes, expression of which is induced by oxygenlimitation. The anaerobic induction of hmprequires the ResD-ResE signal transduction pairsand nitrite. The expression is also induced byexogenous nitric oxide through ResDE-dependentand -independent mechanisms. The detailedregulatory mechanism of ç expression and itsfunctional role in anaerobiosis are underinvestigation. Nakano

Distribution of Organic Compounds Between theGas and Urban Aerosol Particulate Phases

The behavior of organic compounds in theatmosphere depends in large part on the extent to which they partition from the gas phase toaerosol particulate matter. Processes that areaffected by this partitioning process includeprecipitation scavenging of gases and particles as well as dry deposition of gases and particles.Fundamental gas/solid sorption theory is beingused to investigate important aspects ofatmosphericgas/particle partitioning. The studyinvolves the investigation of basic partitioningbehavior of a wide range of representativeatmospheric compounds (including alkanes andpolycyclic aromatic hydrocarbons) on a variety ofrepresentative model particulate substrates,including elemental carbon, organic carbon, silicaand clay. Pankow

Thermodynamics of Inorganic Solid Solutions

The manner in which inorganic solid solutionsbehave is one of the last major research frontiersin ambient temperature aqueous geochemistry.Coprecipitation of metal ions is well known innature, e.g., Sr2+ can form a solid solution incalcium carbonate (CaCO3[s]). Unfortunately, littleis known about the thermodynamics of such solidsolutions. That is, little is known about how theactivity coefficients of metal ions vary as a functionof composition in solid solutions of various types.The values of the activity coefficients are ofinterest because they control the extent to whichthe constituents in the solid solutions will besoluble in water, e.g., the extent to which a toxicmetal ion like Cd2+ that is present in calciumcarbonate will be soluble in water. In this work,activity coefficient values for a variety ofenvironmentally important divalent metal ions arebeing sought as a function of composition incalcium carbonate. Pankow

Fate and Effects of Fuel Oxygenates

The recent realization that oxygenated fueladditives such as MTBE are becoming widelydistributed groundwater contaminants has createda sudden and pressing demand for data on theprocesses that control their environmental fate.Ongoing work in this area includes modeling of

MTBE infiltration to the groundwater, laboratorystudies of MTBE biodegradation, and field studiesof several contaminated sites for MTBE and itspossible breakdown products. For more informa-tion on this work, see www.cgr.ese.ogi.edu/mtbe/.Pankow, Tratnyek, Johnson

Mechanisms of Mammalian Chemical Communicationand Vomeronasal Olfaction

Chemical communication plays a significant role inlife strategies for many mammals. Our researchfocuses on chemical identification of pheromonesfunctioning during reproductive events in the Asianelephant, Elephas maximus. A female-to-malepreovulatory urinary sex pheromone, (Z)-7-dodecen-1-yl acetate, has been identified anddemonstrated to be robust in its synthetic form.This compound is also bioactive in manyLepidoptera, making it a good example ofconvergent evolution of structure and function.Biochemical studies have established the presenceof the pheromone in the serum, and future studieswill investigate its biosynthetic pathways.Considerable progress has been made onestablishing the proteins functioning as pheromonetransporters prior to signal transduction in theneuroreceptive cells of the vomeronasal organ.Radiolabeled analogs, competition experiments andmolecular biological studies have establishedunusual roles for elephant albumin and olfactorybinding protein. A second pheromonal system isactively being investigated. The facial temporalgland, breath and urine exude unusual chemicalcompounds during musth in Asian male elephants.These signals have a role in mate choice by femaleelephants, spatial distribution by male elephantsand other reactions by conspecifics. Utilizingseveral state-of-the-art gas chromatographic/massspectrometric techniques, we are identifyingspecific compounds that have a chemicalcommunication function, i.e., elicit behavioralresponses, and correlating the release of suchcompounds with serum androgen levels.L. Rasmussen

Global Distributions and Mass Balances ofHalocarbons, Nitrous Oxide and Other Trace Gases

Gases such as CCl3F (F-11), CCl2F2 (F-12) CHClF2

(F-22), CF4 (F-14), C2Cl3F3 (F-113), CH3CCl3, CH3Cland N2O are being added to the atmosphere byvarious industrial processes and the public’s useof high-technology products. Such chlorine-containing compounds are believed to threatenthe Earth’s natural ozone layer high in theatmosphere (stratosphere). This research willsystematically obtain a long-time series ofconcentration measurements by a flask samplingsystem. The results are then interpreted withglobal mass balance models and sophisticatedstatistical techniques to quantify the sources andlifetimes of these gases in the environment. Suchdata are now obtained from sites all over the worldextending from the Arctic Circle to the South Pole.R. Rasmussen

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Studies of Past Atmospheres

Atmospheric gases such as N2O, CO2, CO, CH3Cl,carbonyl sulfide (OCS) and CH4 are primarilyproduced by natural processes, but over the pastcentury human activities have been adding growingamounts to their natural abundance. This processcan upset the cycles of these gases and lead topossibly adverse environmental effects such as thewarming of the Earth’s surface (N2O, CO2, CH4).When both natural and anthropogenic processescontribute to the current atmospheric abundanceof a trace gas, it is of interest to determine theamount which existed before human activities hadany effect. Perhaps the only realistic method todetermine the composition of the ancientatmosphere is to analyze the air in bubbles burieddeep in polar ice. The depth of the ice indicates theage of the air in the bubbles. By going far enoughback in time, the relationship between pastatmospheric composition and climate might befound. The novel and simple method of studying theold atmosphere of the earth is beset by manyproblems that complicate the relationship betweenthe gases in the bubbles and the composition of theold atmosphere. Theoretical and experimentalresearch for resolving these problems as well asthe measurement of trace gases are the majorgoals of this project. R. Rasmussen

Ocean-Air Exchange of Gases

Some atmospheric gases are greatly influenced bythe Earth’s oceans. For instance, a large amount ofthe atmospheric methyl chloride (CH3Cl) andmethyl iodide (CH3I) are produced in the oceans,possibly by biogenic processes. It has also beenshown recently that carbonyl sulfide (OCS) isproduced in the oceans and subsequently emittedto the atmosphere. On the other hand, manmadegases such as CCl3F (F-11) can dissolve in theoceans and thus be removed from the atmosphere.This research project is devoted to determining thesolubility of such gases in water and to modelingthe flux of gases into or out of the oceans. Theresults obtained are essential ingredients indetermining the sources and fates of atmospherictrace gases and in estimating the effects of humanactivities on the future warming of the Earth ordepletion of the ozone layer. R. Rasmussen

Studies of Atmospheric Methane

Considerable evidence has been accumulatedshowing that methane (CH4) is increasing in theatmosphere, most likely as an indirect result ofgrowing human population. In the future, such anincrease of CH4 can lead to a global warming byenhancing the Earth’s natural greenhouse effectand create more ozone and carbon monoxide inthe atmosphere. However, it might also preventsome of the destruction of the stratospheric ozonelayer by the manmade fluorocarbons 11 and 12.In this project, experimental and theoreticalresearch is focused on statistical trend analysesfor the global increase of CH4, its seasonalvariation, sources and sinks, models of its effect

on the CO, O3, and OH cycles and its role in thefuture of the environment. R. Rasmussen

Development of Experimental Methods for TraceGas Measurements

At present, some 50 atmospheric gases can bemeasured at the Trace Gas Laboratory. Still, newmethods are needed to improve the accuracy andprecision of measurements and to satisfy thestringent demands of ultra-clean background airsampling. New methods are also being developedfor automated real-time analysis of many tracegases. Research programs include development ofgas chromatographic and mass spectrometricmethods for the analysis of trace gases. At present,GC/MS systems in the laboratory are being used toroutinely measure C2-C12 nonmethane hydrocarbonsat tens of parts-per-trillion levels. Techniques forcollecting and storing air and water samples alsoare being developed. R. Rasmussen

Biogenic Sources of Atmospheric Gases

Living organisms produce and consume a variety ofgases and may therefore form an integral part ofthe global cycle of a trace gas. Selected plants andanimals, living in the sea or on land, are beingstudied to determine their role in the cycles of CH4,N2O, CH3CI, CH3I, isoprene and other hydrocarbons.R. Rasmussen

The Global Cycle of Carbon Monoxide (CO)

Based on 15 years of global sampling and theapplication of modern trend analysis techniques,our data have shown that CO increased in theatmosphere until around 1987 and has sincedeclined. These changes in CO have majorimplications for atmospheric chemistry and therole of biomass burning in causing global increasesof trace gases. Present research includes modelingof the global budgets, seasonal cycles and potentialenvironmental effects. R. Rasmussen

Methane Emissions from Rice Fields

Methane concentrations have nearly tripledcompared to the natural atmosphere of 300 yearsago (based on ice core analyses). The increase ofrice agriculture to sustain an increasingpopulation may be a major contributor to theincrease of methane during the last century. Thisresearch program is designed to determine therole of rice agriculture in the global methanecycle. Field experiments are being conducted inChina, Indonesia and the United States.Laboratory experiments and theoretical researchare being done at the Global Change ResearchCenter (Portland State University) in acomprehensive research program. This workincludes modeling the production, oxidation andtransport of methane in the rice paddy ecosystemand measuring the controlling parameters. R.Rasmussen

Translational Control in Fungal Amino Acid Biosynthesis

A greater understanding of many human healthissues relies on increased knowledge of how cellsexpress genetic information. Gene expression canbe controlled by regulating the synthesis andstability of functional RNA and protein. The goal ofour research is to obtain a greater understandingof how these mechanisms work using theNeurospora crassa arg-2 and Saccharomycescerevisiae CPA1 genes as models. Thesehomologous genes encode the first enzyme inarginine biosynthesis and they are negativelyregulated at both transcriptional and translationallevels in response to the availability of arginine. Anevolutionarily conserved upstream open readingframe (uORF) present in the 5’ leader regions ofthese transcripts is responsible for translationalcontrol. Synthesis of the uORF-encoded peptidecauses ribosomes to stall when the level ofarginine is high, blocking access of ribosomes tothe translation initiation site for the polypeptideencoding the arginine biosynthetic enzyme. Ourcurrent work is focused on developing a molecularunderstanding of how synthesis of this uORF-encoded peptide causes ribosomes to stall, sincethis will provide important insights into thefundamental cellular process of protein synthesis.Sachs

Genome Organization in Fungi

The N. crassa genome and the genomes of otherfilamentous fungi are being sequenced, enablingcomparisons of how these fungi differ from eachother and from the yeasts. We are focusing on thecharacterization of the sub-telomeric regions of N.crassa, since genes in sub-telomeric regions areimplicated in environmental sensing and ininteractions with host species. Sachs

Human-Health Assessment of Water Quality

Since 1991, U.S. Geological Survey (USGS)scientists with the National Water-QualityAssessment (NAWQA) program have beencollecting and analyzing data and information inmore than 50 major river basins and aquifersacross the nation. Their goal is to develop long-term consistent and comparable information onstreams, groundwater, and aquatic ecosystems tosupport sound management and policy decisions.State and national pilot efforts are underway withthe USGS, in collaboration with the U.S.Environmental Protection Agency (USEPA) andstate agencies to develop, test and refine conceptsto more effectively communicate water-qualityinformation in a human-health context. Toccalino

Harvesting Forest Information

We are collaborating with the U.S. ForestService, Bureau of Land Management, Fish andWildlife Service and other government agenciesto build a forest information portal for theAdaptive Management Area (AMA) program. The AMAs develop and test innovative

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approaches to forest management. We aredeveloping an information model to locatedocuments and document fragments and tosearch for documents based on similaritysearches between locations. The Forest projectis primarily housed in the CSE department atOGI, and also includes participants from the MSTdepartment, from UNLV, and from the privatesector. Delcambre, Maier, Toccalino, Phillips,Steckler, Koch, Tolle, Landis, Palmer

Remediation of Halocarbon-Contaminated Groundwater

There is enormous demand for improved ways toclean up aquifers that have been contaminatedwith halogenated hydrocarbon solvents likecarbon tetrachloride and TCE. Recent field-scaletests have shown that technologies based ondechlorination with granular iron may havesubstantial value. The goal of our research inthis area is to provide a sound scientific basisfor designing and operating such technologies bydetermining the mechanisms of dechlorination byiron and the geochemical and microbiologicalprocesses that affect the performance of thistechnique in the field. For more information onthis work, see www.cgr.ese.ogi.edu/iron. Tratnyek

Remediation of Explosives-Contaminated Groundwater

There are numerous facilities where militaryoperations have resulted in contamination ofgroundwater with explosives such as TNT andRDX. Both TNT and RDX react rapidly with zero-valent iron, suggesting that permeable reactivebarriers of zero-valent iron might be useful inremediation of these sites. However, theproducts of these reactions with zero-valent ironmay not present a satisfactory remediation end-point. Therefore, we are investigating thekinetics and mechanisms of this reaction in theexperiments performed in the laboratory and inthe field. See www.cgr.ese.ogi.edu/iron/.Tratnyek and Johnson

Reduction Reactions of Organic Pollutants inAnaerobic Environments

Some organic pollutants undergo rapid reductionin anaerobic sediments, soils and groundwaters.Despite the potential importance of this process,little is known about the natural reducing agentsthat are responsible for these reactions. In thisproject, assays are being developed to identifyand quantify environmental reducing agents insitu. These assays will be used in kinetic studiesof important pollutant reduction reactions.Tratnyek

Oxidation Reactions of Organic Pollutants

Some organic pollutants undergo rapid oxidation innatural waters, when catalyzed by sunlight, and intechnological systems, when chemical oxidants areadded to effect remediation. These reactions areusually mediated by “activated oxygen species”

such as hydroxyl radical. We are studying thekinetics, mechanisms and products of thesereactions with a wide variety of contaminants. Theaim of this work is to help assess the suitability ofvarious advanced oxidation technologies (AOTs) forremediation of groundwater, as well as to betterunderstand the fate of contaminants in naturalwaters that are exposed to sunlight. Tratnyek

Correlation Analysis of Contaminant Reactivity

Quantitative Structure-Activity Relationships(QSARs) are of enormous importance inenvironmental chemistry and toxicology because oftheir predictive power, but they also reveal a greatdeal about reaction mechanisms and the nature ofsubstituent effects. We are involved in thedevelopment of QSARs for a wide range of redoxreactions involving organic contaminants. Thiswork involves the use of computational chemistrymethods as well as advanced statistical techniquesin exploratory data analysis. Tratnyek

Radical Copper Oxidases

Radical copper oxidases are a new class of redoxmetalloenzymes (including the fungal enzymesgalactose oxidase and glyoxal oxidase) containing aprotein free radical directly coordinated to acopper center. This free radical-coupled Cucomplex catalyzes the two-electron oxidation ofsimple alcohols and aldehydes and the reduction ofO2 to hydrogen peroxide, fueling extracellularperoxidases involved in lignin degradation. In theseproteins, the free radical is localized on a tyrosineresidue covalently crosslinked to a cysteinyl sidechain (a Tyr-Cys dimer). The catalytically activeenzyme is an intense green color, the result ofunusual optical spectra arising from electronictransitions within the copper radical complex. Lowenergy transitions in the near IR result frominterligand redox in this metal complex, ligand-to-ligand charge transfer (LLCT) processes that areclosely related to the electron transfer coordinatefor substrate oxidation. The active site metalcomplex is surprisingly flexible, twisting through apseudorotation distortion when exogenous ligandsbind, thereby modulating the basicity of a secondtyrosine ligand that serves as a general base incatalysis. Many of these aspects of electronicstructure and dynamics of the radical copperoxidases are the focus of active research.Whittaker

Manganese Metalloenzymes

Manganese is an essential element for life,forming the active site for a large number ofmetalloenzymes catalyzing hydrolytic or redoxreactions, including the photosynthetic oxygenevolving complex. We are interested in the Mnredox sites in Mn superoxide dismutase (MnSD,mononuclear Mn) and Mn catalase (MnC, dinuclearMn), enzymes that provide protection from toxicoxygen metabolites. The key question is: How dointeractions between the protein, metal ion and

exogenous ligands tune the redox potential andchemistry of these complexes? We are combiningthe powerful tools of molecular biology withadvanced spectroscopic and computationalapproaches to explore the structure and dynamicsof Mn active sites. For MnSD, we find anunexpected temperature dependence for thestructures of anion complexes, which changecoordination as the temperature is raised. Thisthermal transition implies that the stability of theactive site structure is determined by dynamicalfeatures of the complex and that dynamicalexcitation may play an important role in controllingthe energetics of ligand binding and redox. A widerange of projects relating to the chemistry andbiology of Mn are in progress. Whittaker

Electronic Spectroscopy of Biological Metal Complexes

Electronic spectroscopy extends structural studiesof biomolecules beyond the atomic resolution of X-ray crystallography to a level of structural detailthat directly relates to chemistry. The techniquesused in these studies span five decades of theelectromagnetic spectrum, from microwaves to theultraviolet and beyond. At the lowest energy,electron paramagnetic resonance (EPR)spectroscopy gives information on the electronicground state, defining the molecular orbital thatcontains the unpaired electron in a paramagneticcomplex. At higher energy, UV-visible absorptionspectroscopy excites orbital transitions betweenelectronic states, giving information oncharacteristic metal-ligand interaction energiesthat can be understood in terms of a ligand field or molecular orbital analysis. Polarizationspectroscopy (linear dichroism, circular dichroismand magnetic circular dichroism) can give moredetailed information on ground and excited stateelectronic wave functions using geometric featuresof light to probe the active site. These experimentalapproaches can be complemented by spectroscopicmodeling and computational biology methods toprovide a detailed description of a metalloproteincomplex and its interactions. Whittaker

Regulation of Long Chain Fatty Acid Transport andOxidation in Mammalian Heart and Liver

The rate-limiting step in ß-oxidation is theconversion of long-chain acyl-CoA to acylcarnitine,a reaction catalyzed by the outer mitochondrialmembrane enzyme carnitine palmitoyltransferase I (CPTI) and inhibited by malonyl-CoA. Theacylcarnitine is then translocated across the inner mitochondrial membrane by the carnitine/acylcarnitine translocase and converted back to acyl-CoA by CPTII. This reaction in intactmitochondria is inhibited by malonyl-CoA, the firstintermediate in fatty acid synthesis, suggestingcoordinated regulation of fatty acid oxidation andsynthesis. Although CPTII has been examined indetail, studies on CPTI have been hampered by aninability to purify CPTI in an active form fromCPTII. In particular, it has not been conclusivelydemonstrated that CPTI is even catalytically active,

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or whether sensitivity of CPTI to malonyl-CoA is anintrinsic property of the enzyme or is contained ina separate regulatory subunit that interacts withCPTI. To address these questions, the genes forhuman heart muscle M-CPTI and rat liver LCPTIand CPTII were separately expressed in Pichiapastoris, a yeast with no endogenous CPT activity.High levels of CPT activity were present in purifiedmitochondrial preparations from both CPTI- andCPTII-expressing strains. Furthermore, CPTIactivity was highly sensitive to inhibition bymalonyl-CoA while CPTII was not. Thus, CPTcatalytic activity and malonyl-CoA sensitivity arecontained within a single CPTI-polypeptide inmammalian mitochondrial membranes. Ourlaboratory is the first to describe the kineticcharacteristics for the yeast-expressed CPTIs, thefirst such report for a CPTI enzyme in the absenceof CPTII. Both yeast-expressed M-CPTI and L-CPTIare inactivated by detergent solubilization.However, removal of the detergent in the presenceof phospholipids resulted in the recovery ofmalonyl-CoA-sensitive CPTI activity, suggestingthat CPTI requires a membranous environment.CPTI is thus reversibly inactivated by detergents.We have isolated and sequenced the promoterregion of the gene for the human heart M-CPTI. We have mapped the malonyl-CoA and substratebinding sites in human heart M-CPTI and liver L-CPTI by deletion, site-directed mutagenesis andchemical modification studies using residuespecificreagents. Our deletion and point mutation analyseshave demonstrated that glutamate-3 and histidine-5 are necessary for malonyl-CoA inhibition andbinding of CPTI but not for catalysis. We willdetermine the structural basis for the highmalonyl-CoA sensitivity of M-CPTI by constructingchimeras between M-CPTI and L-CPTI and by site-directed mutagenesis. We will prepare milligramquantities of the expressed highly purified humanheart M-CPTI and liver L-CPTI for structuralcharacterization studies. Finally, we plan to studythe regulation of human heart M-CPTI geneexpression by hormonal, developmental and dietaryfactors. Our goal is to elucidate the molecularmechanism of the regulation of fatty acid transportand oxidation in mammalian cells. Woldegiorgis

Prokaryotic Signal Transduction/Gene Regulation

Bacteria can respond in variety of ways to agrowth-restricting environment. Prolongedexposure to a nutritionally poor environmentresults in the induction of antibiotic biosynthesis,functions required for cell motility and processes ofcellular differentiation that give rise to highlyresistant cell types. How cells respond tonutritional stress is profoundly influenced by celldensity. Extracellular signal molecules accumulatein the local environment of densely populated cellcultures and trigger antibiotic production anddevelopmental processes such as sporulation andgenetic competence. The objective of our researchis to understand, in molecular terms, theregulatory networks that cells utilize to choose themost appropriate response to harsh conditions. Inthe spore-forming bacterium, Bacillus subtilis,

establishment of genetic competence is coregulatedwith peptide antibiotic biosynthesis by a complexnetwork of signal transduction pathways thatutilize protein components common to allprokaryotic and most eukaryotic organisms. Zuber

Role of Chaperones/Proteases in the Control ofGene Expression

There is growing evidence that proteincomplexes that function in protein folding,remodeling and degradation interact directlywith the molecular machinery that initiates geneexpression. In mammalian, fungal and bacterialcells, components of ATP-dependent proteasecomplexes have been implicated in the control ofRNA polymerase activity through direct protein-protein interaction. In the spore-formingbacterium, Bacillus subtilis, developmentallyregulated transcription during the early stages ofsporulation, genetic competence developmentand antibiotic biosynthesis is profoundly affectedby members of the heat shock protein family thatnormally function as chaperones and multi-component proteases. Evidence from our studiesindicates that these proteins operate closely withRNA polymerase during the process of regulatedtranscription initiation. Our work is aimed atdetermining the nature of these interactions andtheir effects on the systems controlling bacterialdevelopmental processes. Zuber

RESEARCH CENTERS

C E N T E R F O R C O A S TA L A N D L A N D - M A R G I NR E S E A R C H ( C C A L M R )w w w. c c a l m r. o g i . e d u

The Center for Coastal and Land-MarginResearch (CCALMR) is an interdisciplinaryresearch center affiliated with the Department ofEnvironmental and Biomolecular Systems.CCALMR conducts research, graduate educationand advanced technology development thatdirectly address the need for better scientificunderstanding of coasts, land margins andestuaries. Improved knowledge of these complexsystems is necessary to preserve and enhancetheir environmental integrity, maintain theeconomic viability of communities dependent onthem and protect human populations fromnatural and manmade hazards. Real-worldnatural resource management issues motivateCCALMR research and education activities.Insights drawn from the experience of scienceand engineering professionals in the public andprivate sectors influence the identification ofemerging research challenges, the design ofresearch projects, the development of supportingtools and applications and the transfer ofknowledge and technology. Additional informationabout CCALMR may be obtained from:

A N T Ó N I O M . B A P T I S TA , P H . D .


C E N T E R FA C U LT Y A N D R E S E A R C H S C I E N T I S T S

António M. Baptista, Professor and Director

Arun Chawla, Associate Research Scientist

Wu-Chi Feng, Associate Professor(Computer Science and Engineering)

Wu-Chang Feng, Assistant Professor(Computer Science and Engineering)

Juliana Freire, Assistant Professor(Computer Science and Engineering)

Todd Leen, Professor(Computer Science and Engineering)

David Maier, Professor(Computer Science and Engineering)

Claudio Silva, Associate Professor(Computer Science and Engineering)

Jon Walpole, Professor (Computer Science and Engineering)

Yinglong (Joseph) Zhang, Associate Research Scientist

Mike Zulauf, Assistant Research Scientist

C C A L M R R E S E A R C H FA C I L I T I E S

CCALMR is well equipped to conduct state-of-the-art scientific research. The following is a list offacilities and instruments available in addition tothose available through EBS.

R E A L - T I M E D ATA A C Q U I S I T I O N N E T W O R K

The coastal observatory CORIE includes a real-time data acquisition network with close to 20multisensor oceanographic stations in theColumbia River estuary and plume. Fieldoperations are conducted from the MarineEnvironmental Research and Training Station(MERTS). MERTS is a facility developed inpartnership with and operated by the ClatsopCommunity College (CCC). CCC operates a trainingand research vessel, the 50-foot M/V Forerunner.CCALMR operates a 21-foot research vessel, theR/V CORIE.

O C E A N O G R A P H I C E Q U I P M E N T

• 600-kHz Acoustic Doppler current profilers (RD)

• 500 and 1500 kHz Acoustic Doppler profilers (Sontek)

• Conductivity and temperature pairs (Seabird)

• Conductivity, temperature and pressure sensors(Coastal Leasing and Ocean Sensors)

• Optical backscatter sensors(Downing Associates)

• Wind gauges (Coastal Leasing)

• High-density thermistor chains (CCALMR)

• Differential GPS (Trimble)

• Spread spectrum radio data modems(FreeWave)

C O M P U TAT I O N A L E N G I N E S A N D O N - L I N E S T O R A G E

• 16 parallel Intel dual CPU compute nodes (2.4GHz, 4 Gb)

• 6 single CPU Alpha compute nodes

• 10 TB primary storage

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C E N T E R F O R G R O U N D W AT E R R E S E A R C Hw w w. c g r. e s e . o g i . e d u .

The principal mission of the Center forGroundwater Research (CGR) is to conduct state-of-the-art research in areas relating to thetransport and fate of contaminants in thesubsurface. This is accomplished through acombination of research grants and contracts andcollaboration with other universities, industriesand government agencies.

The Center coordinates a range of projects relatingto the transport and fate of contaminants in soilsand groundwater. The scope of the Center includes,among other things, the development of: 1) newsampling and site characterization techniques; 2)new analytical techniques; 3) improvedgroundwater remediation methods and 4) physicaland numerical models of groundwater- andwatershed-scale processes.

The Center operates the Large ExperimentalAquifer Program (LEAP), which contains theexperimental facilities outlined below. The LEAPfacility provides staff with the capability to conductboth bench-scale experiments and essentially full-scale pilot demonstrations. Students involved inLEAP receive a rare combination of experiences,including full-scale remediation engineering andprocess-level understanding of contaminanthydrology and chemistry.

For additional information about CGR, contact:

R I C H A R D J O H N S O N , P H . D .


C E N T E R FA C U LT Y

Richard Johnson, Associate Professor and DirectorJames F. Pankow, ProfessorPatricia L. Toccalino, Assistant ProfessorPaul Tratnyek, Associate Professor

L E A P E Q U I P M E N T

• Five tanks: one 10 m x 10 m x 3 m; two 10 m x10 m x 5 m; one 10 m x 2.5 m x 0.5 m; and one8 m x 2.5 m x 0.5 m

• In-situ instrumentation, including automatedtemperature, pressure and water-levelmonitoring; multilevel samplers; down-holevideo camera; and automated vapor andproduct-sensing equipment

• Remediation equipment, including soil vaporextraction and air sparging capabilities

• Automated on-site analytical equipment,including capillary GC-MS

RESEARCH FACILIT IESThe EBS department is well equipped to carry on a vigorous research program. Instruments andequipment available in the department include:

• Gas chromatograph/mass spectrometer with computer data system

• High-resolution mass spectrometer

• UV/Visible spectrometer

• Capillary column gas chromatographs with flame ionization detectors

• Fourier transfor-infrared spectrometers

• Fourier transfor-Raman spectrometer with CW Nd:YAG laser

• X-band electron paramagnetic resonance spectrometer

• Ultraviolet/visible/near-infraredspectrophotometers

• Scanning fluorescence spectrophotometers

• Magnetic circular dichroism (MCD) spectrometer

• Diode array UV/Visible spectrophotometer

• Laser Raman spectrophotometer

• Raman spectrograph with CCD detector

• Ar, Kr, HeCd, HeNe and dye lasers

• High-vacuum lines

• Phosphor imager

• Controlled atmosphere reaction chamber

• Super speed centrifuges

• Ultracentrifuges

• HPLCs

• FPLCs

• Fraction collectors

• Liquid scintillation systems

• Gel electrophoresis systems

• Laminar flow hoods for sterile culture

• Growth chambers

• Constant temperature rooms

• Light and electron microscopes

• Ultrafiltration systems

• Autoclaves

• Photographic facilities

• Probe-type sonicators and extruder

See additional research equipment listings in theResearch Centers section.

54

A N T Ó N I O M . B A P T I S TA

Professor and Department HeadDirector, Center for Coastaland Land-Margin ResearchPh.D., Civil EngineeringMassachusetts Instituteof Technology, [email protected]


Integrated understanding andprediction of hydrodynamic and environmental processes in estuaries and coasts. Development of associatedconcepts and technologies: coastal observatories,environmental informationtechnology, numerical methodsand modeling systems, error and uncertainty analysis, and physically based ecological indicators.

R E P R E S E N TAT I V E P U B L I C AT I O N SArcher C., A.M. Baptista and T. Leen,

“Fault Detection for Salinity Sensorsin the Columbia Estuary,” WaterResources Research, to appear in39 (3), 2003.

A.M. Baptista, “EnvironmentalObservation and Forecasting Systems,”in Encyclopedia of Physical Scienceand Technology, 3rd Edition, Vol. 5,Academic Press, 2002.

E.P. Myers and A.M. Baptista,“Inversion for Tides in the EasternNorth Pacific Ocean,” Advances inWater Resources, 24 (5), 505-519,2001.

E.P. Myers and A.M. Baptista,“Analysis of Factors InfluencingSimulations of the 1993 HokkaidoNansei-Oki and 1964 Alaska Tsunamis,”Natural Hazards, 23 (1), 1-28, 2001.

D.C. Steere, A.M. Baptista, D.McNamee, C. Pu and J. Walpole,“Research Challenges in EnvironmentalObservation and Forecasting Systems,”in Proceedings of the 6th AnnualInternational Conference on MobileComputing and Networking (Mobicom2000), Boston, 292-299, 2000.

A. Oliveira, A.B. Fortunato andA.M. Baptista “Mass Balance inEulerian-Lagrangian TransportSimulations in Estuaries,” ASCEJournal of Hydraulic Engineering,126 (8), 605-614, 2000.

N I N I A N J . B L A C K B U R N

Professor Ph.D., Inorganic ChemistryUniversity of Dundee,Scotland, U.K., [email protected]


Structure and function of oxidaseand oxygenase metalloenzymes;spectroscopy of metal sites inproteins with emphasis on EPR,EXAFS, absorption edge and FT-IRspectroscopies; coordinationchemistry and biochemistry ofcopper. Biochemistry of metaltrafficking in cells.

R E P R E S E N TAT I V E P U B L I C AT I O N SF.C. Rhames, N.N. Murthy, K.D. Karlin

and N.J. Blackburn, “Isocyanide Bindingto the Copper(I) Centers of theCatalytic Core of PeptidylglycineMonooxygenase (PHMcc),” J. Biol.Inorg. Chem., 6, 567-577, 2001.

S. Jaron and N.J. Blackburn,“Characterization of a Half-ApoDerivative of PeptidylglycineMonooxygenase. Insight into theReactivity of Each Active Site Copper,”Biochemistry, 40, 6867-6875, 2001.

N.J. Blackburn, F. C. Rhames,M. Ralle and S. Jaron, “Major Changesin Copper Coordination AccompanyReduction of PeptidylglycineMonooxygenase: Implications forElectron Transfer and the CatalyticMechanism,” J. Biol. Inorg. Chem.,5, 341-353, 2000.

J.F. Eisses, J.P. Stasser, M. Ralle,J.H. Kaplan and N.J. Blackburn,“Domains I and III of Human CopperChaperone for Superoxide DismutaseInteract via a Cysteine-BridgedDicopper(I) Cluster,” Biochemistry,38, 7337-7342, 2000.

N.J. Blackburn, M. Ralle, R. Hassettand D.J. Kosman, “SpectroscopicAnalysis of the Trinuclear Cluster in theFet3 Protein from Yeast, a MultinuclearCopper Oxidase,” Biochemistry, 39,2316-2324, 2000.

W I L L I A M H . G L A Z E

ProfessorPh.D., Physical ChemistryUniversity of Wisconsin, Madison, [email protected]


Integration of ecological scienceswith human health sciencesincluding the integration offunctional genomics. Sustainabletechnologies applied to urbandesign and to the energy andtransportation sectors.

R E P R E S E N TAT I V E P U B L I C AT I O N SW.H. Glaze, D.S. Maddox and P. Bose,

“Degradation of RDX by VariousAdvanced Oxidation Processes:I. Reaction Rates,” Water Research,997-1004, 1998.

P. Bose, W.H. Glaze and D.S. Maddox,“Degredation of RDX by VariousAdvanced Oxidation Processes: II.Organic By-Products,” Water Research,1005-1018, 1998.

David R. Pesiri, David K. Morita,William Tumas and William Glaze,“Selective Epoxidation in Dense-PhaseCarbon Dioxide,” Chem. Commun.(Cambridge), Issue 9, 1015-1016,1998.

John L. Ferry and William H. Glaze,“Photocatalytic Reduction of NitroOrganics over Illuminated TitaniumDioxide: Electron Transfer BetweenExcited-State TiO2 andNitroaromatics,” J. Phys. Chem. B102(12), 2239-2244, 1998.

John L. Ferry and William H. Glaze,“Photocatalytic Reduction of NitroOrganics over Illuminated TitaniumDioxide: Role of the TiO2 Surface,”Langmuir, 14(13), 3551-3555, 1998.

H.S. Weinberg and W.H. Glaze,“A Unified Approach to the Analysis ofPolar Organic By-Products of Oxidationin Aqueous Matrices,” Water Research,1555-1572, 1997.

D A V I D A . J AY

Associate ProfessorPh.D., Physical OceanographyUniversity of Washington, [email protected]


River basin, estuarine andcontinental shelf processes,turbulent mixing, tides and tidalanalysis. A unifying theme is theinfluence of hydrodynamicprocesses on ecosystems.

R E P R E S E N TAT I V E P U B L I C AT I O N SKukulka T., and D. A. Jay, “Impacts of

Columbia River Discharge on SalmonidHabitat I. A Nonstationary Fluvial TideModel,” J. Geophys. Res., in press.

Kay, D. J. and D. A. Jay, “InterfacialMixing in a Highly Stratified Estuary.1. Characteristics of Mixing,” J. Geophys. Res., in press.

Kay, D. J. and D. A. Jay, “InterfacialMixing in a Highly Stratified Estuary.2. A Method of Constrained DifferenceApproach for the Determination of theMomentum and Mass Balances andthe Energy of Mixing,” J. Geophys.Res., in press.

Fain, A.M.V., D. A. Jay, D. J. Wilson,P. M. Orton and A. M. Baptista,“Seasonal, Monthly and Tidal Patternsof Particulate Matter Dynamics in theColumbia River Estuary,” Estuaries 24,770-786, 2001.

D.A. Jay, W. R. Geyer andD. R. Montgomery, in An EcologicalPerspective on Estuarine Classification:Estuarine Science, A SyntheticApproach to Research and Practice,J. E. Hobbie, ed., Island Press,pp. 149-175, 2000.

E.P. Flinchem and D. A. Jay, “AnIntroduction to Wavelet TransformTidal Analysis Methods,” Coast.Estuar. Shelf Sci., 51, 177-200, 2000.

D.A. Jay and E.P. Flinchem,“Interaction of Fluctuating River Flowwith a Barotropic Tide: A Test ofWavelet Tidal Analysis Methods,”J. Geophys. Res., 102, 5705-5720,1997.

B.M. Hickey, L.J. Pietrafesa, D.A. Jayand W.C. Boicourt, “The Columbia RiverPlume Study: Subtidal Variability in theVelocity and Salinity Field,” J. Geophys.Res., 103(10), 229-368, 1996.

F A C U L T Y | E N V I R O N M E N TA L A N D B I O M O L E C U L A R S YS T E M S | E B S

FACULTY

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E B S | E N V I R O N M E N TA L A N D B I O M O L E C U L A R S YS T E M S | F A C U L T Y

R I C H A R D L . J O H N S O N

Associate Professor, Director, Center forGroundwater ResearchPh.D., Environmental ScienceOregon Graduate Center, [email protected]


Physical and chemical behavior oforganic contaminants in the air,soil and water; environmentalanalytical organic chemistry;transport and fate of contaminantsat the watershed scale; modelingof contaminant transport.

R E P R E S E N TAT I V E P U B L I C AT I O N SAmerson, I.L. and R.L. Johnson,”

A Natural Gradient Tracer Test toEvaluate Natural Attenuation of MTBEUnder Anaerobic Conditions,”Groundwater Monitoring andRemediation, 23(1), 54-61, 2003.

R.L. Johnson, P.C. Johnson,T.L. Johnson and A. Leeson, “HeliumTracer Tests for Assessing ContaminantVapor Recovery and Air DistributionDuring In-Situ Air Sparging,”Bioremediation Journal, 5(4), 321-336,2001.

R.L. Johnson, P.C. Johnson,T.L. Johnson, Neil R. Thomson andA. Leeson, “Diagnosis of In-Situ AirSparging Performance Using TransientGroundwater Pressure Changes DuringStartup and Shutdown,” BioremediationJournal, 5(4), 299-320, 2001.

R.L. Johnson, P.C. Johnson,I.L. Amerson, T.L. Johnson, C.L. Bruce,A. Leeson and C.M. Vogel, “DiagnosticTools for Integrated In-Situ Air SpargingPilot Tests,” Bioremediation Journal,5(4), 283-298, 2001.

N.R. Thomson and R.L. Johnson,“Air Distribution During In-Situ AirSparging: An Overview of MathematicalModeling,” J. Hazardous Materials 72(2-3), 265-282, 2000.

R.L. Johnson, J.F. Pankow, D. Bender,C. Price and J. Zogorski, “To WhatExtent Will Past MTBE ReleasesContaminate Community Water SupplyWells?” Environ. Science and Technol.,34, 2A-7A, 2000.

L. Slater, A.M. Binley, W. Daily andR.L. Johnson, “Cross-hole ElectricalImaging of a Controlled Saline TracerInjection,” J. Applied Geophysics,44, 85-102, 2000.

P I E R R E M O Ë N N E - L O C C O Z

Assistant ProfessorPh.D., BiophysicsUniversity of Pierre & Marie Curie,Paris VI, [email protected]


Structure-function relationshipswithin proteins. Metallo- andheme-proteins. Spectroscopicstudies of enzyme-active sites andtheir cofactors. Reactionintermediates within catalysis.

R E P R E S E N TAT I V E P U B L I C AT I O N SR.A. Ghiladi, K.R. Hatwell, K.D. Karlin,

H.-w. Huang, P. Moënne-Loccoz, C.Krebs, B.H. Huynh, L.A. Marzilli, R.J.Cotter, S. Kaderli and A.D. Zuberbuhler,“Dioxygen Reactivity of MononuclearHeme and Copper Components Yieldinga High-Spin Heme-Peroxo-Cu Complex,”J. Am. Chem. Soc., 123, 6183-6184,2001.

K. Auclair, P. Moënne-Loccoz and P.R.Ortiz de Montellano, “Roles of theProximal Heme Thiolate Ligand inCytochrome P450cam,” J. Am. Chem.Soc., 123, 4877-4885, 2001.

P. Moënne-Loccoz, O.-M.H. Richter,H.-w. Huang, I. Wasser, R.A. Ghiladi,K.D. Karlin and S. de Vries, “NitricOxide Reductase from Paracoccusdenitrificans Contains an Oxo-BridgedHeme/Non-Heme Diiron Center,” J. Am.Chem. Soc., 122, 9344-9345, 2000.

A. Wilks and P. Moënne-Loccoz,“Identification of the Proximal LigandHis-20 in Heme Oxygenase (HmuO)from Corynebacterium diphtheriae.Oxidative Cleavage of the HemeMacrocycle Does Not Require theProximal Histidine,” J. Biol. Chem.,275, 11686-11692, 2000.

P. Moënne-Loccoz, C. Krebs, K.Herlihy, D.E. Edmondson, E.C. Theil,B.H. Huynh and T.M. Loehr, “TheFerroxidase Reaction of FerritinReveals a Diferric mu-1,2 BridgingPeroxide Intermediate in Common withOther O2-Activating Non-Heme DiironProteins,” Biochemistry, 38, 5290-5295, 1999.

M I C H I K O M . N A K A N O

Research Associate ProfessorPh.D., Cell BiologyUniversity of Tokyo, [email protected]


Anaerobiosis of Bacillus subtilis;oxygen-controlled gene regulation;two-component signal transductionsystem; transcriptional activation;nitrate/nitrite reductases;flavohemoglobin; anaerobicelectron transport; nitric oxidesignaling.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Nakano, M. M. Nakano, Y. Zhang,

M. Leelakriangsak and P. Zuber,“A Regulatory Protein that Interfereswith Activator-Stimulated Transcriptionin Bacteria,” Proc. Natl. Acad. Sci. USA,100, 4233-4238, 2003.

M.M. Nakano and P. Zuber,“Anaerobiosis,” in Bacillus subtilis andIts Closest Relatives, A.L. Sonenshein,J.A. Hoch and R. Losick, eds., AmericanSociety for Microbiology, Washington,D.C., pp. 393-404, 2002.

M.M. Nakano, “Induction of ResDE-dependent Gene Expression in Bacillussubtilis in Response to Nitric Oxideand Nitrosative Stress,” J. Bacteriol.,184, 1783-1787, 2002.

M.M. Nakano and Y. Zhu, “Involvementof the ResE Phosphatase Activity inDown-Regulation of ResD-ControlledGenes in Bacillus subtilis DuringAerobic Growth,” J. Bacteriol., 183,1938-1944, 2001.

M.M. Nakano, Y. Zhu, M. LaCelle,X. Zhang and F.M. Hulett, “Interactionof ResD with Regulatory Regions ofAnaerobically Induced Genes inBacillus subtilis,” Mol. Microbiol.,37, 1198-1207, 2000.

J A M E S F. P A N K O W

ProfessorPh.D., EnvironmentalEngineering ScienceCalifornia Institute of Technology,[email protected]


Physical and analytical chemistryof organic compounds and metalsin natural waters and in theatmosphere; the formation andchemistry of atmospheric aerosols;the chemistry of nicotine intobacco smoke.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.F. Pankow, J.H. Seinfeld, W.E. Asher

and G.B. Erdakos, “Modeling theFormation of Secondary OrganicAerosols. 1. Theory and Measurementsfor the (-Pinene-, (-Pinene-, Sabinene-,(3-Carene, and Cyclohexene-OzoneSystems,” Environ. Sci. Technol., 35,1164-1172, 2001. See also Errata,Environ. Sci. Technol., 35, 3272, 2001.

J.H. Seinfeld, W.E. Asher, G.B.Erdakos and J. F. Pankow, “Modelingthe Formation of Secondary OrganicAerosols. 2. The Predicted Effects ofRelative Humidity on Aerosol Formationin the (-Pinene-, (-Pinene-, Sabinene-,(3-Carene, and Cyclohexene- OzoneSystems,” Environ. Sci. Technol., 35,1806-1817, 2001.

R.L. Johnson, J. Pankow, D. Bender,C. Price and J. Zogorski, “MTBE,To What Extent Will Past ReleasesContaminate Community Water SupplyWells?” Environ. Sci. Technol.,210A-217A, 2000.

J.F. Pankow, B.T. Mader,L.M. Isabelle, W. Luo, A. Pavlick andC. Liang, “Conversion of Nicotine inTobacco Smoke to Its Volatile andAvailable Free-Base Form through theAction of Gaseous Ammonia,” Environ.Sci. Technol., 31, 2428-2433, 1997.

C. Liang and J.F. Pankow,“Gas/ Particle Partitioning of OrganicCompounds to Environmental TobaccoSmoke: Partition CoefficientMeasurements by Desorption,” Environ.Sci. Technol., 30 (9), 2800-2805, 1996.

J.F. Pankow, “An Absorption Modelof Gas/Particle Partitioning in theAtmosphere,” Atmos. Environ., 28,189, 1994.

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L . E . L . ( B E T S ) R A S M U S S E N

Research ProfessorPh.D., NeurochemistryWashington University(St. Louis), [email protected]


Mammalian chemocommunication:the transport, olfactory andvomeronasal organ reception of(Z)-7-dodecenyl acetate, the sexpheromone of the Asian elephant;the origin and synthesis of (Z)-7-dodecenyl acetate; identificationand function of pheromones andchemical signals of theelephantunique temporal gland.

R E P R E S E N TAT I V E P U B L I C AT I O N SL.E.L. Rasmussen, H.S. Riddle and

V. Krishnamurthy, “Mellifluous Maturesto Malodorous in Musth,” Nature, 415,975-976, 2002.

L.E.L. Rasmussen and G. Wittemyer,“Chemosignaling of Musth by IndividualWild African Elephants (Loxodontaafricana): Implications for Conservationand Management,” Proc. Royal Soc.London, 269, 853-860, 2002.

L.E.L. Rasmussen, J. Lazar,D.R. Greenwood and G.D. Prestwich,“Albumin - An Ideal PheromoneCarrier,” Chem. Senses, 26, 1102,2001.

L.E.L. Rasmussen, “Source and CyclicRelease Pattern of (Z)-7-DodecenylAcetate, the Preovulatory Pheromoneof the Female Asian Elephant,” Chem.Senses, 26, 611-623, 2001.

L.E.L. Rasmussen. “ElephantOlfaction,” ChemoSenses, 2, 4-5, 1999.

L.E.L. Rasmussen and T.E. Perrin.“Physiological Correlates of Musth:Lipid Metabolites and ChemosignalComposition,” Physiol. Behav., 67,539-549, 1999.

L.E.L. Rasmussen. “ChemicalCommunication: An Integral Part ofFunctional Asian Elephant (Elephasmaximus) Society, Ecoscience, 5,410-426, 1998.

R E I N H O L D A . R A S M U S S E N

ProfessorPh.D., Botany/Plant PhysiologyWashington University,(St. Louis), [email protected]


Atmospheric chemistry of tracegases; biogenic and anthropogenicemissions of trace gases and theirroles in stratospheric ozonedestruction and troposphericozone formation; measurements oftrace gases at parts per trillion toparts per quadrillion levels;sources and sinks of isoprene andother hydrocarbons.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. Geron, R.A. Rasmussen, R.R. Arnts

and A. Guenther, “A Review andSynthesis of Monoterpene Speciationfrom Forests in the United States,”Atmos. Environ, 34 (11), 1761-1781,2000.

J. Zhang, K.R. Smith, R. Uma, Y. Ma,V.V.N. Kishore, K. Lata, M.A.K. Khalil,R.A. Rasmussen and S.T. Thorneloe,“Carbon Monoxide from Cookstoves inDeveloping Countries: 2. ExposurePotentials,” Chemosphere: GlobalChange Sci., 1 (1-3), 367-375, 1999.

J. Zhang, K.R. Smith, R. Uma, Y. Ma,V.V.N. Kishore, K. Lata, M.A.K. Khalil,R.A. Rasmussen and S.T. Thorneloe,“Carbon Monoxide from Cookstoves inDeveloping Countries: 1. Emissionfactors,” Chemosphere: Chemosphere:Global Change Sci., 1 (1-3), 353-366,1999.

E. Grosjean, R.A. Rasmussen andD. Grosjean, “Toxic Air Contaminantsin Porto Alegre, Brazil,” Environ. Sci.Technol., 33 (12), 1970-1978, 1999.

R.A. Rasmussen, M.A.K. Khalil andF. Moraes, “Permafrost MethaneContent: 1. Experimental Data fromSites in Northern Alaska,”Chemosphere, 26, 591, 1993.

M.A.K. Khalil, R.A. Rasmussen,J.R. French and J. Holt, “The Influenceof Termites on Atmospheric TraceGases: CH4, CO2, CHCl3, N2O, CO, H2and Light Hydrocarbons,” J. Geophys.Res., 95, 3619, 1990.

D.A. Hegg, L.F. Radke, P.V. Hobbs,R.A. Rasmussen and P.J. Riggan,“Emissions of Some Trace Gases fromBiomass Fires,” J. Geophys. Res., 95,5669, 1990.

M AT T H E W S . S A C H S

Associate ProfessorPh.D., BiologyMassachusetts Instituteof Technology, [email protected]


Mechanisms of translational andtranscriptional control thatregulate the expression of theNeurospora crassa arg-2 andSaccharomyces cerevisiae CPA1genes; fungal genomes.

R E P R E S E N TAT I V E P U B L I C AT I O N SSachs, M. S., and Geballe, A. P.,

“Biochemistry. Sense and Sensitivity -Controlling the Ribosome,” Science297, 1820-1821, 2002.

Sachs, M. S., Wang, Z., Gaba,A., Fang, P., Belk, J., Ganesan,R., Amrani, N., and Jacobson, A.,“Toeprint Analysis of the Positioningof Translational Apparatus Componentsat Initiation and Termination Codonsof Fungal mRNAs,” Methods 26,105-114, 2002.

Fang, P., Wu, C., and Sachs, M. S.,“Neurospora crassa SupersuppressorMutants are Amber Codon-specific,”Fungal. Genet. Biol., 36, 167-175,2002.

Gaba, A., Wang, Z., Krishnamoorthy,T., Hinnebusch, A. G., and Sachs,M. S. “Physical Evidence for DistinctMechanisms of Translational Controlby Upstream Open Reading Frames,”EMBO J. 20, 6453-6463, 2001.

D.D. Perkins, A. Radford and M.S.Sachs, The Neurospora Compendium:Chromosomal Loci. Academic Press,San Diego, 2001.

H.S. Kelkar, J. Griffiths, M.E. Case,S.F. Covert, D.A. Hall, C. Keith, J.S.Oliver, M.J. Orbach, M.S. Sachs, J.R.Wagner, M.J. Weise, J.K. Wunderlichand J. Arnold, “The Neurospora CrassaGenome: Libraries Sorted byChromosome,” Genetics, 157,979-990, 2001.

P AT R I C I A L . T O C C A L I N O

Assistant ProfessorPh.D., Environmental Scienceand EngineeringOregon Graduate Institute, [email protected]


Human and ecological riskassessments, water-qualityassessments, contaminant fateand transport in variousenvironmental media.

R E P R E S E N TAT F I V E P U B L I C AT I O N SA N D T E C H N I C A L R E P O R T S

P.L. Toccalino, J. Zogorski, L. Nowell,J. Donohue, C. Eiden, S. Krietzman andG. Post, “Health-based Screening LevelMethodology for State-level Analyses,”technical report to U.S. GeologicalSurvey, U.S. Environmental ProtectionAgency and New Jersey Department ofEnvironmental Protection, 2002.

R. Johnson, D. Grady and P. Toccalino,“Impact of Remediation on Long-termLeaching Due to Recharge in aContaminated Fractured Till,” technicalreport to the American PetroleumInstitute, 2001.

P.L. Toccalino and R. Binder,“Methodologies for PresentingContaminant Concentration Data fromthe Glassboro, New Jersey, Study Areain a Human-Health Risk Context,”technical report to U.S. GeologicalSurvey, U.S. Environmental ProtectionAgency and New Jersey Department ofEnvironmental Protection, 2000.

P.L. Toccalino, K. M. Auer,D. A. Mervyn and B. Stirling, “Phase IIRemedial Investigation/Risk AssessmentReport for Westside Light Rail Transit;Construction Spoils at the Port ofPortland’s Portland InternationalCenter,” Portland, Oregon, 1997.

P.L. Toccalino, “Evaluation of theContained Burn of Two M88 NIKERocket Motors for Environmental Safety& Health Implications,” Nevada TestSite X-Tunnel Facility (U25X), LasVegas, 1997.

P.L. Toccalino, R. L. Johnson andD. R. Boone, “Nitrogen Limitation andNitrogen Fixation During AlkaneBiodegradation in a Sandy Soil,” Appl.Environ. Microbiol., 59, 2977-2983,1993.

FACULTY


57


P A U L G . T R AT N Y E K

Associate ProfessorPh.D., ChemistryColorado School of Mines, [email protected]


Mechanistic and kinetic aspects ofthe fate of organic pollutants inthe environment; degradationreactions involving pesticides,phenols, munitions, dyestuffs andchlorinated hydrocarbon solvents;chemical and microbiologicalprocesses in sediments, soils andgroundwaters as well asphotochemical processes insurface waters; natural andengineered remediation systems.

R E P R E S E N TAT I V E P U B L I C AT I O N STratnyek, P. G., E. J. Weber and

R. P. Schwarzenbach, “QuantitativeStructure-Activity Relationships(QSARs) for Chemical Reductions ofOrganic Contaminants,” Environ.Toxicol. Chem. 22(8), in press.

Canonica, S., and P. G. Tratnyek,“Quantitative Structure-ActivityRelationships (QSARs) for OxidationReactions of Organic Chemicals inWater,” Environ. Toxicol. Chem. 22(8),in press.

Nurmi, J. T., and P. G. Tratnyek,“Electrochemical Properties of NaturalOrganic Matter (NOM), Fractions ofNOM, and Model BiogeochemicalElectron Shuttles,” Environ. Sci.Technol. 36(4), 617-624, 2002.

Gaspar, D. J., A. S. Lea, M. H.Engelhard, D. R. Baer, R. Miehr and P.G. Tratnyek, “Evidence for Localizationof Reaction upon Reduction of CCl4 byGranular Iron,” Langmuir 18(20),7688-7693, 2002.

Agrawal, A., W. J. Ferguson, B. O.Gardner, J. A. Christ, J. Z. Bandstraand P. G. Tratnyek, “Effects ofCarbonate Species on the Kinetics of1,1,1-trichloroethane by Zero-valentIron,” Environ. Sci. Technol. 36(20),4326-4333, 2002.

Tratnyek, P. G., M. M. Scherer, B.Deng and S. Hu, “Effects of NaturalOrganic Matter, AnthropogenicSurfactants, and Model Quinones onthe Reduction of Contaminants by Zero-valent Iron,” Water Research, 35(18),4435-4443, 2001.

K A R E N W ATA N A B EResearch Assistant ProfessorPh.D., Mechanical EngineeringUniversity of California,Berkeley [email protected]


Bioaccumulation in aquaticenvironments, mathematicalmodeling of living systems and health and ecological risk assessment.

R E P R E S E N TAT I V E P U B L I C AT I O N SWatanabe, K.H., Desimone, F.W.,

Thiyagarajah, A., Hartley, W.R. andHindrichs, A.E. (2003). Fish tissuequality in the lower Mississippi Riverand health risks from fish consumption.The Science of the Total Environment302(1-3): 109-126.

Watanabe, K.H. (2002). Fundamentalsof physiologically-based toxicokineticmodels. In: Endocrine Disrupters andCarcinogenic Risk Assessment. L. Chyczewski, J. Niklinski and E. Pluygers, Eds. Amsterdam,Netherlands, IOS Press: 271-280.

Watanabe, K.H. and Chen, C. (2001).The role of physiologically basedtoxicokinetic models in biologicallybased risk assessment. FoliaHistochemica et Cytobiologica39(Suppl. 2): 50-51.

Watanabe, K.H. and Travis, C.C.(1997). Mathematical modeling of skinpapilloma data in SENCAR mice.Toxicology and Applied Pharmacology147: 419-430.

Watanabe, K.H. and Bois, F.Y. (1996).Interspecies extrapolation ofphysiological pharmacokineticparameter distributions. Risk Analysis16(6): 741-754.

Watanabe, K.H. and Bois, F.Y., Daisey,J.M., Auslander, D.M. and Spear, R.C.(1994). Benzene toxicokinetics inhumans — Bone marrow exposure tometabolites. Occupational andEnvironmental Medicine 51(6): 414-420 and Lawrence BerkeleyLaboratory Report LBL-34432/UC-607.

Watanabe, K.H., Bois, F.Y. and Zeise,L. (1992). Interspecies extrapolation: A reexamination of acute toxicity data.Risk Analysis 12: 301-310.

J A M E S W. W H I T TA K E RAssociate ProfessorPh.D., BiochemistryUniversity of Minnesota, [email protected]


Electronic structures anddynamics of metalloenzyme activesites; spectroscopic andcomputational approaches tobiomolecular structure;metalloenzyme mechanisms;enzyme engineering; biology ofmetal ions.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.M. Whittaker and J.W. Whittaker,

“Characterization of RecombinantBarley Oxalate Oxidase Expressed byPichia pastoris,” J. Biol. Inorg. Chem.,7, 136-145, 2002.

V.V. Barynin, M.M. Whittaker, S.V.Antonyuk, V.S. Lamzin, P.M. Harrison,P.J. Artymiuk and J.W. Whittaker,“Crystal Structure of ManganeseCatalase from Lactobacillusplantarum,” Structure, 9, 725-738,2001.

M.M. Whittaker and J.W. Whittaker,“Catalytic Reaction Profile for AlcoholOxidation by Galactose Oxidase,”Biochemistry, 40, 7140-7148, 2001.

R.A. Edwards, M.M. Whittaker, J.W.Whittaker, E.N. Baker and G.B.Jameson, “Outer Sphere MutationsPerturb Metal Reactivity in ManganeseSuperoxide Dismutase,” Biochemistry,40, 15-27, 2001.

M.M. Whittaker and J.W. Whittaker,“Expression of Recombinant GalactoseOxidase by Pichia pastoris,” ProteinExpr. Purif., 20, 105-111, 2000.

M.M. Whittaker and J.W. Whittaker,“Recombinant Superoxide Dismutasefrom a Hyperthermophilic Archaeon,Pyrobaculum aerophilium,” J. Biol.Inorg. Chem., 5, 402-408, 2000.

G E B R E TAT E O S W O L D E G I O R G I S

Associate ProfessorPh.D., Nutritional BiochemistryUniversity of Wisconsin,Madison, [email protected]


Structure-function studies withmitochondrial carnitinepalmitoyltransferases I and II(CPTI and CPTII); regulation ofCPTI gene expression, fatty acidtransport, and oxidation inmammalian cells; role of CPTI indiabetes, obesity, and heartdisease; investigation of themolecular basis of human CPTdeficiency diseases using animalmodels; regulation of cellmetabolism and signaling by long-chain acyl-CoA esters;mitochondrial ion transport andbioenergetics.

R E P R E S E N TAT I V E P U B L I C AT I O N SM. Treber, J. Dai, and G. Woldegiorgis,

“Identification by Mutagenesis ofConserved Arginine and GlutamateResidues in the C-Terminal Domain ofRat Liver Carnitine PalmitoyltransferaseI That Are Important for CatalyticActivity and Malonyl CoA Sensitivity,” J.Biol. Chem., 278, 11145-11149, 2003.

H. Zhu, J. Shi, M. Treber, J. Dai, J.,D.N. Arvidson and G. Woldegiorgis,“Substitution of Glutamate-3, Valine-19,Leucine-23, and Serine-24 with Alaninein the N-Terminal Region of HumanMuscle Carnitine Palmitoyltransferase IAbolishes Malonyl CoA Inhibition andBinding,” Arch. Biochem. Biophys.,413, 67-74, 2003.

J. Dai, H. Zhu and G. Woldegiorgis,“Leucine-764 Near the C-Terminal Endof Carnitine Palmitoyltransferase I IsImportant for Activity,” Biochem.Biophys. Res. Comm., 301, 758-763,2003.

G. Zheng, J. Dai and G. Woldegiorgis,“Identification by Mutagenesis of aConserved Glutamage (Glu487) ResidueImportant for Catalytic Activity in RatLiver Carnitine PalmitoyltransferaseII,” J. Biol. Chem., 277, 42219-42223,2002.

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P E T E R Z U B E R

ProfessorPh.D., MicrobiologyUniversity of [email protected]


Regulation of prokaryotic geneexpression and development inresponse to stress; signaltransduction; regulation andmechanism of peptide antibioticbiosynthesis; regulation of geneticcompetence in Bacillus subtilis.

R E P R E S E N TAT I V E P U B L I C AT I O N SKawulka, K., T. Sprules, R. T. McKay,

P. Mercier, C. M. Diaper, P. Zuber andJ. C. Vederas, “Structure of SubtilosinA, An Antimicrobial Peptide fromBacillus subtilis with Unusual Post-translational Modifications LinkingCysteine Sulfurs to ∂-carbons ofPhenylalanine and Threonine,” J. Am.Chem. Soc. 125, 4726-4727, 2003.

Nakano, M. M., S. Nakano and P.Zuber, “Spx (YjbD), a Negative Effectorof Competence in Bacillus subtilis,Enhances ClpC-MecA-ComKInteraction,” Mol. Microbiol. 44, 1341-1350, 2002.

Nakano, S., G. Zheng, M. M. Nakanoand P. Zuber, “Multiple Pathways of Spx(YjbD) Proteolysis in Bacillus subtilis,”J. Bacteriol. 184, 3664-3670, 2002.

Zuber P., “Control of Gene Expressionin Gram-positive Bacteria: Extensionsof and Departures from EntericParadigms,” Front. Biosci. 2002 Aug1;7:D1857-66, 2002.

Nakano, S., M. M. Nakano, Y. Zhang,M. Leelakriangsak and P. Zuber, “ARegulatory Protein that Interferes withActivator-stimulated Transcription inBacteria,” Proc. Natl. Acad. Sci. (Mar17, e-pub ahead of print), 2003.

Nakano, M. M., F. Hajarizadeh, Y. Zhuand P. Zuber, “Loss-of-FunctionMutations in yjbD Result in clpX- andclpP-independent CompetenceDevelopment of Bacillus subtilis,” Mol.Microbiol., 42, 383-394, 2001.

T H O M A S M . L O E H R

Professor EmeritusPh.D., Inorganic ChemistryCornell University, [email protected]


Metallobiochemistry; biologicalrole of transition metals;molecular and electronicstructures of metalloenzyme activesites; chemistry of O2 metabolism;metal-oxo intermediates;resonance and FT-Raman, FT-IRand EPR spectroscopy.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Taoka, E.L. Green, T.M. Loehr and

R. Banerjee, “Mercuric Chloride-Induced Spin or Ligation State Changesin Ferric or Ferrous HumanCystathionine beta-Synthase InhibitEnzyme Activity,” J. Inorg. Biochem.,87, 253-259, 2001.

L.K. Lightning, H. Huang, P. Moënne-Loccoz, T.M. Loehr, D.J. Schuller, T.L.Poulos and P.R. Ortiz de Montellano,“Disruption of an Active Site HydrogenBond Converts Human HemeOxygenase-1 into a Peroxidase,” J. Biol.Chem., 276, 10612-10619, 2001.

J. Hirst, S.K. Wilcox, J. Ai, P. Moënne-Loccoz, T.M. Loehr and D.B. Goodin,“Replacement of the Axial HistidineLigand with Imidazole in Cytochrome cPeroxidase. 2. Effects on HemeCoordination and Function,”Biochemistry, 40, 1274-1283, 2001.

J. Baldwin, W.C. Voegtli, N. Khidekel,P. Moënne-Loccoz, C. Krebs, B.A. Ley,B.H. Huynh, T.M. Loehr, A. C.Rosenzweig and J.M. Bollinger, Jr.,“Rational Reprogramming of the R2Subunit of Escherichia coliRibonucleotide Reductase into a Self-Hydroxylating Monooxygenase,” J. Am.Chem. Soc., 123, 7017-7030, 2001.

E.L. Green, S. Taoka, R. Banerjeeand T.M. Loehr, “Resonance RamanCharacterization of the Heme Cofactorin Cystathionine beta-Synthase.Identification of the Fe-S(Cys) Vibrationin the Six-Coordinate Low-Spin Heme,”Biochemistry, 40, 459-463, 2001.

J O A N N S A N D E R S - L O E H R

Professor EmeritusPh.D., BiochemistryCornell University, 1969


Investigation of the role of metalions in proteins by resonanceRaman spectroscopy; oxygenactivation and metabolism; active-site structures and redox reactionsof iron proteins, copper proteinsand quinone-containing proteins.

R E P R E S E N TAT I V E P U B L I C AT I O N SF.J. Rotsaert, J.D. Pikus, B.G. Fox,

J.L. Markley and J. Sanders-Loehr,“N-Isotope Effects on the RamanSpectra of Fe(2)S(2) Ferredoxin andRieske Ferredoxin: Evidence forStructural Rigidity of Metal Sites,”J. Biol. Inorg. Chem. 8, 318-326, 2003.

E.L. Green, N. Nakamura,D.M. Dooley, J.P. Klinman andJ. Sanders-Loehr, “Rates of Oxygenand Hydrogen Exchange as Indicatorsof TPQ Cofactor Orientation in AmineOxidases,” Biochemistry, 241,687-696, 2002.

I.M.C. van Amsterdam, M. Ubbink,M. van den Bosch, F. Rotsaert,J. Sanders-Loehr and G.W. Canters,“A New Type-2 Copper CysteinateAzurin. Involvement of an EngineeredExposed Cysteine in Copper Bindingthrough Internal Rearrangement,”J. Biol. Chem., 277, 44121-44130,2002.

C.S. Farmer, D.M. Kurtz, Jr.,Z.J. Liu, B.C. Wang, J. Rose, J. Aiand J. Sanders-Loehr, “The CrystalStructures of Phascolopsis gouldii WildType and L98Y Methemerythrins:Structural and Functional Alterationsof the O2 Binding Pocket,” J. Biol.Inorg. Chem., 6, 418-429, 2001.

M.L. Alvarez, J. Ai, W. Zumft,J. Sanders-Loehr and D.M. Dooley,“Characterization of the Copper-SulfurChromophores in Nitrous OxideReductase by Resonance RamanSpectroscopy: Evidence for SulfurCoordination in the Catalytic Cluster,”J. Am. Chem. Soc., 123, 576-587,2001.

RESEARCH SCIENTISTSW I L L A M A S H E RPh.D., Environmental Scienceand EngineeringOregon Graduate Center

A R U N C H A W L APh.D., Civil EngineeringUniversity of Delaware

W E N TA I L U OPh.D., Environmental Scienceand EngineeringOregon Graduate Instituteof Science & Technology

T O D D S A N D E R SPh.D., Physical OceanographyUniversity of Delaware

Y I N G L O N G ( J O S E P H ) Z H A N GPh.D., Applied Mathematicsand Fluid Mechanics University of Wollongong, Australia

M I C H A E L Z U L A U FPh.D., MeteorologyUniversity of Utah

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PROFESSOR EMERITUS


JOINT FACULTYD A V I D R . B O O N EEnvironmental BiologyPortland State University

J A M E S M . C R E G GKeck Graduate Instituteof Applied Life Sciences

B E R N A R D A . F O XEarle A. Chiles Research InstituteProvidence Medical Center

S T E P H E N B . H A L LPulmonary and CriticalCare MedicineOregon Health &Science University

J A M E S J . H U N T Z I C K E RCenter for ProfessionalDevelopmentOGI School of Science& Engineering

R I C H A R D L . S T O U F F E ROregon National PrimateResearch Center andDepartment of Physiologyand PharmacologyOregon Health &Science University

ADJUNCT FACULTYB R U C E H O P EEnvironmental ToxicologistOregon Department ofEnvironmental Quality

J A M E S K . H U R S TDepartment of ChemistryWashington State University

A S L A M K H A L I LDepartment of PhysicsPortland State University

G E O R G E D . O L S E NOregon Health &Science University

J E F F R E Y R I N GPort of Portland

K E N N E T H R O S E N B A U MEnvironmental Law InstituteWashington, D.C.

S T E W A R T R O U N D SU.S. Geological Survey

B R U C E S T I R L I N GOregon Department ofEnvironmental Quality

J O H N C . W E S TA L LDepartment of ChemistryOregon State University

RESEARCH ASSOCIATESL U I S A A N D R U Z Z I Ph.D., Polymer Chemistry University of Pisa, Italy

T O M C H I S H O L MPh.D., Marine ScienceCollege of William and Mary

H O N G YA N L I UPh.D., ImmunologyNorman Bethune Universityof Medical SciencesChina

R O S E M A R I E M I E H RPh.D., ChemistryTechnical University,Munich, Germany

J A I M I E P O W E L LPh.D., Entomology University of Wisconsin

M A R T I N A R A L L EPh.D., ChemistryUniversity of Bonn, Germany

N I C K D . R U B I EPh.D., ChemistryUniversity of New Mexico

M E I M . W H I T TA K E RPh.D., BiochemistryUniversity of Minnesota

REASEARCH STAFFD E E P A L I D AT TAM.Sc., ZoologyDelhi University, India

K A I T L I N G R A M M E RB.S., GeologyUniversity of Alaska-Fairbanks

J O N G R A V E SM.S. Oceanography andMarine Resource ManagementOregon State University

L O R N E M . I S A B E L L EM.S., ChemistrySan Francisco State University

G U A N G Z H I L I UM.S., Computer Scienceand EngineeringOregon Health &Science University

M A R Y M AY F I E L D - G A M B I L LB.S., MicrobiologyOregon State University

S T E FA N M I N A S I A NB.A., ChemistryReed College

C O L E M C C A N D L I S HM.S., Atmospheric SciencesOregon State University

J I M M O H A NM.S., Management inScience and TechnologyOregon Graduate Institute

J U L I A N O R M A NM.S., Environmental Scienceand EngineeringOregon Health &Science University

S H U N J I N A K A N OB.S., Molecular BiologyNagoya University, Japan

P H I L L I P B . P E A R S O NM.S. Environmental Scienceand EngineeringOregon Graduate Institute

R O B Y N P H I L L I P SM.S., EnvironmentalManagement/ToxicologyDuke University

C H A R L E S S E AT O NM.S. Environmental Scienceand Engineering Oregon Graduate Instituteof Science & Engineering

R O B E R T ( B R A D ) T H O M SM.S. Environmental Scienceand EngineeringOGI School of Science& Engineering

M I C H E L L E T R E B E RB.S., Biological SciencesCalifornia PolytechnicState University

P A U L J . T U R N E RB.S. MathematicsBoise State University

E T H A N VA N M AT R ESoftware EngineeringKennedy Western University

B O B W AT K I N SB.S., Chemical EngineeringWashington State University

M I C H A E L W I L K I N

B.Sc. (Hons),Oceanography and GeologyUniversity of Southampton,U.K.

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THE DEPARTMENT OF MANAGEMENT IN

SCIENCE AND TECHNOLOGY focuses oneducating leaders and managersin a technology-intensive world.All MS in Management courseshave a strong technology focus,meeting the educational needs ofstudents working in high-technology industries and/ortechnology-intensive professions.Our curriculum also emphasizesleadership and the communicationand teamwork skills needed towork effectively with people.

WHAT SETS MANAGEMENT IN SCIENCEAND TECHNOLOGY APART?

The M.S. in Management is:

Te c h n o l o g y - f o c u s e d . Our graduatemanagement program is designed with a very specific intent: to prepare students toeffectively lead and manage in a technology-intensive organization. Compared to atraditional MBA, the learning from the M.S. in Management is much more relevant to the student’s professional situation. Go tohttp://www.ogi.edu/MST/degreechart.html for a more detailed comparison of the M.S. in Managment with traditional M.B.A. andM.S. in Engineering Management degrees.

R e l e v a n t . Management in Science andTechnology courses are taught by facultywith outstanding professional and academiccredentials. Faculty have developed theirexpertise through years of professional work in the private sector as well as indistinguished research careers. Each class is designed to deliver cutting-edge knowledgeabout best practices. Managers andexecutives from the region’s high-technologycompanies visit classes to share theirexperience with the students. Students andmanagers alike tell us that the “M.S. inManagement classes offer knowledge you can apply Monday morning.”

F l e x i b l e . We designed the program forworking people, making it possible forstudents to attend intensive weekend orweeknight classes and continue to fulfill their

commitments at work and home. Studentsmay begin taking classes in any quarter, andmay take individual courses for professionaldevelopment prior to enrolling in the degreeprogram. Our online presence makes ourdegree program available to students around the world, as well as to thosestudents from our region for whom onlinecourses are more convenient.

C o l l a b o r a t i v e . Management in Science andTechnology equips students with thefunctional expertise and the people skills to manage cross-boundary partnershipseffectively. The curriculum and facultyemphasize the development of leadership and communications skills that are critical to collaboration between people fromdifferent functions, companies, and countries.Team projects, group exercises and oralpresentations are emphasized throughout the curriculum. In addition, small class sizes make interactions and discussionsbetween faculty and students an enrichinglearning experience.

E n t r e p r e n e u r i a l . The M.S. in Managementprogram emphasizes entrepreneurshipthrough the integrative Capstone experience,culminating in the Jim Hurd New VentureCompetition. Students form managementteams and develop business plans requestinginvestment from a panel of distinguishedventure capitalists who evaluate their oraland written presentations.

INDIVIDUAL COURSES FORCAREER DEVELOPMENT

Each Management in Science and Technologycourse has been designed as a valuableprofessional development experience forworking professionals. Project Management(MST 512), Managing OrganizationalRelationships (MST 520) and Leadership and Communication Skills (MST 541), forexample, may be taken as stand-alonecourses. We encourage non- matriculatedstudents to join our courses for their owncareer development in specific areas.

ONLINE COURSES, REMOTECLASSROOM SITES AND ALLIANCES

Management in Science and Technologydelivers challenging and engaging versionsof its courses over the Internet.

Department ofManagement in Science

and Technology

www.ogi.edu/MST/

I N T E R I M D E P A R T M E N T H E A D Jack Ra i ton


D E P A R T M E N T A D M I N I S T R AT O R Shel ly Char les


A D M I N I S T R AT I V E A S S I S TA N TStac i Sutton


P R O G R A M A D M I N I S T R AT O RMaryann Burn ingham


G E N E R A L I N Q U I R I E S


M.S. in Management student Dav id Kennedypresents h is team’s bus iness p lan in theJ im Hurd New Venture Compet i t ion as partof the Capstone course.

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M S T | M A N AG E M E N T I N S C I E N C E & T E C H N O L O G Y

U.S. News & World Report chose MST-Onlineas one of the “Best of the Online GradPrograms” in 2001. This is an excellentoption for students facing time pressures orworking in locations where travel to campusis not feasible. The course delivery system isbased on interactive Web pages, multimedialectures and lessons, and online discussions,all in a seamless browser-centricenvironment. Students can take individualcourses, enroll in the Certificate inManagement in Science and Technologyprogram or apply for the full Master ofScience degree. Courses offered online willhave a “D” designation as the section numberfollowing the course number. For furtherinformation, visit the Management in Science and Techonology Web site atwww.ogi.edu/MST/. Links from this Web sitewill lead a student directly to our onlineeducational administration partner, Cenquest.

The M.S. in Management program also offerson-site courses at our remote classroomlocation at the Wilsonville Training Center,29353 Town Center Loop East, Wilsonville,OR 97070. Currently, one or two MSTcourses per term are offered at theWilsonville Training Center. Please refer tothe department’s Web site at www.ogi.edu/MST/for updated course schedule information.

The Management in Science and Technologydepartment has established an alliance withthe Engineering Technology Managementgraduate program at Portland State University.Students from either degree program maycross-register and receive full course credittransferable to his or her matriculated degreeprogram. ETM students will need to receivefaculty advisor approval first.

FOR-CREDIT CERTIF ICATE PROGRAMS

A D M I S S I O N R E Q U I R E M E N T S F O R M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G Y C E R T I F I C AT E P R O G R A M S

The Management For-Credit CertificatePrograms require the following for admission:

• A completed application with $25nonrefundable application fee

• At least two years of relevant professional experience

• For non-native speakers of English, a score of 625 or better on the TOEFL examination

Individual courses are open to interestedpersons without the need to matriculate intothe degree or certificate programs. Enroll-ment is available to any qualified student.

M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G Y C E R T I F I C AT E

The Management in Science and Technologydepartment offers a six-course certificate in Management in Science and Technology.The following five courses, plus an additional management elective coursechosen in consultation with a faculty advisor,are required:

MST 510 (D) Principles and Trends in . . . . . . 3 creditsTechnology Management

MST 512 (D) Project Management . . . . . . . . . 4 creditsMST 520 (D) Managing Organizational . . . . . . 4 credits

RelationshipsMST 571 (D) Managerial and Financial . . . . . 4 credits

Accounting for Scienceand Technology

MST 573 (D) Technology Marketing: . . . . . . . . 4 creditsPlanning for Market

Elective to be chosen after consultation . . . . . 3-4 creditswith faculty advisor

H E A LT H C A R E M A N A G E M E N T C E R T I F I C AT E

The Management in Science and Technologydepartment’s graduate-level certificate inHealth Care Management is designed forworking professionals in administration,reimbursement or management roles inhealth care organizations. The programprovides an overview of the financial, policy,organizational and operational environmentof health care-related enterprises. Studentsgain focused skills for designing andmanaging organizations engaged in thedelivery of health care.

The Management in Science and Technologydepartment blends the unique managementand planning expertise within the M.S. inManagement faculty with those of recognizedprofessionals in the health care community at OHSU and elsewhere.

The program consists of six courses,including four core (required) courses, andtwo elective choices, for a total of at least 20 credits, as listed below.

H E A LT H C A R E M A N A G E M E N T C E R T I F I C AT E C O R E( 1 6 c r e d i t s )

MST 560 The Organization, Financing, . . . 4 creditsand History of Health Care Delivery in the United States

MST 561 Managerial and Financial . . . . . . 4 creditsAccounting for Health Care Professionals

MST 562 Health Care Program . . . . . . . . 4 creditsManagement

MST 563 The Regulation and Legislation . . 4 creditsof Health Care Delivery

E L E C T I V E S : Two of the following courses are required(4-8 credits)

MST 564 Business Planning and Strategy . . 4 creditsin the Health Care Industry

MST 565 Human Resources . . . . . . . . . . . 4 creditsin Health Care

MST 566 Health Care Information . . . . . . 4 creditsSystems Management

MST 567 Health Care Technology – . . . . . 4 creditsNew Medical Advances

MST 568 New Trends in Health . . . . . . . 2-4 creditsCare Delivery

MST 507HC Seminar for Health . . . . . . . . . . 2 creditsCare Management

The following courses from MST and other OHSUdepartments may also be used as electives, as mayother Oregon University System courses, by petition ofthe department.

D E P A R T M E N T O F M A N A G E M E N TI N S C I E N C E & T E C H N O L O G Y :

MST 512 (D) Project Management . . . . . . . . . 4 creditsMST 520 (D) Managing Organizational . . . . . . 4 credits

RelationshipsMST 522 (D) Change Leadership for . . . . . . . 3 credits

Building Effective OrganizationsMST 541 Leadership and . . . . . . . . . . . . . 3 credits

Communication SkillsMST 542 Business Ethics and . . . . . . . . . 3 credits

Corporate Social Responsibility

D E P A R T M E N T O F M E D I C A L I N F O R M AT I C S& O U T C O M E S R E S E A R C H :

MINF 510 Introduction to Medical InformaticsMINF 517 Organizational Behavior and

Management in InformaticsMINF 518 Project Management in Informatics

S C H O O L O F N U R S I N G :

NURS 531 Ethical Decisions in Health CareManagement Marketing

NON-CREDIT CERTIF ICATE PROGRAMS

ESSENTIALS OF GENERAL MANAGEMENT FOR EMERGINGHIGH TECHNOLOGY LEADERS: A Partnership betweenOGI, PSU and AeA

The Essentials of General Managementprogram is an excellent foundation for thosebound for senior management. It bringstogether the region’s rising stars of high-technology, offering a high-quality, local,affordable foundation for entry into senior-level management.

This unique executive development workshopseries is ideal for functional managers andhigh-potential employees who are on theirway up. It lays the groundwork for the nextlevel of leadership training, making future

investments in more extensive managementprograms even more valuable andmeaningful. In addition, the program providesan excellent environment for networking.

The format includes intensive one-dayworkshops taught by senior executives andacademics who are highly respected in thetechnology industry, an interactive onlineforum, immediate application and feedbackand a graduate ceremony. For moreinformation, contact Jack Raiton [email protected] or 503 748-3075.

M.S. DEGREE PROGRAM

A D M I S S I O N R E Q U I R E M E N T S F O R T H EM . S . D E G R E E P R O G R A M

In addition to the general admissionrequirements for the institution, theManagement in Science and Technologydepartment requires:

• A minimum of two years of full-time work experience-preferably at theprofessional, supervisory or manageriallevel-in a technical, scientific, business or related area

• Recommended TOEFL score of 625 (paper-based test) if English is not theapplicant’s first language. Scores are notrequired for students who earned anundergraduate degree in the United States,or who have worked for at least two yearsfor a business where the primary businesslanguage is English. For more informationon the computer-based score scale, pleasevisit www.toefl.org.

GMAT or GRE scores are not required.

Part-time students may apply for admission to the M.S. in Management program duringany quarter. Full-time students are stronglyrecommended encouraged to apply in thewinter or summer quarter and begin in thespring or fall quarter.

D E G R E E R E Q U I R E M E N T S

OGI offers a non-thesis M.S. in Managementin Science and Technology. Students elect one of two areas of emphasis within thedegree program: Managing the TechnologyCompany or Managing in the SoftwareIndustries. Students must complete aminimum of 52 credits with an average GPA of 3.0 or better.

M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G YC O R E S E Q U E N C E

All M.S. students must take the coresequence, consisting of the followingcourses or their equivalent (35 credits).The courses listed below are offered bothon-campus and online. Either is acceptablefor the M.S. in Management degree. If youintend to take only online courses, pleasesee the Online Degree Requirements afterthis section.

MST 510 (D) Principles and Trends in . . . . . . 3 creditsTechnology Management

MST 512 (D) Project Management . . . . . . . . . 4 creditsMST 513 (D) Operations Management . . . . . . 3 credits

and PracticesMST 520 (D) Managing Organizational . . . . . . 4 credits

RelationshipsMST 530 (D) Strategic Management . . . . . . . 4 credits

and PlanningMST 550 (D) Capstone Project: . . . . . . . . . . . 4 credits

Business Plan MST 571 (D) Managerial and Financial . . . . . . 4 credits

Accounting for Science and Technology

MST 572 (D) Financial Management for . . . . . 4 creditsScience and Technology

MST 573 (D) Technology Marketing: . . . . . . . . 4 creditsPlanning for Market

MST 590 (D) Effective Business Writing . . . . . . 1 creditfor Management

– OR –

MST 591 (D) Effective Business Writing for . . . 1 creditNon-native Speakers

Based on experience, certain courses aremore beneficial when taken earlier or later in a student’s program of study.

It is strongly recommended that studentstake MST 512, Project Management; MST 520, Managing OrganizationalRelationships; and MST 590, EffectiveBusiness Writing for Management or MST 591, Effective Business Writing for Non-native Speakers, as early as possible in their studies.

For the best possible Capstone experience,students form teams at least six months inadvance of the quarter in which they plan totake MST 550 Capstone Project: BusinessPlan. Past Capstone students strongly recom-mend taking MST 573, Technology Marketing:Planning for Market, late in their studies andforming a Capstone team prior to completingMST 573 assignments. Elective MST 574,Going to Market: Delivering Value toCustomers and Shareholders, is also highlyrecommended as a follow-on to MST 573, to

be taken together with one’s Capstone team.MST 530, Strategic Management andPlanning, and MST 550, Capstone Project:Business Plan, both should be taken as closeto the end of a student’s studies as possible.

A R E A S O F E M P H A S I S

Both emphasis areas require the completionof the 35-credit M.S. core sequence. Specificcourses required for each emphasis area areas follows.

M A N A G I N G T H E T E C H N O L O G Y C O M P A N Y S E Q U E N C E

Core Sequence plus three of the following six coursesare required (9–10 credits):

MST 511 (D) Quality Management . . . . . . . . . 3 creditsMST 514 (D) Issues in R&D Management . . . 3 creditsMST 522 (D) Change Leadership for . . . . . . . 3 credits

Building Effective OrganizationsMST 540 (D) International Management in . . . 3 credits

Science and TechnologyMST 541 Leadership and . . . . . . . . . . . . 3 credits

Communication SkillsMST 574 Going to Market: Delivering . . . . 4 credits

Value to Customers and Shareholders

E L E C T I V E S : Two or three elective courses, including anycourse in the above list not already taken and/or any ofthe following (8–10 credits):

EBS 547 Uncertainty Analysis . . . . . . . . . 4 creditsEBS 583 Environmental Law . . . . . . . . . . 3 credits

and RegulationCSE 517 Software Engineering . . . . . . . . . 3 credits

ProcessesCSE 568 Empirical Research Methods . . . 3 creditsMST 506 Special Topics . . . . . . . . . variable credits

(special electives offered on a one-timeonly basis)

MST 509 Commercialization Practicum . . . 3 credits

MST 515 Supply Chain Management . . . . 3 creditsMST 516 Global Logistics and Financial . . 3 credits

Management MST 517 Supply Chain Management . . . . 3 credits

Advanced ModelingMST 521 (D) Human Resource Management . . 3 credits

in Science and TechnologyMST 523 New Product Development . . . . . 4 creditsMST 524 eBusiness: Strategy and . . . . . . 4 credits

RoadmapMST 531 Software Commercialization . . . . 3 creditsMST 542 Business Ethics and Corporate . . 3 credits

Social ResponsibilityMST 544 (D) Strategic Alliances . . . . . . . . . . 3 creditsMST 549D Applied Business Forecasting . . 4 creditsMST 577 Principles for Process . . . . . . . . 4 credits

Development and Introductionto Manufacturing

Students may petition the department for elective credit for other OGI academic courses relevant to the theory orpractice of management.

M A N AG E M E N T I N S C I E N C E & T E C H N O L O G Y | M S T

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M S T | M A N AG E M E N T I N S C I E N C E & T E C H N O L O G Y

MANAG ING IN THE SOFTWARE INDUSTR IES SEQUENCE

Core Sequence plus the following two courses arerequired (6 credits):

CSE 516 Introduction to Software . . 3 creditsEngineering

MST 531 Software Commercialization . . 3 credits

Elect ives: Four of the following elective courses arerequired (12–13 credits):

CSE 514 Introduction to Database . . 3 creditsSystems

CSE 517 Software Engineering . . . . . . 3 creditsProcesses

CSE 518 Software Design . . . . . . . . 3 creditsand Development

CSE 519 Object-Oriented Analysis . . 3 creditsand Design

CSE 560 Ar tificial Intelligence . . . . . 3 creditsCSE 564 Introduction to Human . . . . 3 credits

Computer InteractionCSE 567 Developing User-Oriented . . 3 credits

SystemsMST 511 (D) Quality Management . . . . . 3 creditsMST 514 (D) Issues in R&D . . . . . . . . . 3 credits

ManagementMST 522 (D) Change Leadership . . . . . . 3 credits

for Building Ef fective Organizations

MST 540 (D) International Management . . 3 creditsin Science and Technology

MST 541 Leadership and . . . . . . . . . 3 creditsCommunication Skills

MST 574 Going to Market: . . . . . . . . 4 creditsDelivering Value to Customers and Shareholders

Students may petition the department head for electivecredits for other OGI academic courses relevant to thetheory or practice of management.

O N L I N E D E G R E E R E Q U I R E M E N T S

The Department of Management in Scienceand Technology recommends that studentstake at least two on-campus courses. Aproctored comprehensive exam may berequired at or near the completion of theM.S. in Management Online degreerequirements. Students must complete aminimum of 52 credits with an average GPAof 3.0 or better.

O N L I N E M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G YC O R E S E Q U E N C E

All online M.S. students must take the Management coresequence, consisting of the following courses or theirequivalent (35 credits):

MST 510D Principles and Trends . . . . . . . 3 creditsin Technology Management

MST 512D Project Management . . . . . . . . . 4 creditsMST 513D Operations Management . . . . . . 3 credits

and PracticesMST 520D Managing Organizational . . . . . . 4 credits

Relationships

MST 530D Strategic Management . . . . . . . 4 creditsand Planning

MST 550D Capstone Project: . . . . . . . . . . . 4 creditsBusiness Plan

MST 571D Managerial and Financial . . . . . . 4 creditsAccounting for Scienceand Technology

MST 572D Financial Management for . . . . . 4 creditsScience and Technology

MST 573D Technology Marketing: . . . . . . . . 4 creditsPlanning for Market

MST 590D Effective Business Writing . . . . . . 1 creditfor Management

– OR –MST 591D Effective Business Writing . . . . . . 1 credit

for Non-native Speakers

O N L I N E M A N A G I N G T H E T E C H N O L O G YC O M PA N Y S E Q U E N C E

OGI currently offers the Managing the Technology Companyemphasis to students who take only online classes. TheOnline Core Sequence plus three of the following fourcourses are required (9 credits):

MST 511D Quality Management . . . . . . . . . 3 creditsMST 514D Issues in R&D Management . . . 3 creditsMST 522D Change Leadership for . . . . . . . 3 credits

Building Effective OrganizationsMST 540D International Management in . . . 3 credits

Science and Technology

Electives: Three elective courses, including any course inthe above list not already taken and/or any of the following(9–10 credits):

MST 521D Human Resource . . . . . . . 3 creditsManagement in Scienceand Technology

MST 544D Strategic Alliances . . . . . . 3 credits MST 549D Applied Business . . . . . . . 4 credits

Forecasting

Students may petition the department head for electivecredits for other OGI academic courses relevant to thetheory or practice of management.

64

J A C K R A I T O N

Senior Fellow and InterimDepartment HeadMBA, Finance and StatisticsUniversity of Washington, [email protected]

Having previously served as chieffinancial officer of Planar Systemsand as corporate controller ofTektronix, Jack brings a wealth ofhigh-level management experiencein local industry to the MSTdepartment. He is active in theleadership of the AmericanElectronics Association andFinancial Executives International,and serves on the Advisory Boardsof Compli, Inc, StoriedLearnings,and two high tech start-ups. Jackearned his BS in Mathematicsfrom Oregon State University in1966 and his MBA in Finance andStatistics from the University ofWashington in 1967. He attendedHarvard University’s AdvancedManagement Program, and passedthe CPA exam in 1979.

A R E A S O F E X P E R T I S E

Performance measurement,capital structure, stock optionsand incentive plans, forensicaccounting

M A R I A N N E K O C H

Visiting Associate ProfessorPh.D., Human ResourceManagement andIndustrial RelationsColumbia University, 1989 [email protected]


The human side of technologytransfer; work/family policies andpractices; coaching faculty in thedevelopment and teaching of e-learning courses.

R E P R E S E N TAT I V E P U B L I C AT I O N S :M. Koch and D Moshavi, “The

Adoption of Family-Friendly Policiesin Family-Owned Firms: Paragonor Paradox,” Proceedings of the2001 Southern ManagementAssociation Annual Meeting, NewOrleans, LA, 2001.

M. Koch and G. Hundley, “The Effectsof Unionism on Recruitment andSelection Practices,” IndustrialRelations, 36(3), 349–370, 1997.

M. Koch and R. McGrath, “ImprovingLabor Productivity: Human ResourceManagement Policies Do Matter,” 1996,Strategic Management Journal, 17,335–354, 1996. (Awarded an AnbarElectronic Intelligence Citation ofExcellence Award for 1997).

M. Koch, L. Long, and A. Meyer,“Adoption of Innovations in Hospitals:Exploring the Validity of a Multi-StageModel,” forthcoming, InternationalJournal of Technology Management;also in Academy of Management BestPapers Proceedings, August 1996.

M. Koch. “Hiring Practices and LaborProductivity,” Garland Publishing, NewYork, 1995.

F R E D Y O U N G P H I L L I P S

ProfessorPh.D. ManagementScience/Business AdministrationUniversity of Texas at Austin, [email protected]


Market research, marketinginnovation and high-technologyproducts, managing the newproduct development process,incubation and commercializationof new technologies, strategic andinnovative use of computers.

R E P R E S E N TAT I V E P U B L I C AT I O N SF. Phillips, The Conscious Manager:

Zen for Decision Makers, GeneralInformatics, 2003.

L. Delcambre, T. Tolle, D. Maier,F. Phillips, P. Toccalino, N. Steckler, M. Koch, L. Shapiro, E. Landis, B. Banga, S. Bowers, J. Brewster, A. Gutema, W. Howe, S. Murthy, J. Norman, R. Tummala, M. Weaver,and K. Zillman. 2003. “HarvestingInformation to Sustain our Forests.”Communications of the ACM. 46(1):38-39.

F. Phillips, Market-OrientedTechnology Management: Innovatingfor Profit in Entrepreneurial Times,Springer-Verlag, Heidelberg, 2001.

F. Phillips and S. Tuladhar, “Measuresof Organizational Flexibility,”Technological Forecasting & SocialChange 64/1, May 2000.

F. Phillips, L. Ochs and M. Schrock,“The Product is Dead; Long Live theProduct-Service,” Research TechnologyManagement, 42(4), 51–56, July-August 1999.

S. Thore, G. Kozmetsky and F. Phillips,“DEA of Financial Statements Data: The U.S. Computer Industry,” Journal ofProductivity Analysis, 5(3), 229, 1994.

F. Phillips, “Conditional InformationCharacterization of Brand Shifting in aHierarchical Market Structure,”Journal of the Operational ResearchSociety, 45(8), 901, 1994.

N I C O L E A . S T E C K L E R

Associate ProfessorPh.D., Organizational BehaviorHarvard University, [email protected]


Information-sharing acrossorganizational boundaries; leadingorganizational change;interpersonal communication andinfluence in organizations; andtools for diagnosing and improvingleadership effectiveness.

R E P R E S E N TAT I V E P U B L I C AT I O N SD.B. Drake, M.J. Koch, and N.A.

Steckler, “Scientist, Politician, andBureaucrat Subcultures as Barriers toInformation-Sharing in GovernmentAgencies,” Proceedings of the 2003National Conference on DigitalGovernment Research, May 18-21,2003, Boston, MA.

N.A. Steckler and N. Fondas,“Building Team Leader Effectiveness:A Diagnostic Tool,” OrganizationalDynamics, 23, 20–35, Winter/Spring1995.

J. White, S. Jacobson, R. Jacques,N. Fondas and N.A. Steckler, “YouJust Don’t Understand: GenderedInteraction and the Process of ‘Doing’Organizational Scholarship,” Journal ofManagement Inquiry, 4(4), 370–379,December 1995.

N.A. Steckler and A. Donnellon,“Review of Peter K. Manning’s‘Organizational Communication’,”Academy of Management Review, 18,374–377, 1993.

N.A. Steckler and R. Rosenthal, “SexDifferences in Nonverbal and VerbalCommunication with Bosses, Peers, andSubordinates,” Journal of AppliedPsychology, 70, 157–163, 1985.

N.C. Ware, N.A. Steckler andJ. Leserman, “Undergraduate Women:Who Chooses a Science Major?”Journal of Higher Education, 56,73–84, 1985.

FACULTY

F A C U L T Y | M A N AG E M E N T I N S C I E N C E & T E C H N O L O G Y | M S T

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A LV I N H . T O N G

Professor

Ph.D., Electrical EngineeringUniversity of Minnesota, [email protected]

Alvin Tong has 30 years of workingexperience in the computer andrelated industries, which includesserving as chief operating officerof Acer, Inc., a Taiwan-basedmanufacturer of personalcomputers. While with Acer, healso served as President of AcerVenture, their venture capital arm.Previously, he worked for 14 yearsat IBM in New York as engineeringand marketing manager. He alsohad a significant role as the firstDeputy Director-General of theHsin-chu Science-Based IndustrialPark (SBIP) in Taiwan. Alvin hasconducted numerous management-training seminars and isfrequently invited to speak andlecture on the subject ofglobalization and high-techScience-Based Industrial Parks.

R E P R E S E N TAT I V E P U B L I C AT I O N SP. Schumann, D. Prestwood, A. Tong

and J. Vanston, Innovate!, McGraw-Hill,New York, 1994.

ADJUNCT FACULTY

K E N A N T H O N YIndustrial DesignConstruction (IDC)

J E A N - C L A U D E B A L L A N DJCB Associates

G R E G C H A R L E SIndependent Consultant

M A R K C H E NSoftech Innovation LLC

L I N D A C R A F T SCumulus Resources LLC

T U G R U L D A I MIntel Corporation

J E R R Y D A V I E SEPIC Aviation, LLC

K AT H Y M A N G E L D A V I SProfessionally Speaking

D E A N D E R R A HRV Kuhns & Associates

D A V I D D R A K ECatalyst Communications, Inc.

W I L L I A M D R E S S E L H A U SDresselhaus Design Group

T O M F L O R AOHSU – CFO, School of Medicine

R I C H A R D F O U R N I E RKaiser FoundationHealthplans Northwest

R I C H A R D G O L D G A RTexas Education Agency

S T E P H E N G O M E SCEO2Inc.

J U L I A N G R E S S E RLogosNet

F R A N K H A L LEntreDigm Consulting

R O B E R T H A R M O NPortland State University

J I L L B . K E L LYJK Editing

R I TA L A X T O NIMMEDIAD’sChildRom Productions

D O N L E W I SLewis and Lewis Consulting

K AT H Y L O N G H O L L A N DLongSherpa/Eco-D

M I C H A E L M C L E A NAC Transit

D E I R D R E M E N D E ZForeign BusinessManagement Consultants

R A J M E R C H A N TStrategy@work

P A U L N E W M A NCooper Mountain Research, Inc.

LY L E O C H STechnology & InnovationManagement, Inc.

J E F F O LT M A N NSynergy Professional Services

J E S S E R E E D E RLeadership Dynamics

A D R I A N R O B E R T SIndependent Consultant

J AY S H U T T E RMomentum Research Group

W I L L I A M S E I D M A NCerebyte, Inc.

L E S L I E S M I DWaggener Edstrom

T H O I T R U O N GCNF Inc.

H A R V E Y U T E C HIndependent Consultant

J O H N W A L L N E RTektronix, Inc.

A R T H U R W A R DIBM

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CROSS-INSTITUTIONALPROGRAMSAND COURSESMost courses at the OGI School ofScience & Engineering areapplicable to a specific programof study. However, the followingprograms and subjects are notidentified with any onedepartment or program. Theseprograms and courses arerelevant for students in variousdepartments and academicprograms, and are accessiblefrom more than one department.

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PROGRAMS OF STUDY IN SPOKENLANGUAGE UNDERSTANDING

The research program of the Centerfor Spoken Language Understanding encompassesa broad range of speech technologies.Such research is inherentlymultidisciplinary, and the center bringstogether a team with expertise in signalprocessing, speech recognition, speechsynthesis, dialog modeling, naturallanguage processing, multimodalsystems, linguistics and human-computer interaction.

This program focuses on specificproblem areas such as: multimodal,interactive reading tutors for childrenwith reading or hearing problems;robust methods for enhancing speechin noisy environments; large vocabulary recognition of continuousspeech, as in broadcast news; unitselection and voice conversion for more realistic speech synthesis; robust parsing and interpretationof spoken and multimodal input;modeling of disfluencies in spontaneousspeech; and effective methods fordialog management.

The Center for Spoken LanguageUnderstanding participates in themaster’s and Ph.D. programs of study in the Departments of BiomedicalEngineering and Computer Science and Engineering. Students who areinterested in earning a master’s orPh.D. degree in biomedical engineering,computer science and engineering, or electrical engineering, withspecialization in spoken languageunderstanding, should consult thecatalog information for thosedepartments and consult an advisor in the Center for Spoken LanguageUnderstanding, the Department ofBiomedical Engineering or theDepartment of Computer Science and Engineering.

APPLIED COMPUTING COURSES

Applied computing (APC) courses provide the skills needed to accomplish specific goals and provide prerequisiteknowledge for more advanced courses.Students should check with theiradvisors to determine whether thesecourses should be taken and checkwith their departments to determinewhether applied computing credit hours can be used to satisfy degreerequirements in their programsof study.

APPLIED MATHEMATICS COURSES

Applied math (MATH) courses provideprerequisite knowledge for moreadvanced courses. Students shouldcheck with their advisors to determinewhich, if any, of these courses areneeded for their programs of study and check with their departments to determine whether appliedmathematics credit hours can be used to satisfy degree requirements in their programs of study.

GENERAL EDUCATION COURSES

General education (GEN) courses are provided as a service to the academiccommunity. They are intended toimprove the general academic skills of participants. Credit hours earnedfrom general education courses do not usually apply toward degreerequirements. Students should check with their advisors concerningthe desirability of taking generaleducation courses.

OGI facu l ty adv isors work c lose ly w i th studenttsto take advantage of the school ’s cross-d isc ip l inaryeducat iona l opportun i t ies . Here, MST professorNico le Steck ler counse ls a prospect ive student .

COURSE DESCRIPTIONSEffective Fall quarter 2003,the OGI School has renumberedmany of its courses to betteralign course numbers with theOregon Health & ScienceUniversity standard numberingscheme. To assist in relating thenew course numbers to coursesoffered in the past, a coursenumber crosswalk is availableonline at www.ogi.edu/schedule/crosswalk.shtml.

5xx Graduate courses offered primarily insupport of master’s programs. May beused towards a doctoral program asappropriate.

6xx Graduate courses offered primarily insupport of doctoral programs. May beused towards a master’s program asappropriate.

Master’s and certificate students shouldregister for the 5xx class and doctoralstudents should register for the 6xx classwhen available.

APPLIED COMPUTING

APC 514/614 Applications Programming in C++(Formerly APC 505a and APC 505b)This course provides an introduction to program-ming in C++, which is widely used for developingengineering and business applications. This courseintroduces students to the C++ language, and coversfundamental concepts such as classes, compositionand inheritance, polymorphism, virtual functions,overloading and overriding, abstract classes, purevirtual functions, streams, exceptions, operatoroverloading and templates. The course is suitablefor students in engineering, science and finance whowish to gain an understanding of the language. Oncompletion, students will be in a position to con-tribute to the design and development of systemsusing the main features in C++. Assignments includewriting programs and a programming project.Prerequisites: Knowledge of a programming language.

3 credits

APC 515/615 Data Structures and Discrete MathematicsThis course covers fundamental topics in data struc-tures and discrete mathematics. The topics arepresented in an integrated manner that provides thediscrete math foundations for data structures andcomputing applications of discrete mathematics

concepts. Topics include stacks, queues, linked lists,trees, algorithms for searching and sorting, finitestate automata, and concepts of computability anddecidability. Topics from discrete math include setsand various types of relations (functions, graphs,trees, lattices), recursion and inductive proofs,Boolean logic, relational algebra, predicate calculus,series and limits, and asymptotic behavior ofsearching and sorting algorithms. Programmingexercises are assigned throughout the course.Prerequisites: APC 514 or equivalent knowledge of Cor C++. 3 credits

BIOMEDICAL ENGINEERING

BME 501 M.S. Non-Thesis ResearchSupervised project research for Master’s studentswho are not pursuing a thesis.

Variable and repetitive credit

BME 502/602 Independent StudyIndependent study allows a student to work one-on-one with a faculty member on selected topic(s) ofinterest. Registering for independent study requirespre-approval from the faculty member and the stu-dent’s academic department.


BME 503 M.S. Thesis ResearchSupervised original research towards a thesis forthe Master’s degree. Variable and repetitive credit

BME 504/604 Professional InternshipProfessional internship credits provide students anopportunity to earn credit for relevant work experi-ence in industry. Students gain valuable industrialexperience that allows them to both apply theknowledge gained in the classroom and prepare forcareers following graduation. Students on F-1 or J-1 visas must obtain prior written approval forinternships from OGI’s Office of InternationalStudents and Scholars before enrolling. Enrollmentrequires a faculty advisor and is limited by the num-ber of internship opportunities available.


BME 505/605 Readings in Biomedical EngineeringThis course is designed to teach critical evaluation ofinformation in the field of Biomedical Engineering.Students will read articles and papers on timely top-ics related to the student’s area of interest. Studentswill be required to present a summary of the read-ings to the class. 1 credit, repetitive

BME 506/606 Special TopicsSpecial topics courses are offered in areas of par-ticular relevance to the research interests of facultyor in response to industry needs. Special Topiccourses are subject to change and are offered intermittently. Variable and repetitive credit

BME 507a/607a Biomedical Engineering SeminarThis seminar course will feature presentations anddiscussions on topics in biomedical engineering thatexemplify the wide range of applications of biomed-ical engineering to science and medicine. The goals

are to provide the students with an overview of thediverse opportunities for research and application,to foster development of critical analysis and think-ing, and to stimulate creative problem solving andresearch planning. Both faculty and students willpresent topics and lead discussions. Students will berequired to write a short paper that introduces atopic and proposes an original project.

1 credit, repetitive

BME 507b/607b Current Topics in Tissue EngineeringThis course is a seminar course with both criticalevaluations of papers in tissue engineering litera-ture and guest speakers presenting their recentresearch. Specific topics will change with students’interests and developments in the field.Prerequisites: Molecular and Cellular Biology forBiomedical Engineering. 1 credit, repetitive

BME 507c/607c Readings in Neurologyand NeuroscienceThis course is intended to develop skills in criticalanalysis of the basic and clinical neuroscience liter-ature through readings, presentations, anddiscussions. Topics will vary with the individualinterests of the students and faculty and develop-ments in the field. 1 credit, repetitive

BME 511/611 Biochemistry for Biomedical EngineeringThe course will introduce the basics of biochemistry,emphasizing the chemical structure and physio-chemical behavior of biochemicals such as sugarsproteins, nucleic acids, water, various polymers andother common components of cells and tissues. Anoverview of the basic metabolic pathways of cellsand the integrated chemistry of different organs inthe whole body will be presented. A biochemical per-spective on processing of biomaterials will bepresented, drawing examples from tissue engineer-ing and cooking. The goal is to give an introductionto biochemistry that enables the biomedical engi-neer to better communicate with medicalresearchers and clinicians, while also offering aunique engineering perspective on the biochemicalnature of biomaterials. 3 credits

BME 513/613 Biomedical Signal Processing IThis series covers the analysis of biomedical signals.The first course introduces the basic tools for con-tinuous- and discrete-time signal analysis andmodeling: Laplace and continuous-time Fouriertransform, z-transform and discrete time Fouriertransform, Fourier series, discrete Fourier trans-form, continuous time filter design, FIR and IIR filterdesign, wavelet transform. Applications areas cov-ered are ECG, IEGM, blood pressure measurement,cardiac impedance measurement, and heart ratevariability. Tool: MATLAB with Simulink.Prerequisites: undergraduate signal and systemcourse covering Laplace and Fourier transform.

3 credits

BME 514/614 Biomedical Instrumentation —Signals and SensorsThis course covers the concept and application ofinstrumentation techniques to biomedical subjects.Areas studied will include biopotentials, sensors,

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stimulators, amplifiers, filters, displays, safety, andinstrument design. This course includes a laborato-ry and a design project. Prerequisites: Calculusthrough differential equations. 3 credits

BME 522/622 Biomedical Optics I: Tissue OpticsLight propagation in tissue: This course treats light transport in scattering and absorbing mediasuch as biological tissue. Light transport is modeledusing a variety of theories and computational tech-niques, including Monte Carlo simulations andapproximate solutions of the radiative transportequation. Steady- state and time-dependent prob-lems are treated. Spectroscopy and fluorescencemeasurements are introduced. Optical imagingtechniques are presented. Students learn the basicsrequired for design of optical devices for therapyand diagnostics. 3 credits

BME 523/623 Biomedical Optics II:Laser-Tissue InteractionsPhysics of laser-tissue interactions: The coursetreats the immediate physical processes thataccompany the absorption of light by biological tissues, including photochemical reactions, heatingand tissue coagulation, vaporization, creation ofplasmas, and production of stress waves in tissue.Such processes are modeled using finite-differencetechniques. Applications in medicine and biology are discussed. Prerequisite: BME 522/622Biomedical Optics I, or permission of instructor.

3 credits

BME 524/624 Biomedical Optics III: Engineering DesignThe students work as a team in preparing five business plans throughout the quarter. Each busi-ness plan is devoted to a potential medical device orprotocol using optical technologies. The team isdivided into a CEO, scientific officer, marketingmanager, regulatory affairs manager, and manufac-turing manager. The roles are rotated amongst thestudents for each business plan. Feasibility studiesare conducted in a laboratory exercise designed bythe students. The team formally presents a businessplan every two weeks. Prerequisite: BME 523/623Biomedical Optics II, or permission of instructor.

3 credits

BME 525/625 Optical Nondestructive EvaluationThis course is aimed at introducing the field of opti-cal NDE to engineering students. The course focusesprimarily on coherent light techniques such as inter-ferometry, holography, and laser speckle methods.Moiré, photo-elastic, and structured light methodsare also discussed. Specific applications to biomed-ical engineering, semiconductor, and electronicmaterials will be presented. 3 credits

BME 526/626 Computational Approaches to LaserInteractions with Biological TissuesLasers and light from alternative conventionalsources interact with biological tissues or othercomplex media through photochemical, photother-mal and photomechanical mechanisms. This coursewill employ computational methods to simulateinteraction of lasers with tissues. Compartmentalmodeling will model photochemical interactions.

Green’s function and finite difference techniques willmodel thermal and water diffusion, surface evapo-ration, and explosive vaporization. Arrhenius rateprocess calculations will model thermal damage,thermoelastic expansion and velocity potential mod-els will simulate pressure wave generation andpropagation, spallation/cavitation models will modelinitiation and growth of laser-induced materialdefects leading to fragmentation. These methodsprovide a tool kit for handling a wide variety of lasereffects in biological tissues. 3 credits

BME 527/627 Computational Approaches to LightTransport in Biological TissuesUnderstanding the movement of light through com-plex biological tissues or other complex media is thefirst step in design of optical devices or clinical pro-tocols in medical applications of lasers and light.This course will use various computational methodsto simulate such light propagation: (1) wave theoryto discuss the early loss of coherence and polariza-tion as light initially enters tissue; (2) small anglescattering to discuss the transition of ballistic pho-tons into scattering photons; (3) Monte Carlosimulations to discuss a variety of issues in energypropagation, including irregular boundary condi-tions; (4) diffusion theory to predict light fieldsdistant from sources; (5) perturbation theory toapproximate optical heterogeneities with absorptionand scattering properties that vary from the back-ground medium properties. These methods provide atool kit for handling a wide variety of optical prob-lems encountered in design of optical systemsinvolving tissues. 3 credits

BME 528/628 Physical and Geometrical OpticsFirst-order Gaussian optics and thin-lens systemlayout. Photometric theory applied to optical sys-tems. Topics include: the eye, magnifiers,microscopes, matrix optics, Seidel aberrations,scalar diffraction theory; Fresnel and Fraunhoferdiffraction, and interferometry. 3 credits

BME 541/641 Biomaterials IThe first of a two part series aimed at a graduatelevel introduction to the composition, properties,manufacture, design and application of syntheticand naturally derived materials for the replacementor augmentation of human tissue. Biomaterials I isfocused on a rigorous treatment of elastic and vis-coelastic theory, the mechanics of natural hard andsoft biological tissues, and numerical methods formaterials evaluation. 3 credits

BME 542/642 Biomaterials IIThis is the second course in a two-class sequence onbiomaterials. Biomaterials II covers an in-depthanalysis of specific materials used for implantatiowithin the human body. Topics that will be coveredinclude biocompatibility, tissue engineering for hardand soft tissues, applications of metals, ceramicsand polymers, and finite-element methods for bio-materials evaluation. Prerequisite: BME 541/641Biomaterials I. 3 credits

BME 543/643 Advanced Tissue Engineering TechniquesThis course is designed to teach the techniques nec-

essary to perform advanced research in TissueEngineering. Techniques include the latest in imag-ing, stem cell isolation, growth factor treatmentsand mechanical stimulation of engineered tissues.Prerequisites: BME 511/611 Molecular and CellularBiology for Biomedical Engineering, BME 541/641Biomaterials I, and BME 542/642 Biomaterials II.

3 credits

BME 544/644 Advanced BiomaterialsThis course is a seminar-style course in which stu-dents critically evaluate key papers in thebiomaterials literature. Specifics topics will changewith developments in the field as well as with thestudents’ interests. Students may take this coursemore than once. Prerequisites: BME 541/641Biomaterials I and BME 542/642 Biomaterials II.

3 credits

BME 545/645 Biocompatibility: Host-Implant InteractionsThis course provides the student with a firm under-standing of how the body reacts to implantedbiomaterials at the cell, tissue, organ, and systemiclevels. In addition, specific characteristics that hin-der or improve the biocompatibility of materials willbe addressed. Prerequisites: BME 511/611Molecular and Cellular Biology for BiomedicalEngineering and BME 542/642 Biomaterials II.

3 credits

BME 561/661 Neuronal Control SystemsThis course explores various neuronal control sys-tems from an engineering perspective. Topicsinclude: control system theory; neuronal plasticityand state dependence; sympathetic nervous systemcontrol of cardiovascular functions, temperature,and respiration; and vestibulooculomotor control.

3 credits

BME 562/662 Motor ControlThis course is intended to introduce the student tosimple and complex mechanical, electronic, and dig-ital control systems using human and animalskeletomuscular systems and robotics as model sys-tems. The course will consist of three parts: first,the physiology and neural control of the neuromus-cular system; second, control problems faced indesigning robots with complex mechanical systemsand the relation to problems faced by the mam-malian motor control system; third, background anddesign of clinical devices and procedures for motordisorders, including stroke, spinal cord injury, bal-ance disorders, and neuroprostheses. 3 credits

BME 563/663 Mathematic and Computational Modelingof Neuronal SystemsThis course introduces mathematical and computa-tional techniques for modeling the dynamics ofbiological systems. Topics will include analytical,numerical, and agent-based simulations using ordi-nary and partial differential equations, stochasticdynamics, and discrete methods. Applications willbe drawn from topics including neural dynamics atthe cellular and circuit level, circulation, respira-tion, and immune system response, molecularevolution, enzyme kinetics, and development.

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Discussion will include techniques for validatingmodels and for incorporating experimental data, andthe roles of simulation and theory in the effort tounderstand biological systems. 3 credits

BME 564/664 Methods in Neuromedicine This course includes topics on methods related tothe diagnosis, treatment and intraoperative assess-ment of the nervous system in humans. Topicsinclude: electrical stimulation (neuronal excitability,diagnostic testing of nerves and brain structures,surgical monitoring, neuronal rehabilitation, andfunctional electrical stimulation); safety (coupling tobiological tissues, excitotoxicity, neuronal vulnera-bilities, and special considerations with diseasestates); drug targeting; blood brain barrier; andbasic neuro-imaging. 3 credits

BME 565/665 Introduction toComputational NeurophysiologyOverview of basic cellular neurophysiology, includ-ing action and membrane potentials, channels andchannel blockers, gates, and ion pumps. Biophysicalmodels of the neuron including Hodgkin-Huxley andCable models. Models of synaptic function and plas-ticity. Central pattern generators and simpleinvertebrate circuits. Organization of receptivefields and topographic neural maps. Models ofneural development, ocular dominance, and orienta-tion columns. 3 credits

BME 566/666 Biomedical Signal Processing IIThe course covers advanced techniques of digitalsignal processing for solving biomedical signal prob-lems. Time and frequency domain filteringtech-niques, adaptive and optimal systems, detec-tion of biomedical waveforms, spectral estimationand system modeling are covered. Applications toproblems in ECG and EEG are featured.Prerequisites: BME 513/613 Biomedical SignalProcessing and I and EE 582/682 Introduction toDigital Signal Processing. 3 credits

BME 567/667 Visual Sensory SystemsIn this course, the anatomy, physiology and functionof visual systems are examined with emphasis onthe dynamic processing of visual inputs and on tech-nological approaches to functional analysis and onmethods for diagnosis of eye diseases. Topics to becovered include optics, anatomy of the eye, retinalphysiology, signal processing, plasticity, perception,functional assessment with complex visual stimuliand evoked potentials, and new developments invisual prosthetic systems. 3 credits

BME 568/668 Auditory and Visual Processing by Human and MachineInteraction between humans and machines could begreatly enhanced by machines that could communi-cate using human sensory signals such as speechand gestures. Knowledge of human information pro-cessing including audition, vision, and theircombination is, therefore, critical in the design ofeffective human-machine interfaces. The courseintroduces selected phenomena in auditory andvisual perception, and motor control. Students learnhow to interpret empirical data, how to incorporatethese data in models, and how to apply these mod-

els to engineering problems. The anthropomorphic(human-like) signal processing approach is illustrat-ed on engineering models of perceptual phenomena.

3 credits

BME 571/671 Speech SystemsSpeech is one of the most natural means for com-munication and carries information from manysources. The explosive growth of communicationsand computer technologies puts new demands ontechniques for machine extraction of informationcontent of speech signals, for its storage or trans-mission, and for reconstruction of the speech signalfrom its parametric representation. The course cov-ers techniques for processing of speech signal usedfor speech coding and synthesis, enhancement ofdegraded speech, speech recognition, speakerrecognition, and language identification. 3 credits

BME 572/672 Speech SynthesisThis course will introduce students to the problem ofsynthesizing speech from text input. Speech synthe-sis is a challenging area that draws on expertisefrom a diverse set of scientific fields, including sig-nal processing, linguistics, psychology, statistics,and artificial intelligence. Fundamental advances ineach of these areas will be needed to achieve truly“human-like” synthesis quality and advances inother realms of speech technology (like speechrecognition, speech coding, speech enhancement).In this course, we will consider current approachesto sub-problems such as text analysis, pronuncia-tion, linguistic analysis of prosody, and generation of the speech waveform. Lectures, demonstra-tions, and readings of relevant literature in the areawill be supplemented by student lab exercises usingthe Festival text-to-speech system and other hands-on tools. 3 credits

BME 581/681 Fourier AnalysisFourier analysis is used in nearly every field of engi-neering, including biomedical engineering. Itprovides a unifying mathematical approach to thestudy of networks, electrical and mechanical sys-tems, linear systems, image and signal processing,as well as many other systems. This course will pro-vide a solid introduction to application of Fouriertheory in biomedical engineering. Topics include:convolution and correlation; Fourier theorems;Numerical transforms; Sampling and series;Discrete Fourier transform and the FFT; Relatedtransforms. Prerequisites: one year of calculus.

3 credits

BME 599/699 Reciprocity CourseOGI students admitted to a degree program have theopportunity to take classes at other OregonUniversity System schools under the Joint CampusAgreement or Reciprocity Agreement. Contact theDepartment of Graduate Education for details.Courses taken under these agreements are listed as599/699. Variable and repetitive credit

BME 601 Prequalifying Ph.D. ResearchSupervised Ph.D. research prior to passing thedepartment’s qualifying exam.


BME 603 Ph.D. Dissertation ResearchResearch toward the dissertation for the Ph.D.degree occurring after passing the qualifying exam.


COMPUTER SCIENCE & ENGINEERING

CSE 501 M.S. Non-thesis Research(Formerly CSE 610)Supervised research for up to 6 credits as a compo-nent of the non-thesis master’s degree. Students arerequired to produce concrete research deliverables,including a final report equivalent to a CSE techni-cal report. Each 3 credits of CSE 501 may count asone class to fulfill the M.S. non-thesis graduationrequirements. Variable and repetitive credit

CSE 502/602 Independent StudyIndependent study allows a student to work one-on-one with a faculty member on selected topic(s) ofinterest. Registering for independent study requirespre-approval from the faculty member and the stu-dent’s academic department.


CSE 503 M.S. Thesis Research(Formerly CSE 700)Research toward the thesis for the M.S. degree.


CSE 504/604 Professional Internship(Formerly CSE 620)These courses provide an opportunity to earn creditfor relevant work experience in industry. Studentsgain valuable industrial experience that allows themto both apply the knowledge gained in the classroomand prepare for careers in computer science. Awritten report must be submitted to the CSE facultyadvisor at the end of the experience. Enrollmentrequires a faculty advisor and is limited by the num-ber of internship opportunities available.

1 to 3 credits per quarter

CSE 506/606 Special Topics(Formerly CSE 58X)Under this number, we offer courses of particularrelevance to the research interests of faculty or instate-of-the-art subjects of interest to the communi-ty. Some recent offerings include:Advanced Functional ProgrammingBuilding Secure SystemsFormal Verification of SoftwareHigh Assurance Software EngineeringInformation IntegrationInformation Retrieval on the InternetInternet TechnologyNetworking PracticumPrinciples of Database Systems3D GraphicsReal-time Rendering Using Modern GraphicArchitectureScientific VisualizationSecurity ProtocolsWeb Data Management

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CSE 511/611 Principles of Compiler DesignThis course introduces the basics of building a com-piler using a multiphase translation process. Itcovers lexical analysis, parsing and translation toabstract syntax using modern parser generatortechnology. It discusses binding of identifiers andsymbol table organization, and a variety of interme-diate representations that are suitable for back-endanalysis. It investigates back-end transformationsand optimizations for a number of languages. Othertopics include type checking, static analysis andbasic run time support. Compiling is essentially aprocess of symbolically manipulating program rep-resentations represented by tree and graph-likedata structures. Because of this, we will use toolsthat facilitate symbolic manipulation and definitionof such structures as parser and lexical generators,and tools for generating code from pattern-baseddescriptions. Prerequisite: CSE 533. 3 credits

CSE 512/612 Compiling Functional LanguagesA project-oriented course on the theory and designof a compiler for a typed, functional programminglanguage. Topics include understanding a formaldefinition of programming language semantics, com-piling pattern analysis, lifting abstractions,continuation-passing style of implementation,abstract machines, code generation and addressassignment, register allocation and assignment ongeneral-register machines, run-time storage admin-istration, data-flow analysis and code improvement.Prerequisite: CSE 511. 3 credits

CSE 513/613 Introduction to Operating SystemsA study of the design and implementation of modernoperating systems. The course concentrates onoperating system kernel design and includes the fol-lowing topics: concurrent processes, interprocesscommunication, synchronization, scheduling,resource allocation, memory management, the con-cept of virtual memory and the required underlyinghardware support, secondary storage management,file systems and security. We will use the Linuxoperating system to ground the discussion ofabstract concepts. Interested students will beencouraged to read the Linux source code for dis-cussions in class. 3 credits

CSE 514/614 Introduction to Database SystemsA survey of database fundamentals emphasizing theuse of database systems. Topics include databasedesign, data dependencies and normalization, sec-ondary storage structures, SQL, relational algebra,query processing, query optimization, transactions,recovery and embedded SQL. This course focuses onrelational database systems and the SQL query lan-guage. Students participate in a project to design,populate and query a database. Prerequisites: Data structures, discrete mathematics and mathe-matical logic. 3 credits

CSE 515/615 Distributed Computing SystemsThis course concentrates on distributed computingfrom a systems software perspective. Major topicsinclude communications middleware (remote proce-dure call, remote method invocation and causalbroadcast), operating system support, distributed

file systems, distributed transaction processing,load balancing, distributed programming languagesand systems, fault-tolerance and replication algo-rithms, distributed timing issues and distributedalgorithms. Prerequisites: CSE 513, Introduction to Operating Systems as well as a basic under-standing of computer communications problems and protocols. 3 credits

CSE 516/616 Introduction to Software Engineering(Formerly CSE 500)Software engineering is concerned with the ways inwhich people conduct their work activities and applytechnology to produce and maintain software prod-ucts and software-intensive systems. Issues ofconcern include specification, design, implementa-tion, verification, validation and evolution ofsoftware artifacts. Related topics include softwaremetrics, project management, configuration man-agement, quality assurance, peer reviews, riskmanagement and process improvement. This coursepresents an integrated view of these topics andrelated issues. It is an essential course for anyoneworking in development, maintenance, managementor related areas in a software organization.

3 credits

CSE 517/617 Software Engineering Processes(Formerly CSE 503)This course is concerned with examining andimproving the software development processes,including the technical, managerial and culturalprocesses, used by organizations to develop andmaintain high-quality software systems in a timelyand economical manner. Various process models,including the SEI Capability Maturity Models, theISO SPICE model, the Team Software Process, andthe Personal Software Process are studied and con-trasted. Tailoring of process models to fit localsituations and various approaches to softwareprocess improvement are presented. Studentsselect and complete term projects that address top-ics in software process improvement. 3 credits

CSE 518/618 Software Design and DevelopmentContemporary, object-oriented software design,using the Java programming language. An introduc-tion to the eXtreme Programming softwaredevelopment methodology, which is based upon theprinciple that change is inevitable and successfulsoftware designs undergo continual evolution.Techniques to be covered include program refactor-ing, automated unit testing, pair programming,participatory design and managing short productdevelopment cycles. These principles and tech-niques will be illustrated in a term-length projectthat provides design and implementation experience.

3 credits

CSE 519/619 Object-Oriented Analysis and Design(Formerly CSE 504)This course presents an integrated set of techniquesfor software analysis and design based on object-oriented concepts. The techniques focus onproducing the artifacts and work products,expressed in UML, appropriate for the analysis anddesign phases of the software development lifecycle.

We adopt a use case model for requirements and aresponsibility-driven approach for the developmentof object models. Design patterns and frameworksare also emphasized. Note that CSE 529/629 Object-Oriented Programming is intended as a follow-oncourse for CSE 519/619. 3 credits

CSE 520/620 Software ArchitectureThe architecture of a software system specifies thecomponents, visible properties of the components,and the structural and behavioral relationshipamong the components of a software program orsystem. There are many different architecturalstyles, including pipes and filters, layers, client-server, OO frameworks, embedded-systems,plug-and-play, remote procedure call, and data-driv-en architectures. Different styles satisfy differentconstraints and influence the system’s performance,reliability, safety, security, and other quality-of-service attributes. Systematic architectural designfacilitates software reuse and the development ofproduct families. In this course, we will study archi-tectures and architectural styles from both thestructural and behavioral viewpoints. In addition,we will examine design methods and tools for devel-oping software architectures. Students will learnthe strengths and weaknesses of various architec-tures and will understand the circumstances underwhich various architectural styles might be used.The course will include lectures plus reading anddiscussion of papers from the literature of softwarearchitecture. Each student will conduct an in-depthinvestigation of an architecture or architecturalstyle and prepare a term paper based on the inves-tigation. Prerequisites: Prior knowledge of UML isdesirable but not required. 3 credits

CSE 521/621 Introduction to Computer ArchitectureThis course provides a broad introduction to com-puter architecture. It covers a large amount ofmaterial in moderate depth, providing a good under-standing of the basic issues in computer systemdesign. Specifically, the course covers instructionset design, pipelining, the memory hierarchy, I/Osystems, networking issues and multiprocessors.Example systems include the Intel x86, MIPS andDEC Alpha processors. Prerequisites: Experiencewriting software, preferably with some C or assem-bler programming. NOTE: Computer architecturehas become a quantitative science, so there will beconsiderable algebraic manipulation involved in theperformance analysis component of the course.

3 credits

CSE 522/622 Advanced Computer ArchitectureThis course is a follow-up to CSE 521/621. It coversadvanced computer architecture topics such as SMP(Shared Memory Multiprocessors) and NUMA (Non-Uniform Memory Access) Architectures. It alsolooks at new trends in designing high-performanceclusters with examples. Specific topics to be cov-ered include: fundamentals of parallel architectures(communication paradigms, programming models,etc.), snoopy-based multiprocessors (cachecoherency, bus designs, multilevel caches, etc.),directory-based multiprocessors (NUMA and hybridarchitectures), interconnection networks (routing,

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switch designs, virtual lanes, etc.). Examples ofcommercial and prototype architectures such asIBM NUMAQ, InfiniBandTM and ServerNet.Prerequisite: CSE 521/621. 3 credits

CSE 524/624 TCP/IP Internetworking ProtocolsThis course provides an overview of the structureand algorithms used in the TCP/IP networking pro-tocols that make up the foundation of the Internet.Protocols and technologies covered will include anintroduction to the link layer, ARP, IP, ICMP, UDP,TCP, routing protocols and application protocols andsystems like the DNS, NFS, SMTP, FTP, HTTP andmulticasting protocols and applications. Providesarchitectural insight into protocol design issues andoperating system implementation techniques, typi-cally in terms of the Berkeley UNIX socketprogramming model. Provides socket programmingexperience with the client/server model. Providesexperience reading Internet RFC’s and/or drafts.Prerequisites: Familiarity with the functions of amodern multiuser operating system such as is cov-ered in CSE 513/613 or PSU’s CS 533; familiaritywith C programming on modern UNIX computers.

3 credits

CSE 525/625 Advanced NetworkingThis course is a seminar-style course targeted atlearning about advanced Internet technology andInternet research. In particular, we will choose froma range of contemporary papers and topics dealingwith gigabit switching and routing, web switching,firewalls, traffic engineering, MPLS, lambda switch-ing, issues in wide-area networking, internetrouting, packet classification, fast IP routinglookups, content-addressable networks, peer-to-peernetworking, wireless networking, Internet mappingand measurement, content distribution networks,overlay networks, sensor networks, ad hoc networks,power-aware networking, intrusion detection sys-tems, distributed denial of service attacks andprevention, web and application server technology,browser technology, and web cashing. Prerequisites:CSE524 TCP/IP Internetworking Protocols. 3 credits

CSE 526/626 Advanced Topics in Operating SystemsThis course includes an in-depth study of modernoperating system design. The course is based onreading recent research papers, and includes anemphasis on evaluating the papers in addition tounderstanding the systems they describe. Topicsvary from year to year but typically include micro-kernel operating systems, lightweight inter-processcommunication, extensible operating systems, filesystems, mobile computing, ubiquitous computing,workstation clusters, adaptive resource manage-ment, and OS support for multimedia applications.Prerequisites: CSE 513 and CSE 521. 3 credits

CSE 527/627 Principles and Practices of System SecurityIn the Internet age, host system security is essentialand difficult. This course explains the principles andpractices of securing host systems. Students learnthe principles of how to build secure systems andhow various real systems succeed and fail in livingup to these principles. We will study various securi-ty- enhancing technologies, in each case relating the

security enhancement to the principles of securesystems. Prerequisite: CSE 513. 3 credits

CSE 528/628 CryptographyThis course covers the major modern cryptographictechniques — the core technology for the area ofinformation security. We start with an overview ofclassical cryptography and information theory. Thenwe examine in-depth the most widely used cryp-tosystems: symmetric systems such as DES (DataEncryption Standard) and AES (Rijndael, the newstandard), and public-key systems, notably RSA.Discrete log systems and standard digital signatureschemes are also covered, including elliptic curvecryptography. The course should be accessible to any-one who is willing to encounter some number theory.

3 credits.

CSE 529/629 Object-Oriented Programming(Formerly CSE 509)This course provides a rigorous introduction to theconcepts behind object-oriented programming. It isfor students who are already familiar with the con-cept of object-orientation and with object-orientedanalysis and design techniques. One way to learnthis background material is by taking CSE 519/619,Object-Oriented Analysis and Design. In CSE 509,students gain a thorough understanding of incre-mental programming, type-safety, polymorphism,encapsulation and set-based abstraction, and applythese concepts through a variety of programmingprojects. We study several programming languages,including Java and Smalltalk, so students areexposed to different realizations of these conceptsand gain an appreciation for the programming lan-guage design space. We also look at publishedobject-oriented design patterns and see how theycan be implemented in different object-oriented pro-gramming languages. Students are required to readappropriate research papers, complete severalshort programming assignments, complete a sub-stantial programming project and write some shortessays. Prerequisite: CSE 519/619 or equivalent.

3 credits

CSE 530/630 Introduction to Mathematical LogicProvides a theoretical foundation for the logic ofcomputation. Propositional and first-order predi-cate calculi, soundness and completeness,incompleteness and incomputability, the Church-Turing thesis, term-rewriting systems and appli-cation to program verification. 3 credits

CSE 531/631 Foundations of SemanticsFormal semantics aims to answer two importantquestions: 1) when are two programs equal and 2)when does a program faithfully implement a mathe-matical specification? The course exploresdenotational semantics, operational semantics andprogram logic, studying how they are related andhow they can answer the motivating questions.Programming language concepts, such as impera-tive programming, functional programming,call-by-name, call-by-value and continuations, arecontrasted and explained in terms of their semanticfoundations. Key concepts include full abstractionand the use of least fixed-point constructions to

solve recursive equations. The course is designedfor students interested in the mathematical founda-tions of programming languages and programminglogics. Prerequisite: Discrete mathematics.

3 credits

CSE 532/632 Analysis and Design of AlgorithmsAn introduction to the design and analysis of algo-rithms. The course covers design techniques, suchas dynamic programming and greedy methods, aswell as fundamentals of analyzing algorithms forcorrectness and time and space bounds. Topicsinclude advanced sorting and searching methods,graph algorithms and geometric algorithms. Otherareas vary from year to year and may include com-putational geometry, matrix manipulations, stringand pattern matching, set algorithms, polynomialcomputations and the fast Fourier transform. Pre-requisites: Data structures and discrete mathematics.

3 credits

CSE 533/633 Automata and Formal LanguagesAutomata theory introduces fundamental modelsthat are used over and over again in computer sci-ence for programming languages, in compilerconstruction and in algorithms. These models are avaluable part of the repertoire of any computer sci-entist or engineer. This course introducesprogressively more powerful models of computation,starting with finite automata and moving throughcounter, stack and Turing machines. It also presentsthe regular, context-free, recursive and recursivelyenumerable languages and shows how they corre-spond to the various models of computation and togeneration mechanisms such as regular expressionsand grammars. The emphasis is on understandingthe properties of these models, the relationshipsamong them and how modifications such as nonde-terminism and resource bounds affect them. Thecourse includes application of these concepts toproblems arising in other parts of computer science.Prerequisite: Discrete mathematics. 3 credits

CSE 534/634 Computability and IntractabilityComputability and complexity theory identify class-es of languages based on characteristics ofmachines that recognize them. The course presentselementary results from recursive function theory,including recursive and recursively enumerablesets, and degrees of undecidability. Using recursiontheory as a model, it develops the classical resultsof complexity theory, including time and space com-plexity classes, hierarchy theorems and elementaryresults from parallel complexity. The course con-cludes by studying classes of problems that areprovably intractable, with a particular emphasis onNP-complete problems. Prerequisite: CSE 532 orCSE 533. 3 credits

CSE 535/635 Categories in Computer ScienceCategory theory provides a powerful and concisenotation for abstract properties of functions.Originally developed for algebraic topology, it hasfound widespread application in computer science.This course introduces the basic notions of categorytheory, including functors, natural transformations,products, sums, limits, colimits, monads and

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adjunctions. These concepts are illustrated withexamples from computer science and mathematics,including the relationship between Cartesian closedcategories and the lambda-calculus. Familiarity withdiscrete mathematics is an essential prerequisite.

3 credits

CSE 536/636 Functional Programming(Formerly CSE 502)In functional programming, we shift our focus fromdata objects and their representations to functionsthat act on data. Programs are formulated as com-positions of functions, rather than as sequences ofstatements. This leads to a programming methodol-ogy that is quite different from that learned in usingstatement-oriented languages. This course intro-duces the student to functional notation, recursion,higher-order functions, reasoning about functionsand polymorphic-type systems. Functional program-ming languages are known for their increasedproductivity and reliability, due in part to the higherlevels of abstraction provided by functional lan-guages. Course is taught by lecture with smallweekly programming assignments. Experience isgained by programming in the functional languageHaskell or one of its close derivatives. Recentadvances in functional programming languagesallow them to use updatable state in a safe mannerand to cause effects on the real world. Students gainexperience by writing programs using these featuresto program interactive window-based programsusing an embedded “widget” library. 3 credits

CSE 540/640 Neural Network Algorithmsand ArchitecturesThis course introduces the fundamentals of connec-tionist and neural network models. Paradigms forsupervised, unsupervised and reinforcement learn-ing are covered. Topics include LMS andbackpropagation algorithms, network optimizationtechniques, theoretical and practical tools toaddress generalization and complexity control, prin-cipal components and independent componentanalysis, mixture models and clustering. The courseaims to develop the student’s statistical understand-ing of the use of neural network techniques.Applications to classification, time series predic-tion, regression and data clustering are treatedusing real world data. 3 credits

CSE 541/641 Database ImplementationThis course explores the internals of relationaldatabase management systems. This course willgive students a strong grounding in the designtradeoffs and implementation issues that areaddressed by large database systems. The coursewill also help DBA’s understand how the tuningparameters of commercial databases can affectperformance, and will help database applicationprogrammers to create applications better tuned totake advantage of the database internals. Typicaltopics discussed include file and index implementa-tion, buffer management, query processing,cost-based query optimization, concurrency con-trol, transaction processing, and logging andrecovery implementations. The class includeshands-on programming assignments. Prerequisite:

CSE 514; UNIX and C programming experience isstrongly recommended. 3 credits

CSE 542/642 Object Data ManagementA variety of products for managing object data have emerged in the marketplace. Object-orienteddatabase systems and persistent programming lan-guages have been joined by object-relationaldatabases and middleware component technologies,such as Enterprise Java Beans. Other storageengines, such as LDAP and XML servers, have anobject flavor. This course begins with the conceptsin types, data models and languages that underlieobject data management. It then looks at exampleprototype and commercial systems, and examinesdesign dimensions such as data model, persistence,encapsulation, hierarchies, query languages andtransactions. It touches on application developmentand data management issues and concludes withtreatment of software architecture, implementationand benchmarking techniques. Students will do aproject using a commercial product. Prerequisite:CSE 514 or other introductory database course.

3 credits

CSE 545/645 Advanced Neural and Adaptive AlgorithmsAn advanced treatment of architectures and algo-rithms for pattern recognition, regression,timeseries prediction and data mining. Typical top-ics include convergence, effects of noise,optimization methods, probabilistic framework(including Bayesian estimation), generalization abil-ity and regularization and pruning, Hebbian learningand clustering and density modeling. Prerequisite:CSE 540 or instructor permission. 3 credits

CSE 546/646 Data and Signal CompressionThe need for signal and data compression is ubiqui-tous in image, video and speech processing, financeand computational science. Where data storesbecome very large (e.g. video, finance, earth sci-ence), the need is not met by simple lossless filecompression schemes, and we must turn to sophis-ticated coding techniques. This course addressesboth the theoretical basis and practical algorithmsfor data and signal compression. Topics include loss-less entropy-based coding, including Huffman andLempel-Ziv, and lossy compression techniquesincluding scalar quantizers, transform coding(Karhunen-Loeve, DCT and nonlinear transformcodes), predictive coding, vector quantization, adaptive codes and wavelets. The relation betweencompression schemes and probabilistic data modeling is emphasized in conjunction with eachtechnique. Application to speech, image and videocoding are discussed. Students will have the opportunity to design compression schemes for such diverse applications as earth science data,finance, speech or video, depending on their inter-ests. Prerequisites: Undergraduate calculus,introductory probability and statistics, some pro-gramming experience. 3 credits

CSE 547/647 Statistical Pattern RecognitionTheory and practice of statistical pattern recogni-tion. Students will learn fundamental theory andpractices that are common to a broad range of pat-

tern recognition applications and technologies, andapply principles to real-world examples. Theemphasis is on developing theoretical and practicaltools that provide grounding in pattern recognitionproblems and methods, rather than on showcasingparticular technologies. The course will benefitthose whose work may use any of a variety of recog-nition technologies in broad-ranging applicationssuch as speech and image processing, data mining,finance. Topics include: random vectors, detectionproblems (binary decision problems), likelihoodratio tests, ROC curves, parametric and non-para-metric density estimation, classification models,theoretical error bounds and practical error estima-tion through cross-validation. Maximum likelihoodand Bayesian parameter estimation, model-basedclustering, feature extraction for dimensionalityreduction and for classification. 3 credits

CSE 550/650 Spoken Language SystemsSpoken language systems will revolutionize howpeople interact with machines, replacing the key-board and mouse with natural conversations. Thesesystems will act like helpful human assistants andteachers for information access, commercial transac-tions, and learning. You’ll review the state of the artin building spoken language systems. You will gainhands-on experience using toolkits for building suchsystems, as well as learn the technologies needed fornext-generation systems, such as robust parsing,semantic processing, dialogue management, andagent architectures. Class projects will be done usingthe CSLU toolkit, Tcl/Tk, and VoiceXML. 3 credits

CSE 551/651 Structure of Spoken LanguageSpeech is considered a key component in the futureof human-computer communication. However, thesuccess of speech recognition and text-to-speechsynthesis systems depends on development of thetechnology as well as further research advances.Research and development of spoken-language tech-nology is facilitated by an understanding of theacoustic and symbolic structure of language, as wellas the capabilities and limitations of current sys-tems. This course will present some of what isknown about speech in terms of phonetics, acoustic-phonetic patterns, and models of speech perceptionand production. The goals are for the student tounderstand how speech is structured, understandand identify acoustic cues (especially in differentphonetic contexts), and understand how this infor-mation may be relevant to automatic speechrecognition or generation systems. 3 credits

CSE 552/652 Hidden Markov Models forSpeech Recognition(Formerly ECE 580-HMM)Hidden Markov Model-based technology is usedwidely in today’s speech recognition systems. Thiscourse is an introduction to speech recognitionusing HMM technology. Topics include the theory ofHidden Markov Models (discrete, semi-continuous,and continuous) and their applications to speechrecognition, along with the basic mathematics(probability theory, statistics, stochastic process,information theory, and signal processing) that arenecessary for speech recognition. The course is

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focused on understanding the theory behind thesefundamental technologies, and applying the technol-ogy to develop speech recognition systems.Prerequisite: Some knowledge of engineering math-ematics (calculus and linear algebra) is required; Cprogramming experience is necessary. 3 credits

CSE 558/658 Evolutionary ComputationThe field of evolutionary computation encompassesmachine learning methods inspired by biologicalevolution, as well as the computational modeling ofevolutionary processes in nature. The techniques ofevolutionary computation include genetic algo-rithms, genetic programming, evolvable hardware,evolutionary robotics, and related methods. Thesemethods have been used to solve problems in engi-neering design and optimization, robot control,bioinformatics and drug design, financial prediction,and image processing, to name a few applications.They are beginning to be widely used in the scientif-ic and commercial worlds. This course is a hands-onintroduction to these techniques and the theorybehind them. Students will learn the basics of evo-lutionary computation by implementing variousmethods themselves and applying them to simpleversions of real-world problems (when possible,related to the students’ own research or applica-tions interests). More advanced topics will includecoevolutionary learning, agent-based and artificiallife simulations, and the theoretical foundations ofevolutionary computation. Prerequisites:Programming experience in any high-level language.

3 credits.

CSE 559/659 Machine LearningThis course provides a broad introduction to tech-niques for building computer systems that improvethrough experience. It provides both conceptualgrounding and practical experience with severallearning systems. The course provides grounding foradvanced study in statistical learning methods, andfor work with adaptive technologies used in speechand image processing, robotic planning and control,diagnostic systems, complex system modeling, anditerative optimization. Topics include: learning para-digms and concept learning, decision trees, artificialneural networks, statistical sampling and empiricalerror estimation, Bayesian learning (including anintroduction to belief networks), clustering, princi-pal and independent component analysis,generalization theory, memory-based (instance)techniques, evolutionary computation, and rein-forcement learning. Students will gain practicalexperience implementing and evaluating systemsapplied to pattern recognition, prediction, and opti-mization problems. Prerequisites: Some experiencewith multi-variate calculus and linear algebra, atleast one high-level programming language, and anelementary undergraduate course in probability andstatistics. 3 credits.

CSE 560/660 Artificial IntelligenceThis course surveys the foundations and applica-tions of symbolic approaches to artificialintelligence. The approach emphasizes the formalbasis of automated reasoning and includes an intro-duction to programming in Prolog. Fundamentals

covered include search, knowledge representation,automated inference, planning, nonmonotonic rea-soning and reasoning about belief. Applicationsinclude expert systems, natural language processingand agent architectures. 3 credits

CSE 561/661 DialogueThis course provides an in-depth treatment of themajor theories of dialogue, including finite-state,plan-based and joint action theories. Dialogue isexamined at a level general enough to encompassconversations between humans, between humanand computer, and among computers, while at thesame time being precise enough to support imple-mentations. The course introduces basic speech acttheory, planning and reasoning through a number ofclassic papers. Plan-based theories are examined indetail, including their incorporation into spoken dia-logue systems and their potential effects uponspeech recognition components. Students will devel-op dialogue components and integrate them intoworking systems. Prerequisite: CSE 560. 3 credits

CSE 562/662 Natural Language ProcessingAn introduction to artificial intelligence techniquesfor machine understanding of human language. Thecourse introduces key aspects of natural language,along with the analyses, data structures and algo-rithms developed for computers to understand it.Computational approaches to phonology, morpholo-gy, syntax, semantics and discourse are covered.Programming assignments are written in Prolog.Prerequisite: CSE 560 or equivalent. 3 credits

CSE 563/663 Multi-Agent SystemsThis course covers the emerging theory and practiceof multiagent systems: semi-autonomous, semi-intelligent distributed computing systems that canbe organized ad hoc to meet the immediate needs ofa user. The course covers a variety of individual andmultiagent architectures, including the Contract Netprotocol, distributed blackboard systems and mobileagents. Also discussed are principles for buildingnetworks of heterogeneous agents, ranging fromsimple rule-based systems to databases andhumans. In order to collaborate to solve a user’sproblem, agents need to communicate. We examineagent communication languages, including KQMLand FIPA, as well as the underlying general speechact theories. Students learn how to model these sys-tems formally and will develop and programindividual agents that can participate in a multia-gent system. 3 credits

CSE 564/664 Introduction to Human-Computer InteractionThis course emphasizes the experience of comput-ing, which centers on an understanding of real usersand the specific tasks they need to accomplish whencomputing. In the pursuit of optimal user support, amultidisciplinary approach to system design andevaluation is stressed. The course reviews basicresearch methods, terminology, viewpoints, andactivities in the broad field of human-computerinteraction. It includes coverage of research onhuman computer interaction, as well as practicalissues in system interface design. Students gain

hands-on experience by critiquing existing inter-faces, as well as hearing reports from experts inindustry on the state of the field. An introduction tothis topic is essential for everyone working in thefield of computer science. 3 credits

CSE 565/665 Advanced Topics in Human-Computer InteractionThis course reviews advanced topics and currentresearch in the field of human-computer interaction,surveys key research challenges that exist, and dis-cusses emerging trends in next-generation systemdesign. Topics include advanced research anddesign methods, new recognition-based and multi-modal interfaces, conversational interfaces andanimated character design, mobile interfaces, ubiq-uitous and tangible interfaces, adaptive interfaces,advanced user modeling and design for universalaccess, and other key issues. Topics are coveredfrom a broad multidisciplinary perspective, with anemphasis on real-world users and usage contexts. Inaddition to weekly classroom lectures, guest lec-tures, and discussion, this class includes a hands-onpracticum component in which students participatein state-of-the-art research and interface design tocomplete a team project. Pre-requisites: CSE564 orinstructor’s consent. 3 credits

CSE 567/667 Developing User-Oriented SystemsThis course explores a range of issues and methodsneeded to design and evaluate user-oriented soft-ware applications. Topics focus on field andethnographically based design studies, participatorydesign methods, user laboratory studies and usabil-ity testing. The purpose is to have access to a rangeof methods that help uncover opportunities, break-downs and interactions that affect the design anduse of developing systems. Students are challengedto evaluate the underlying perspectives of theapproaches and decide which approach or combina-tion of approaches works best for particularproblems. They apply the methods in field and class-room exercises and produce a real-world project orpaper using course methods. The intended result isto make students more effective not only at gatheringrelevant user-based information, but also at inte-grating it into the development process. 3 credits

CSE 568/668 Empirical Research MethodsThis course introduces principles of experimentaldesign and data analysis for empirical research.Topics include the goals and logic of experimentaldesign, hypothesis formation and testing, probabili-ty and sampling theory, descriptive statistics,correlation and regression, basic parametric andnonparametric tests of statistical significance (e.g.,Binomial, t-test, chi-square, analysis of variance),standard designs for single- and multi-factor exper-iments, and strategies of scientific investigation(e.g., Exploratory vs. Directed). The course is fun-damental for anyone who plans to conductindependent research or needs to evaluate critical-ly the research of others. Students participate indesigning and analyzing data to answer scientificquestions and present the results of these activitiesboth orally and in writing. 3 credits

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CSE 569/669 Scholarship SkillsScientific results have little value if they are notcommunicated clearly or are disconnected fromprior work in a field. This course teaches studentsto research, write, present and review effectivelyfor the computer sciences. It emphasizes learningby doing, and students have frequent writing andpresentation assignments. Students learn how tolocate and organize background materials, how towrite clearly about technical topics, how to organ-ize Web content, the structure and stylisticconventions of scientific documents (such as con-ference abstracts, journal papers, theses andproposals), how to prepare and deliver short andlong presentations, the refereeing process, and howto prepare and respond to a review. This course isrequired for Ph.D. students and strongly recom-mended for master’s students, especially thosepursuing the thesis option. It also is useful for professionals who must write or speak to a techni-cal audience. 3 credits

CSE 599/699 Reciprocity Course(Formerly CSE 595)OGI students admitted to a degree program have theopportunity to take classes at other OregonUniversity System schools under the Joint CampusAgreement or Reciprocity Agreement. Contact theDepartment of Graduate Education for details.Courses taken under these agreements are listed as599/699. Variable and repetitive credit

CSE 601 Research(Formerly CSE 600)Ph.D. supervised research activity.


CSE 603 Ph.D. Dissertation Research(Formerly CSE 800)Research toward the dissertation for the Ph.D. degree.


ENVIRONMENTAL ANDBIOMOLECULAR SYSTEMS

EBS 501 M.S. Non-Thesis Research(Formerly BMB 610 and ESE 610)Supervised research as a component of the M.S.non-thesis degree. The plan of research and finaldeliverables must be approved by the research advi-sor and the SPC. Deliverables include a writtenreport and/or seminar given as part of EBS 507A. Amaximum of 8 credits from EBS 501 may be appliedto a degree. Variable and repetitive credit

EBS 502/602 Independent StudyTypically involves a scholarly and critical review ofan advanced scientific topic by one or more studentstogether with one or more faculty members.Requirements of the student typically include a writ-ten review paper and/or a seminar to be given aspart of EBS 507A/607A - EBS 507B/607B - EBS507C/607C. Selection of this course for credit andthe topic to be investigated must be approved bythe SPC. Variable and repetitive credit

EBS 503 M.S. Thesis Research(Formerly BMB 700 and ESE 700)Research toward the M.S. thesis degree.


EBS 504/604 Professional Internship(Formerly BMB 620 and ESE 620)Professional internship credits provide students anopportunity to earn credit for relevant work experi-ence in industry. Students gain valuable industrialexperience that allows them to both apply theknowledge gained in the classroom and prepare forcareers following graduation. Students on F-1 or J-1 visas must obtain prior written approval forinternships from OGI’s Office of InternationalStudents and Scholars before enrolling. Enrollmentrequires a faculty advisor and is limited by the num-ber of internship opportunities available.


EBS 506/606 Special Topics(Formerly BMB 58X and ESE 58X)Special topics courses are offered in areas of par-ticular relevance to the research interests of facultyor in response to industry needs. Special Topiccourses are subject to change and are offered inter-mittently. Variable and repetitive credit

EBS 507A/607A EBS Department Seminar(Formerly BMB 591 and ESE 599)Weekly seminars by invited guests. Public visitorsare welcome. Schedules are available on the WorldWide Web at www.ebs.ogi.edu/seminars/, or byrequest at [email protected]. 1 credit, repetitive

EBS 507B/607B Student Seminar: Metallobiochemistry(Formerly BMB 594)Presentations and discussions of selected topicsfrom the recent literature and of ongoing researchprojects in the department. 2 credits, repetitive

EBS 507C/607C Student Seminar: Molecular Biology/Biochemistry(Formerly BMB 596)Presentation and discussion of journal articles fromthe recent literature in molecular biology, geneticsand biochemistry. 2 credits, repetitive

EBS 510/610 Aquatic Chemistry(Formerly ESE 510)General acid/base concepts (mono- and polyproticsystems); pH; making activity corrections; numeri-cal calculations; titration concepts as applied tonatural systems; buffer intensity; dissolved CO2chemistry; acidity and alkalinity in open CO2 sys-tems; minerals and their role in controlling naturalwater chemistry; solubility characteristics of oxideand hydroxides; introduction to redox chemistry innatural systems; pe-pH diagrams. 4 credits

EBS 511/611 Advanced Aquatic Chemistry(Formerly ESE 511)Role of complexing ligands in solution chemistry;redox chemistry in natural systems; pe-pH diagramconstruction and use; solid/solution interfacial con-siderations; the electrical double layer; and selectedadvanced topics. Prerequisite: EBS 510/610.

4 credits

EBS 512/612 Biochemistry I: Proteins and Enzymes(Formerly BMB 527)Primary, secondary and tertiary structure of pro-teins; enzyme mechanisms; enzyme kinetics.

4 credits

EBS 513/613 Biochemistry II: Introduction to Molecular Biology(Formerly BMB 528)DNA replication, RNA synthesis and protein synthe-sis; genetic code; gene regulation. 4 credits

EBS 514/614 Biochemistry III:Metabolism and Bioenergetics(Formerly BMB 529)Metabolism of carbohydrates, lipids and aminoacids; bioenergetics; photosynthesis; oxidativephosphorylation. 4 credits

EBS 518/618 Metals in Biochemistry(Formerly BMB 537)Comprehensive study of the chemistry and biochem-istry of metal ions in biological molecules and livingsystems. Topics include metalloprotein structure,metal ion specificity, biological oxidation mecha-nisms, metal ion catalysis in enzymes, metal iontransport and gene regulation. 4 credits

EBS 520/620 Coordination Chemistry(Formerly BMB 538)Structures and stabilities of transition metal coordi-nation compounds with mono- and multi-dentateligands; coordination compounds as models for bio-logical metal centers; strategies for synthesis oftransition metal complexes. 4 credits

EBS 523/623 Chemical Group Theory(Formerly BMB 539)Properties of mathematical groups; symmetry prop-erties of molecules; symmetry groups,represen-tations, and character tables. Applications of grouptheory to the study of structure and spectroscopy oforganic and inorganic molecules; Hückel molecularorbital theory; ligand field theory; electronic spec-troscopy and vibrational spectroscopy. 4 credits

EBS 525/625 Bioenergetics and Membrane Transport(Formerly BMB 532)Critical evaluation of the chemiosmotic theory withspecific reference to oxidative phosphorylation,photophosphorylation and metabolite transport.Biochemical mechanisms of energy transductioncommon to bacterial and mitochondrial respiration,and bacterial and plant photosynthesis are reviewed.

4 credits

EBS 528/628 Enzyme Structure, Functionand Mechanisms(Formerly BMB 533)Provides an in-depth analysis of the structural ori-gins of protein interactions and catalysis that are thebasis for biological function. The course develops thebasic principles of structural biology through anoverview of X-ray crystal structures and foldingprocesses, acquainting the students with computa-tional resources for protein structure analysis. Thestructural foundation is expanded into a detailed

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investigation of enzyme active sites, including theapplication of kinetic approaches to understandingenzymatic reaction mechanisms. 4 credits

EBS 530/630 Introduction to Bioinformatics(Formerly BMB 544)Primary literature of computational biology andhands-on experience in data manipulation fromlocal and remote databases. 3 credits

EBS 535/635 Distribution and Fate of Organic Pollutants(Formerly ESE 514)Discussion of the physico-chemical processes thatcontrol the partitioning of organic chemicals in theenvironment. This introductory course considers allenvironmental compartments, water, soil and air,and partitioning between those phases. Recom-mended prerequisite: EBS 510/610. 4 credits

EBS 537/637 Chemical Degradation and Remediation(Formerly ESE 516)A thorough introduction to the transformation reac-tions that contribute to the fate of organicsubstances in the environment. The course coverspathways, mechanisms and kinetics of hydrolysis,oxidation, reduction, elimination, conjugation, etc.Treatment is balanced to reflect the importance ofthese processes in all types of environmental watersranging from engineered systems to groundwater,surface water, rain and fog. Recommended prepara-tion: EBS 511/611 and 535/635. 4 credits

EBS 538/638 Air Pollution:Origins, Chemistry and Control(Formerly ESE 519)This course will focus on tropospheric air pollutionwith particular emphasis on the urban and regionalscales. It will discuss the following items: basicstructure of the atmosphere and relevant meteoro-logical considerations; sources of tropospheric airpollutants; atmospheric photochemistry; the ozone,oxide of nitrogen and hydrocarbon chemical cycles;chemistry of toxic organic compounds in the atmos-phere; gas and aqueous phase chemistry of sulfurdioxide; size distributions, lifetimes, origins and for-mation mechanisms of aerosols; measurement andcontrol of atmospheric pollutants. 3 credits

EBS 540/640 Instrumental Methods in Biophysics I(Formerly BMB 534)Theory and application of physical techniques toproblems in biochemistry. Optical, fluorescence, cir-cular dichroism, infrared and Raman spectroscopyof chromophoric groups. Magnetic susceptibility andnuclear magnetic resonance of metalloproteins.

4 credits

EBS 541/641 Instrumental Methods in Biophysics II(Formerly BMB 535)Investigation of physical techniques particularlyuseful for studying metalloproteins. Electron para-magnetic resonance, electron spin echo, magneticcircular dichroism and X-ray absorption spec-troscopy. The course has significant “hands-on”exposure to both instrumentation and computersimulation techniques. 4 credits

EBS 547/547 Uncertainty Analysis(Formerly ESE 504)A survey of basic probability concepts followed byintroductions to several statistical advanced tech-niques that play an important role in environmentaldata analysis. Topics may include distribution func-tions, propagation of error, hypothesis testing,analysis of variance, experimental design, samplingtheory, regression analysis, time-series analysis andspatial statistics techniques. The course provides abalance of theory and application using environmen-tal data sets. 4 credits

EBS 550/650 Environmental Systems Analysis(Formerly ESE 506)Introduction to techniques of systems analysisapplied to environmental quality management.Emphasis is on development and application ofmathematical models with computer simulation andoptimization. Analysis includes efficient computa-tional algorithms and search techniques. Linear andseparable programming applied to evaluate man-agement alternatives. Applications to air, water,solid and hazardous waste management.Prerequisites: Computer programming and calculus.

4 credits

EBS 555/655 Computational Fluid Dynamics(Formerly ESE 508)This course describes advanced topics in computa-tional fluid dynamics, including specialized discretemethods (e.g., for advection-dominated problems),formal analysis of stability and accuracy, and select-ed simulations of complex environmental andbiological systems. Prerequisites: Advanced calcu-lus and EBS 545/645. 4 credits

EBS 560/660 Introduction to EnvironmentalObservation and Forecasting Systems(Formerly ESE 520)This course introduces environmental observationand forecasting systems and their applicationtoward the enhanced understanding and manage-ment of natural resources. Emphasis is on estuariesand coasts. Students are exposed to a novel, cross-disciplinary culture for understanding andinteracting with environmental systems. This cul-ture relies heavily on “real-time” generation ofmodeling and observational data, which are inte-grated and distributed through informationnetworks designed to bring the right environmentalinformation at the right time to the right user.Prerequisite: Instructor permission. 4 credits

EBS 561/661 Introduction to Spatial Sciences(Formerly ESE 522)Students will learn theoretical and practical appli-cations of geo-spatial sciences within the contextof Environmental Sciences and Engineering.Geographic Positioning Systems (GPS) will bestudied while performing practical, hands-on labo-ratory experiments using the latest in GPSequipment. Classroom discussions will focus onrelating location on the Earth’s surface to a com-mon graticule. Horizontal and vertical datum,theoretical spheroids and ellipsoids, geoids and

map projections will be discussed. Spatial rela-tionships, or analysis, of continuous and categor-ical data will be addressed through the applicationof standard statistics and probability. ARCVIEW, apopular Geographic Information System (GIS) soft-ware tool, will be stressed. 4 credits

EBS 562/662 Introduction to Remote Sensing ofthe Environment(Formerly ESE 523)This course will explore the acquisition, analysisand visualization of remotely sensed data. Thephysics behind the collection of remotely senseddata will be introduced as will both airborne-plat-form and satellite-platform sensors. Fundamentalsof aerial photogrammetry, single-band, and multi-spectral and thermal infrared data will beaddressed. Concepts of image statistics, radiometricand geometric corrections, spatial filtering and spe-cial transformations like the Normalized DifferenceVegetation Index are explored. Supervised andUnsupervised classification schemes will be dis-cussed as will change detection. The coursepedagogy is designed to address the needs of theadvanced Environmental Science and Engineeringgraduate student. While there is no prerequisite, thecourse incorporates many topics from EBS 561/661,“Introduction to Spatial Science.” It is therefore rec-ommended that students who are unfamiliar withclassification methods and the fundamental con-cepts of Geographic Information Systems completeEBS 561/661 or equivalent. 4 credits

EBS 570/670 Groundwater and Watershed Hydrology(Formerly ESE 540)Hydrologic cycle, principles of unsaturated and sat-urated flow in the subsurface; characterization ofgroundwater/surface interactions, water balance,modeling of watershed-scale processes. 4 credits

EBS 571/671 Groundwater Modeling(Formerly ESE 541)Applied groundwater modeling using the finite dif-ference method. Introduction to numerical methodsfor solving the partial differential equations for sat-urated and unsaturated subsurface flow. Modelexecution and calibration. Prerequisite: EBS570/670. 4 credits

EBS 572/672 Contaminant Hydrology(Formerly ESE 542)Processes controlling subsurface contaminantmovement in porous and fractured media, includinggroundwater flow, dispersion, diffusion, sorption,and degradation. Parameter estimation, mathe-matical and laboratory modeling of aquifers isalso covered. 4 credits

EBS 573/673 Modeling in Contaminant Hydrogeology(Formerly ESE 543)This course is designed to be taken concurrentlywith EBS 572/672. It emphasizes the hands-on useof common mathematical models for groundwaterflow and transport (e.g., MODFLOW/MODPATH/MT3D/RT3D) to examine real groundwater contami-nation problems. Prerequisite: EBS 572/672.

4 credits

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EBS 574/674 Introduction to EnvironmentalForecasting Systems(Formerly ESE 538)This course addresses the composition and noveluses of observation and forecasting systemstowards the enhanced understanding and manage-ment of natural resources. Students are exposed toa novel, cross-disciplinary culture for understandingand interacting with environmental systems. Thisculture relies heavily on “real-time” generation ofmodeling and observational data, which are inte-grated and distributed through informationnetworks designed to bring the right environmentalinformation at the right time to the right user.Prerequisite: Instructor permission. 4 credits

EBS 575/675 Transport Processes(Formerly ESE 530)An introductory course in the physics of transportprocesses in the natural environment. The courseexamines heat, mass and momentum transport viaconservation principles and the Reynolds TransportTheorem, but strongly emphasizes the environmen-tal applications of these processes. Example studiesinclude atmospheric and oceanic circulation, flowand dispersion in rivers, and heat budgets for lakesand reservoirs. 4 credits

EBS 578/678 Methods in Estuarine Oceanography:Field Observation(Formerly ESE 539)This course covers the fundamentals of estuarineand coastal oceanographic data collection using ves-sels and remotely moored equipment. Topics includevessel logistics and sampling, navigation systems,interfacing of instruments with personal computers,types of moorings and their deployment and recov-ery, and telemetry. 4 credits

EBS 580/680 Physics of Pacific NorthwestCoastal Ecosystems Thie course considers the impacts of climate,hydrology, and coastal, estuarine and fluvial circula-tion on Pacific Northwest coastal ecosystems.Special attention will be given to human impacts onecosystem through alteration of their physical con-text. Examples will include downstream effects ofwater withdrawal, the interaction of climate changeand climate cycles with salmonids and the coastalupwelling ecosystem, and the interaction ofmicrobes, particles, consumers and estuarine circu-lation in estuarine turbidity maxima. Prerequisites:EBS 575/675 Transport Processes. 4 credits

EBS 581/681 Ecosystem Management and Restoration This course will provide an overview of ecosystemmanagement and restoration at the local and regional scale. It will follow the hydrologic cyclefrom upland watersheds through streams, rivers and estuaries to the ocean and will trackimportant system parameters such as water flowand temperature. 4 credits

EBS 583/683 Environmental Law and Regulation(Formerly ESE 586)A survey of environmental law and regulation con-cepts essential to practicing scientists andengineers. Topics covered include the theory and

practice of environmental regulation, environmentallitigation, and legislation including Superfund (CERCLA), the Clean Water Act, the ResourceConservation and Recovery Act (RCRA), the CleanAir Act, and the Toxic Substances Control Act (TSCA). 3 credits

EBS 585/685 Advanced Molecular Biology(Formerly BMB 540)An in-depth study of the molecular mechanisms gov-erning the replication, recombination, transcription,and translation of genetic material. Emphasis isplaced on experimental approaches that have led toour understanding of these fundamental processes.

4 credits

EBS 586/686 Molecular Genetics of Development(Formerly BMB 541)A focused study of selected topics examining theregulation of gene expression during cellular differ-entiation. Emphasis is placed on the molecularnature of cell-cell interactions and the genetic con-trol of complex cellular responses to developmentaland environmental stimuli. 4 credits

EBS 587/687 Molecular Cell Biology(Formerly BMB 542)The techniques of molecular biology have created anexplosion in knowledge of cell structure and func-tion. This course examines the following topics:cellular organization; cell signaling; cell differentia-tion; cell evolution. Knowledge of the cell is obtainedthrough combining core readings and lectures withstudent-led discussions of primary research papers.

4 credits

EBS 590/690 Environmental Microbiology(Formerly ESE 550)Introduction to environmental microbiology, withemphasis on the role of microbes in the environ-ment and in remediation processes. Microbes andtheir interaction and activities in soil and aquaticenvironments will be discussed, as well as elemen-tal cycling as influenced by microbes. Microbiallymediated transformation of organic pollutants,transformation kinetics and remediation technolo-gies will be considered. In 2003-2004, may beoffered in combination with EBS 593/563.

4 credits

EBS 593/693 Biodegradation and Bioremediation(Formerly ESE 554)A process-oriented survey of microbially medi-ated transformations of organic pollutants.Transformations occurring in the natural environ-ment as well as in remediation technologies areconsidered. Emphasis is on the pollutant properties,microbiological factors, and medium properties thatdetermine the pathways and kinetics of biodegradation.Recommended preparation: EBS 590/690. 4 credits

EBS 596/696 Principles of Toxicology and Risk Assessment(Formerly ESE 570)This course applies toxicological principles to bothhuman and ecological risk assessments. The princi-ples and methodologies for risk assessments arepresented within a regulatory context. Topics

include hazard identification, exposure assessment,dose-response relationships, deterministic andprobabilistic risk assessments, responses of variousreceptors to different contaminants, and environ-mental management decisions. 3 credits

EBS 597/697 Ecosystem Ecology(Formerly ESE 562)Principles of ecology and of ecosystem process,description, and measurement, with emphasis onecosystem health assessment. Simulation modeling ofecosystem processes; transport and transformation.

4 credits

EBS 598/698 Current Topics in Proteomics(Formerly BMB 543)Proteomics is a new area of molecular biology whichaims to identify and map the total protein comple-ment of a genome. It expands the scope of biologicalinvestigation from studying single proteins to sys-tematically studying all proteins. Proteomics hasbroad applications in disease diagnosis, drug dis-covery, and agriculture. The key technologies usedin proteomics are 2-dimensional gel electrophore-sis, mass spectrometry (ESI-MS, MALDI-TOF),imaging, and database. This course will focus onelectrophoresis, mass spectrometry, and applica-tions, using lectures, student seminars, andliterature readings. 3 credits

EBS 599/699 Reciprocity CourseOGI students admitted to a degree program have theopportunity to take classes at other OregonUniversity System schools under the Joint CampusAgreement or Reciprocity Agreement. Contact theDepartment of Graduate Education for details.Courses taken under these agreements are listed as599/699. Variable and repetitive credit

EBS 601 Ph.D. Prequalifying Research(Formerly BMB 600 and ESE 600)Research toward the dissertation for the Ph.D. degreebefore completing the comprehensive examinations.


EBS 603 Ph.D. Dissertation Research(Formerly BMB 800 and ESE 800)Research toward the dissertation for the Ph.D. degree after completing the comprehensiveexaminations. Variable and repetitive credit

ELECTRICAL ENGINEERING COURSES

EE 501 M.S. Nonthesis Project Research(Formerly ECE 610)Supervised project research for master’s studentswho are not pursuing a thesis. A student’s academicdepartment may have additional requirements orrestrictions. Please contact your academic depart-ment for further details.


EE 502/602 Independent Study(Formerly ECE 591)Independent study allows a student to work one-on-one with a faculty member on selected topic(s) ofinterest. Registering for independent study requires

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pre-approval from the faculty member and the student’s academic department. Each departmentmay have additional requirements or restrictions.Please contact your academic department for further details. Variable and repetitive credit

EE 503 M.S. Thesis Research(Formerly ECE 700)Research toward the thesis for the M.S. degree.

Variable and repetitive credit.

EE 504/604 Professional Internship(Formerly ECE 620)Professional internship credits provide students anopportunity to earn credit for relevant work experi-ence in industry. Students gain valuable industrialexperience that allows them to both apply theknowledge gained in the classroom and prepare forcareers following graduation. Students on F-1 or J-1 visas must obtain prior written approval forinternships from OGI’s Office of InternationalStudents and Scholars before enrolling. Enrollmentrequires a faculty advisor and is limited by the num-ber of internship opportunities available.


EE 506/606 Special Topics (Formerly ECE 580-XXX)Special topics courses are offered in areas ofparticular relevance to the research interests offaculty or in response to industry needs. SpecialTopic courses are subject to change and are offered intermittently. Variable and repetitive credit

EE 511/611 Analytical Scanning Electron Microscopy(Formerly ECE 565)This course introduces the operation and theory ofSEM and covers sources, lenses, accelerating volt-age, detectors, image formation, beam-specimeninteractions, beam-produced signals, the combinedeffects of signal-to-noise ratio and spot size in deter-mining resolution, and stereo imaging SEM. Theprocess of specimen preparation, metallo-graphicgrinding and focused ion beam-produced transversecross sections, planar sections, coating techniquesfor nonconductors, sampling of powders, and isola-tion of contaminants are some of the topics covered.Students are encouraged to work on materials theyprovide. The course covers the operation of energydispersive X-ray detectors, qualitative analysis,quantitative analysis, elemental mapping, spectrumartifacts, and contaminant and compound identifica-tion. The lecture portion of this course can bepresented on site at companies in a 6-week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the SEM at the students’convenience during the remainder of the quarter anda written report is the basis for a grade. 3 credits

EE 512/612 Focused Ion Beam Technology(Formerly ECE 566)This course covers operation and theory of a FIBworkstation, including ion sources, acceleratingvoltage, electrostatic lenses, beam-material interac-tions, resolution, beam intensity distribution, beamproduced signals, detectors, metal and oxide depo-sition, and enhanced etch. FIB-produced

site-specific SEM transverse cross sections, thelocation and sectioning of micron and sub-micronscale structures on the surface and buried in multi-layered stacks or bulk materials, cross sections inmetals, semiconductors, ceramics, and compositesare covered. The location and sectioning of micronand submicron surface and buried structures to cre-ate electron transparent foils with little or nodamage in metals, semiconductors, ceramics, andcomposites, and artifacts of specimen preparationare presented. Ion beam lithography and microfab-rication of structures on the micron and sub-micronscales are also covered. This course uses a combi-nation of lectures and hands-on practice to coverthese topics. The lecture portion of this course canbe presented on site at companies within a six-weekperiod. Corresponding lab sessions are done at OGI.A project requiring operation of the FIB at the stu-dent’s convenience during the remainder of thequarter and a written report is the basis for a grade.

3 credits

EE 513/613 Transmission Electron Microscopy(Formerly ECE 567)Electron microscopy is a continually evolving disci-pline that has developed a wide range of techniquesto solve specific problems. This course is designedto help the student develop a broad appreciation andknowledge of the important techniques for theanalysis of crystalline and amorphous materials.Modern transmission electron microscopes can givethe investigator detailed information of crystalstructure, crystal defects and quantitative localchemistries on a nanometer scale. This informationis often critical to the understanding of materialproperties. Principles, methods and application oftransmission electron microscopy to crystallinematerials are covered as well as the constructionand design of electron microscopes, electron dif-fraction, reciprocal lattice and Ewald Sphereconstruction. Kinematic and dynamic theories ofimage formation will be introduced. Combining lec-tures with hands-on laboratory practice, studentswill be instructed in the use of sample preparationequipment and an analytical transmission electronmicroscope. Students will be expected to carry outbasic experiments on selected materials that illus-trate fundamental concepts covered of the lecture.The lecture portion of this course can be presentedon site at companies within a six-week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the SEM at the student’sconvenience during the remainder of the quarter anda written report are the basis for a grade. 3 credits

EE 514/614 Failure and Reliability in Microelectronics(Formerly ECE 568)The failure and reliability of microelectronicsdepends on the stability of thin films and the purityof the bulk semiconductors. Contamination, filmthickness, diffusion and phase changes all drivemechanisms of failure. Characterization of a faileddevice depends on analysis of thin film structure,crystalline structures, contaminant identificationand microchemistry. This requires a variety ofmicroanalytical techniques involving the SEM, TEMand FIB. This course covers the potential defects,

failure mechanisms and the methodology used toanalyze them. Case studies also are discussed. Thelecture portion of this course can be presented onsite at companies within a six-week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the SEM at the student’sconvenience during the remainder of the quarterand a written report are the basis for a grade.

3 credits

EE 525/625 Introduction to Electromagnetics forModern Applications(Formerly ECE 507)This series (EE 525/625-527/627) cover essentialsof electromagnetic theory for modern practitionersin such areas of engineering and applied science assemiconductor devices; IC design; optics, lasers,and optoelectronics; wireless and optical communi-cations; electronic displays; electron and ion beamtechnology; vacuum electronic devices; and variousbiomedical applications. The course is practicallyoriented, and presents both analytical and numeri-cal methods. The first course introduces basicexperimental laws and theoretical concepts.Laplace and Poisson equations for static electricand magnetic potentials. Basic properties of elec-tromagnetic materials. Maxwell equations for staticand time-varying fields. Wave equations andPoynting theorem. Finite-difference numerical solu-tion of boundary-value problems. Prerequisite:Some undergraduate electromagnetism, calculusthrough ordinary and partial differential equations,some vector calculus, or consent of instructor.

4 credits

EE 526/626 Electromagnetics for Modern Applications II(Formerly ECE 508)This course introduces additional mathematicaltools and covers topics basic to circuit design, semi-conductor device operation, IC design, optics,transmission lines, and antenna design. Waves inconductors and skin effect are included. Retardedpotentials for time-varying fields. Electromagneticsof lumped-element circuit theory. Plane wave prop-agation, reflection, and refraction. Polarizationstates and Stokes parameters. Analytical methodsfor boundary-value problems and numerical solutionby boundary-element method. Introductory (TEM)field theory of transmission lines and its relation tocircuit model. Prerequisite: EE 525/625 and somelinear algebra or consent of instructor. 4 credits

EE 527/627 Electromagnetics for Modern Applications III(Formerly ECE 509)This course covers advanced transmission line andwave guide field theory for high speed intercon-nects, microwave and optical wave guides; resonantcavities for frequency control and lasers; and radia-tion basics for communications and optics. Topicsinclude TE and TM transmission line and wave-guidemodes. Field theory of multiple-conductor transmis-sion lines: Modes, coupling, crosstalk, andtermination. Dielectric wave guides. Resonant cavi-ties. Radiation from antennas and apertures.Additional topics as time permits, chosen from:electromagnetic properties of materials; variationalformulation of field problems and finite element

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numerical solution; analytical and numerical calcu-lation of charged-particle motion in electromagneticfields; suggestions of students. Prerequisite:ECE526/626 and some linear algebra or consent of instructor. 4 credits

EE 528/628 Introduction to Electronic Materials(Formerly ECE 515)The fundamental properties and concepts needed tounderstand electronic materials are introduced inthis course. We begin with crystals, their structureand bonding, and thermal properties. We then exam-ine electron interactions in metal andsemiconductor crystals. The physics behind theenergy bandgap in semiconductors are examined,and used to ultimately derive the energy band struc-ture, effective mass, and equilibrium carrierstatistics. Next, we use these statistics to definecarrier transport in semiconducting materials.Finally, we study and understand dielectrics andinsulators, magnetic properties, superconductivity,and the optical response of semiconductors. Thiscourse is recommended if you have never taken asemiconductor device course (or if you need arefresher). The materials covered will provide youwith background for other semiconductor device,processing, and characterization courses offered at OGI. Although quantum mechanics is notrequired, taking the course will help achieve a moreadvanced understanding of the concepts discussedin this class. 4 credits

EE 529/629 Fundamentals of Semiconductor Device Structures (Formerly ECE 516)Semiconductor bulk, junction and surface proper-ties. We develop the fundamentals of semiconductorstructures; bulk defects; mechanisms affecting elec-tron/hole transport at low and high electric fields;junction formation/stability (p-n, metal-semiconduc-tor, and metal-insulator); and relationships betweensemiconductor properties and device performance.The underlying concepts of minority carrier andmajority carrier devices are expounded and clarified.

4 credits

EE 530/630 Advanced Semiconductor Devices:Structures and Materials (Formerly ECE 517)The complex interplay between materials proper-ties, fabrication technologies, and deviceperformance is examined in the context of elucidat-ing such current technology developments as siliconon insulator (SOI), high-K dielectrics, SiGe hetero-junctions, heterojunction bipolar transistors (HBT),pseudomorphic high electron mobility transistors(PHEMT), Vertical Cavity Surface Emitting Lasers(VCSEL), quantum dots, single electron transistors,and organic semiconductors. 4 credits

EE 531/631 Introduction to Quantum Mechanics forElectrical and Computer Engineers(Formerly ECE 510)Courses EE 531/631-532/632 present basic quan-tum theory for understanding practical applicationssuch as solid state devices, lasers and other opto-electronic devices, properties of electronic

materials, band-gap engineering, quantum effectsdue to shrinking IC feature sizes, quantum-dot andquantum-well devices, and quantum computing. Thefirst course introduces basic concepts and resultsessential to understanding solid-state band struc-ture, devices based on tunnelling, and quantum-welldevices. Topics include a review of classicalmechanics. The Schroedinger equation, postulatesof Quantum Mechanics, and basic Hilbert-Dirac for-malism. The free particle. One-dimensionalquantum-well bound states and tunneling throughpotential barriers. Bloch functions in periodicpotentials and the origin of solid-state band struc-ture. Prerequisite: Calculus through ordinary andpartial differential equations, or consent of instructor.

4 credits

EE 532/632 Advanced Quantum Mechanics for Electricaland Computer Engineers(Formerly ECE 511)This course covers two- and three-dimensionalapplications, and introduces new physical phenom-ena, mathematical formulations, and tools essentialfor understanding materials science, lasers, solidstate devices, quantum optics, and quantum com-puting. Covered are two- and three-dimensionalquantum wells. The simple harmonic oscillator andalgebraic methods. Angular momentum and spin.Matrix formulation of Quantum Mechanics. Atomicstructure. Approximation methods, including per-turbation theory. Interaction of matter andelectromagnetic waves. Prerequisite: EE 531/631plus some linear algebra, or consent of instructor.

4 credits

EE 533/633 Advanced MOSFET Analysis I: DC Models(Formerly ECE 512)“No IC designer’s education is complete withoutdetailed exposure to MOS transistor operation andmodeling” (J.Tsividis). This is the first part of athree-course sequence addressing this importantneed. Starting with contact potentials and proper-ties of semiconductor surfaces, we analyze, (withinthe charge sheet and depletion approximations), thecharges and potentials in MOS capacitors fromaccumulation to flat band to inversion (including therole of oxide charge). With these results we discussvarious MOSFET dc current models based on thegradual channel approach: Symmetric (body-refer-enced) models and the concept of extrapolatedpinch-off potential, source-referenced models andthe concept of extrapolated threshold voltage(including body effect); more compact models forstrong inversion and for sub-threshold behavior(weak inversion); interpolation models for moderateinversion. The compact models are then modified ina semi-empirical way to describe the effects of ion-implanted channels (including buried channels), aswell as those due to small channel dimensions(channel length modulation, effective modification ofthreshold voltage in short and narrow channels,velocity saturation, series resistance effects, thinoxide/shallow deletion effects). Breakdown andpunch-through are discussed qualitatively.Prerequisites: basic electrostatics, semiconductorsand circuits. 4 credits

EE 534/634 Advanced MOSFET Analysis II: Dynamic Models.(Formerly ECE 513)Based on EE 533/633 the dynamic large-signal andsmall-signal models of MOSFET operation aredeveloped for digital and analogue applicationsrespectively: Large-signal modeling is analyzed indetail for quasi-static operation (neglecting transit-time effects) in terms of the charges flowing in andout of all four MOSFET terminals covering the vari-ous charge conditions in the semiconductor(accumulation to inversion); non-quasi-static model-ing is introduced to include transit-time effects inhigh-speed applications and is illustrated for achannel in strong inversion. Small-signal modelingfor the description of equivalent circuit elementsstarts with a simplified quasi-static analysis at lowand medium frequencies at all channel conditions(weak to strong inversion). Then this model isextended to high frequencies in a complete quasi-static mode that includes transcapacitors at highestfrequencies near gain cut-off. Non-quasi-static mod-eling is discussed and applied to channels in stronginversion. Finally, noise models are developed tosupplement the derived equivalent circuits with theproper noise source elements. Prerequisite: EE 533/633. 4 credits

EE 535/635 MOSFET Modeling for VLSI Circuit Design(Formerly ECE 514)A comprehensive study of state of the art compactmodels used in circuit simulators for VLSI designand their underlying physics. Topics covered includehigh speed and high frequency (non quasi-static)models, quantum effects, high field and hydrody-namic effects. Substrate current and gate currentmodeling with applications for reliability modelingin circuit simulators and circuit design impact.Discussion of device scaling issues, fundamentallimits to mos device and circuit performance. Areview of novel device architectures for future mosdevices, in particular SOI devices, double gatedevices, their physics and operation in terms of ana-lytic models. Study of parameter extraction,optimization and device characterization techniquesrequired for developing compact models. Develop-ment of statistical and mismatch models for themosfet. Radio frequency models for the mosfet and Sparameter characterization. Review and comparisonof existing mosfet models such as BSIM4, EFLKV,PCIM. Implementation of mos models in circuit sim-ulators. Project work will include evaluating variousmodels in SPICE, and their impact on circuits, aswell as understanding device operation using a 2Ddevice simulator (MINIMOS) and a coupled 1DSchrodinger-Poisson Solver (SPIN). 4 credits

EE 536/636 Operation of Semiconductor Devices(Formerly ECE 580-OSD)This class is aimed at professionals and full timestudents who wish to gain physical insight into oper-ation of semiconductor devices. Emphasis will be onconceptual understanding of the underlying princi-ples. The course content will include a review ofjunctions and MOS structures, followed by examina-tion of basic IC devices, including memory and

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power devices. Students seeking in-depth coverageof BJTs and MOSFETs are recommended to take theEE 533/633-535/635 series. 4 credits

EE 537/637 Thin Film Deposition and Applications inSemiconductor Fabrication(Formerly ECE 535)Covers thin film deposition topics, such as thermalevaporation, plasma deposition, chemical vapordeposition (CVD and MOCVD), molecular beam epi-taxy (MBE), atomic layer epitaxy (ALE),electrochemical deposition, and electroless deposi-tion. Thin film deposition forms the basis formanufacture of modern integrated circuits; knowl-edge of methods available for thin film deposition isessential for IC process engineers. Course isdesigned to cover the theory and applications ofmain deposition techniques in use or being consid-ered for future IC fabrication processes. 4 credits

EE 538/638 Surface Science forSemiconductor Technology(Formerly ECE 536)The study of gas-solid surface science with empha-sis on understanding semiconductor systems andthe mechanisms of epitaxial growth of semiconduc-tor films by molecular beam epitaxy (MBE),metal-organic molecular beam epitaxy (MOMBE),atomic layer epitaxy (ALE), etc. The study of ther-mal desorption, surface diffusion. Surface electronicproperties such as work function. Physical absorp-tion, the growth of multilayer films and theapplication of these phenomena to the study of theBET equation as a tool for the determination of sur-face area. 4 credits

EE 539/639 Computer-Aided Analysis of Circuits(Formerly ECE 557)This course covers the algorithms and techniquesfor formulation and solution of circuit equations forlarge-scale VLSI circuits. Topics include equationformulation, linear AC and DC networks, linear tran-sient networks, and stability analysis. Solution ofnonlinear DC and transient problems. Frequencydomain (AWE) techniques for VLSI interconnections,Sensitivity analysis, harmonic balance, circuit opti-mization, and statistical design. The implementationof device models in circuit simulators and conver-gence issues is covered. Assignments stresscomputer-aided implementation techniques and useof simulators such as PSPICE. 4 credits

EE 540/640 Microelectronic Device Fabrication I(Formerly ECE 560)This course is the first in a full-year, three-termsequence that treats both the science and practice ofmodern microelectronic fabrication. The principlesof crystal growth and wafer preparation, ion implan-tation, doping and diffusion, and oxidation are allcovered. Emphasis is placed on understanding thebasic chemistry, physics, and material science ofwafer processing. This includes crystal structure anddefects, heterogeneous chemical reactions, the ther-modynamics and kinetics of diffusion, etc. Inaddition, the practical implementation of theseprocesses is also discussed. This includes

realistic process flows, physical metrology, devicestructure and electrical behavior, trade-offs, etc. Thecourse is intended to serve both working processengineers and matriculating graduate students.

4 credits

EE 541/641 Microelectronic Device Fabrication II(Formerly ECE 561)The second class of this series emphasizes metal-lization and dielectrics. Metallization issues includesilicides, barrier layers, interconnects (e.g., Cu),multilevel metallization, and low k dielectrics. Thisfollowed by discussion of deposition and propertiesof different dielectric films. Finally, processingissues of epitaxial growth and properties of SOIdevices are covered. Class assignments includecomputer simulation of device fabrication.

4 credits

EE 542/642 Microelectronic Device Fabrication III(Formerly ECE 562)This class starts with electron beam, x-ray, and pho-tolithography, including discussion of resisttechnology (e.g., chemically amplified resists). Thisfollowed by fundamentals and applications of plas-mas for etching and deposition (e.g., high-densityplasmas), including plasma damage. Other topicsconsidered are process integration, which includesseveral devices such as BiCMOS and memories.Finally yield and reliability statistics as related tomicroelectronic device fabrication are discussed.Class assignments include computer simulation ofdevice fabrication and testing. 4 credits

EE 543/643 Plasma Processing of Semiconductors I(Formerly ECE 563)Fundamental plasma properties. Plasma produc-tion, properties, and characterization. DC and RFplasmas. Sputtering. Sputtering as a depositionprocess for the growth of thin films. Multicomponentfilms. Plasma etching. 4 credits

EE 544/644 Chemical Mechanical Planarization(Formerly ECE 580-CMP)Chemical Mechanical Planarization (CMP) is rapid-ly growing in use within the microelectronicsindustry to planarize wafers as one of the process-ing steps. While simple in concept - chemical andmechanical material removal processes, the CMP isa complex tribological system. Mechanical abrasionand polishing mechanisms interact and co-exist withchemical layer removal processes. This course willpresent some of the historical background to CMPfrom its inception to the current state of knowledge,the underlying concepts behind the tribologicalprocesses of abrasion, grinding, and polishing mech-anisms and the principles behind the chemicalphenomena. Building on these fundamental con-cepts, this course will examine oxide CMP, tungstenCMP, and the role of CMP on the planarization ofcopper and other materials. 4 credits

EE 545/645 Electronic Materials andDevice Characterization(Formerly ECE 569)This class is designed for engineers and scientistswho wish to understand the basic principals behind

the electrical and optical techniques used to char-acterize semiconductor materials and devices.These techniques are crucial in determining thecauses of failure in semiconductor devices. Amongthe parameters covered are contact resistance, car-rier mobility and lifetime, defects, oxide andinterface trapped charges, as well as series resist-ance, channel length /width, threshold voltage andhot carriers in MOSFETs. This class includes somelab time. 4 credits

EE 546/646 Design of Digital Communication Circuits(Formerly ECE 580-DDC)Digital communications concepts including trans-mission, media, encoding, and synchronization.Review of BJT and CMOS circuit design and analy-sis. Amplifiers, filters, amplitude control,equalization. Phase locked loops, clock and datarecovery. Transmitter and receiver design.Networks. Project: complete design of a serial opti-cal link. 4 credits

EE 547/647 Statistical Process Control and DOE(Formerly ECE 580-DOE)Over the past 30 years design of experiments (DOE)has proven to be an extremely value tool allowingUSA manufacturing to re-gain its lead as the highestquality producer in the world. Course is geared forengineers in any industry/discipline seeking a prac-tical understanding of design of experiments. Classwill cover a review of basic statistical techniques, T-test, F-Test, full factorial design, Yates Algorithm,ANOVA, Hadamard designs, fractional factorialdesigns, block designs, Latin squares, regressionanalysis and response surface methodology.Emphasis will be on practical applications of tech-niques to real world problems and how to avoidsome of the typical errors made in designing, exe-cuting and analyzing an experiment. Actualindustrial examples will be used throughout theclass to allow the student to see the value of thesetechniques. Class project will involve the studentactually running a DOE on a topic of interest.

4 credits

EE 548/648 Fundamentals of Sensors andMEMS Fabrication(Formerly ECE 580-FSM)The market for Micro-Sensors and MEMS devices isexpanding at an ever-increasing rate. Ranging fromsimple environmental sensors to electronic noses tomicro-actuators, the applications are diverse. Whileconventional integrated circuit processing can bemodified and utilized for Micro-sensors and MEMSfabrication, these devices can also be constructedusing a wide variety of non-CMOS techniques and inmany cases using non-CMOS materials. This coursewill explore micro-fabrication for Micro-Sensorsand MEMS from the variety of photolithographyprocesses (conventional, LIGA, soft lithography,micro-contact printing), additive processes (CVD,PVD coatings, electroplating), and subtractiveprocesses (chemical etching, DRIE and RIE) whichhave been used to construct devices ranging fromaccelerometers to chemical sensors to actuatorsand microfluidic pumps. 4 credits

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EE 549/649 Introduction to Nanomaterials(Formerly ECE 580-IN)As the transistor gate length approaches 50nanometers, its electrical properties are subjectedto novel quantum effects, necessitating a paradigmshift in design and fabrication of related semicon-ductor devices. This introductory course focuses onapplications of nanomaterials in a range of disci-plines spanning from semiconductors and displaysto biochips. The topics covered will include synthe-sis, fabrication and optoelectronic characterization.Selected device applications will emphasize (1)transistors based on silicon quantum dots and car-bon nano-tubes, (2) displays, and (3) DNA/Proteinbiochips. This cross-disciplinary course is for elec-trical engineering as well as biologists wishing tolearn the complementary technologies and assess-ing the impact of nanostructured materials on theirrespective disciplines. 4 credits

EE 550/650 Introduction to Sensor Microfabrication(Formerly ECE 580-ISM)Tired of simulating and modeling everything that youhave ever learned about semiconductor devices?This course brings you into the lab to give you theopportunity to build microsensors. We will coverfundamental processing methods and introducesome background information on sensor operation.The rest of the course will be spent learning how togrow oxides, dope semiconductors, carry out a fullphotolithography process, evaporate metal, andperform chemical processes that result in a fullyoperational sensor. By the end of the course, youwill have fabricated and tested your devices. Thiscourse is recommended if you have an interest inthe MEMS and Semiconductor Sensors courses. Labfee of $100 is required. 4 credits

EE 551/651 Introduction to Liquid Crystal Displays(Formerly ECE 580-LCD)Introduction to nematics, cholesterics, smectics,and polymer-dispersed liquid crystals. Courseemphasizes methods used to probe electro-opticproperties of liquid crystals related to display deviceapplications. Course delineates anisotropic interac-tion of liquid crystals with applied electromagneticfields. Consequences of liquid crystal-electric fieldresponses in relation to various addressing schemes(passive vs. active) used in twisted nematics, super-twisted nematics, and ferroelectric liquid crystaldisplays, are discussed. LIQUID, a general-purposeLCD simulation software, is used to simulate activematrix liquid crystal displays properties, switchingspeeds and viewing angles of LCD’s. Includes lab.

4 credits

EE 552/652 Micro-electro-mechanical Systems(Formerly ECE 580-MEM)Combining the miniaturization and processing tech-niques of semiconductor technology withmechanical structures, MEMS offer new opportuni-ties for ‘devices’ and solutions. Graduating frominitial development as electro-mechanical locks,MEMS devices are now ubiquitous in mirror assem-blies for digital projectors, and optical handlers.Other applications include micro-manipulators,fluid handling units, micro-turbines, and even rock-

et engines. This course covers the types, design,processing, and analysis of MEMS devices.

4 credits

EE 553/653 Modern Photolithographic Engineering(Formerly ECE 580-MPE)An in-depth course designed for students and indus-try engineers seeking a better understanding of thephotolithographic process as used to fabricate inte-grated circuits. All material presented is supportedwith examples from actual processes used by indus-try leaders. 4 credits

EE 554/654 Reliability and Failure of ElectronicDevices, Packages, and Assemblies(Formerly ECE 580-RFD)An overview of electronic devices, packages andtheir reliability. Defects, contaminants, and yield;the mathematics of failure and reliability; masstransport-induced failure; electronic charge-induced damage; environmental damage toelectronic products; packaging materials, processand stresses; degradation of contacts and packageinterconnections; degradation and failure of electro-optical materials and devices; characterization andfailure analysis of materials and devices; futuredirections and reliability issues. 4 credits

EE 555/655 Simulation & Modeling of VLSI Interconnect(Formerly ECE 580-SMV)Review of Maxwell’s equations and mathematicalmethods relevant for computational electromagnet-ics for VLSI. Boundary element / method ofmoments, finite difference (2D/3D), finite elementand stochastic methods for computation of capaci-tance and resistance. Fast capacitance simulationusing multipole and random walk methods.Inductance simulation using partial equivalent ele-ment models (PEEC). Introduction to finitedifference time domain (FDTD) and full-wave solu-tion techniques. Large-scale extraction ofcapacitance, resistance and inductance from layout:algorithms and models. Construction of equivalentcircuits and network reduction techniques.Wireability issues in VLSI circuits. Rents rule andstochastic wiring distribution models. Circuit designissues related to interconnect: a discussion basedon analytical models and metrics for noise anddelay. Inductance effects in high speed digital cir-cuits. Interconnect issues related to clockdistribution and power grid networks. Brief reviewof circuit simulation algorithms relevant to inter-connect such as AWE and scattering parameterbased methods. Simulation of frequency dependentelements using convolution techniques. Review oflossy transmission line algorithms in SPICE .Thermal and reliability issues and models relevantto VLSI interconnect. The course will include proj-ects where students will implement algorithms andalso use existing simulators and extractors to obtainhands on experience. 4 credits

EE 556/656 Semiconductor Sensors(Formerly ECE 580-SSE)The emergence of MEMS and the continual sizereduction of the transistor have enabled engineersto design micro- and nano-sensor technologies for a

wide range of applications. In this course, we inves-tigate the physics of sensing, the characteristics ofdifferent categories of sensors, and materials andfabrication fundamentals in a case-based format.This course is intended for both electrical engineer-ing students and scientists whose work is expectedto require interaction with sensor technologies.Students will be asked to research and write a sen-sor case study or to research and demonstrate tothe class a specific sensor technology. Although notrequired, it is recommended students take EE550/650, Introduction to Sensor Microfabricationand EE 552/652, Micro-electro-mechanical Systemsin conjunction with this course. 4 credits

EE 557/657 Technology of Photoresists(Formerly ECE 580-TP)Modern semiconductor fabrication relies heavily onthe use of photoresists to fabricate integrated cir-cuits. This course will introduce basic chemical andphoto-physical properties of resists, with a discus-sion of resists that are currently in use. Variousresist-processing steps involved in lithography, suchas surface-preparation, coating, optical/radiationexposure, developing, etching and resist strippingwill be presented. We will conclude with a discus-sion of materials used in emerging soft lithographictechniques that allow nanometers resolution.

4 credits

EE 560/660 Introduction to Electronicsand Instrumentation(Formerly ECE 500)Review of fundamental electronics components anddesign: passive components, transistor circuits, opamps, RC circuits, frequency domain, and timedomain response. Feedback theory, op amp limita-tions, precision op amp circuits. Noise, interference,grounding, and shielding. Phase-locked loops, lock-in amplifiers. Practical advice on componentselection and circuit design. Equipment and circuitdemonstrations in class. Homework includes Pspicecircuit simulation problems. 4 credits

EE 561/661 Analog Integrated Circuit Design(Formerly ECE 571)Design techniques for analog integrated circuits.Silicon bipolar and JFET analog integrated circuitdesign. Technology overview, device structures,Ebers-Moll equations, hybrid-pi model. Single-stageamplifiers, current sources, active loads, outputstages. Operational amplifiers, bandgap references,frequency response, feedback, stability. Design project.

4 credits

EE 562/662 Digital Integrated Circuit Design(Formerly ECE 572)Design techniques for digital integrated circuits.Silicon bipolar and MOS digital integrated circuitdesign. Technology overview, device structures,modeling. Standard logic families. NMOS and CMOSlogic design. Regenerative circuits and memory.Design project. 4 credits

EE 563/663 Analog CMOS Integrated Circuit Design(Formerly ECE 580-AC)Design techniques for CMOS analog integrated cir-

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cuits. Technology overview and models. Single-stageamplifiers, current sources, biasing, active loads,class AB output stages. Low-voltage design,bandgap references, operational amplifiers, fre-quency response, compensation. Design project.

4 credits

EE 564/664 High Speed Interconnect Design (Formerly ECE 558)Analysis, design, and measurement of digital inter-chip interconnects operating at multi-gigabits persecond. Topics include: transmission line analysis,timing analysis, measurement equipment and tech-niques, lossy and coupled transmission lines,frequency domain analysis, differential signaling,equalization, modulation techniques, and designmethodology. A design/research project is used togive students practical insight into high-speed dif-ferential signaling challenges. 4 credits

EE 565/665 Introduction to Wireless IntegratedCircuit Design(Formerly ECE 580-ACD)Analog integrated circuit design for wireless com-munications. Transistor models, biasing, distortion,matching networks, noise modeling, low noise ampli-fiers, mixers, power amplifiers. Design project.

4 credits

EE 570/670 Advanced Logic Design(Formerly ECE 573)This course constitutes a basic introduction to thedesign and implementation of computer logic. Basicprinciples of discrete logic will be presented, includ-ing boolean algebra, finite-state machine design,logic minimization and optimization using bothhand-compiled (Karnaugh maps) and CAD toolbased techniques. Students will apply logic designtechniques to PLD (Programmable Logic Devices)and FPGA (Field Programmable Gate Array)devices. In addition, students will learn the basics ofthe hardware design language Verilog. The last partof the course will include a Verilog design projectusing the ModelSim simulation/compilation tool.This course or its equivalent is a prerequisite to allother EE Electronics Design courses. 4 credits

EE 571/671 System On a Chip (SOC) Design withProgrammable Logic(Formerly ECE 559)Programmable logic, such as FPGA and CPLDdevices, has become a major component of today’sdigital designs. This course builds on skill gained inEE 570 to teach students how to implement complexdigital designs with programmable logic. A design isfirst created in Verilog, a high-level RegisterTransfer Level (RTL) language, and simulated.Synthesis to a targeted programmable logic deviceis then performed. Common synthesis problems arediscussed while presenting the student with a com-prehensive understanding of the operation of thetools. Systems on a Chip (SOC) design will also becovered. The course has a project orientation - stu-dents will take their designs from concept to RTLverification and synthesis, then to programmabledevice implementation. The Mentor Graphics FPGAAdvantage tools will be used. The hardware platform

will be the Altera NIOS Development board and theNIOS soft core processor. Prerequisites: EE570/670 or consent of instructor. 4 credits

EE572/672 Advanced Digital Design — Timing Analysis and Test (Formerly ECE 580-TNT)This course focuses on timing and design-for-testtopics in FPGA and ASIC design and implementa-tion. The course uses industrial EDA tools. Topicscovered include synchronization and crossing clockdomains, metastability and synchronization failure,timing-driven logic synthesis, static timing analysis,skew and jitter analysis, clock distribution, phase-and delay-locked loops, scan testing and automatedtest pattern generation. Prerequisite: EE 571/671or consent of instructor. 4 credits

EE 573/673 Computer Organization and Design (Formerly ECE 580-COD)Basic computer organization. Computer compo-nents: memory systems, including caches, computerarithmetic, number representation, floating pointarithmetic processors, controllers, input/output,buses, DMA. Data formats, addressing modes,instruction sets, and microcode. Study of the designof a small computer from the logic level on up. Thiscourse fills the gap between the EE computer engi-neering design courses and CSE 521/621 Intro-duction to Computer Architecture. Prerequisites: EE 570/670 recommended. 4 credits

EE 574/674 CMOS Digital VLSI Design I(Formerly ECE 574)An introduction to CMOS digital IC design coversbasic MOS transistor theory; operation of basicCMOS inverter; noise margins; switch level model-ing of MOS devices; capacitive characteristics ofMOS devices; introduction to device fabrication,design rules and layout issues; power consumption;gate design/transistor sizing; pass transistors andcomplimentary pass transistor logic; dynamic domi-no and precharge/discharge circuits; memoryelement design (RAM/ROM/flip-flops) and subsys-tem design (adders, multipliers, etc.). Anunderstanding of basic digital design concepts isassumed. Lab exercises use industry-standarddesign tools. Laboratories include circuit validationand characterization. Prerequisite: EE 570/670.

4 credits

EE 575/675 CMOS Digital VLSI Design II(Formerly ECE 575)Concentration on advanced digital VLSI circuitdesign techniques. Architecture and micro-architec-ture of VLSI components, clocking schemes,input/output circuits, and special functional blockssuch as random access memories, read only memo-ries and programmable logic arrays. The coursecovers design tradeoffs, especially considering cost,power and performance. The course devotes a con-siderable amount of time to layout, parasitics andperformance verification. Introduction to design andverification tools with hands-on experience.Prerequisites: EE 574/674, familiarity with MOStransistor operation; computer architecture andorganization; logic design. 4 credits

EE 576/676 Algorithms for VLSI Design & Test(Formerly ECE 580-VDT)Computer-aided Design (CAD) of integrated circuitsrequire complex algorithms and software tools toenable designers develop designs that meet a host ofspecifications such as area, performance, testabili-ty and power to state a few. In this course we reviewthe underlying algorithms and methods used indesign of integrated circuits and provide insight intothe challenges faced today. This course may be ofinterest to graduate students in the area of digitalcircuit design where the students are introduced tounderlying algorithms and principles of design toolsused in design of integrated circuits. This under-standing will enable the designer to makeappropriate educated choices required during thedesign process. The next type of students interestedin this course will be students of computer sciencewho are interested in seeing applications of algo-rithms and optimization techniques to the integratedcircuit design process. 4 credits

EE 580/680 Linear Systems (Formerly ECE 550)This course introduces the State Variable represen-tation of linear dynamical systems and studies alarge body of State Space techniques to reveal bothinner structure and external behavior of the systemsmodeled in this way. The course develops and usesa general framework for treating time-varying linearsystems. Major emphasis is placed, however, on thetime-invariant systems, whose structure anddynamics are investigable and knowable to the veryutmost detail. Both continuous-time and discrete-time linear systems are explicitly studied. Thecourse provides a strong body of foundational mate-rial, which is utilized either explicitly or implicitly invirtually all applications-specific areas pertaining tosystem analysis/design and signal/information pro-cessing. The major topics covered are: canonicalrealizations, equivalent systems, canonical transfor-mations, canonical decompositions, solution of stateequations, stability, controllability and observability,design of asymptotic observers, state-feedback com-pensation schemes. Linear Quadratic Regulator andKalman Filter are also introduced. 3 credits

EE 581/681 Introduction to Signals, Systems andInformation Processing(Formerly ECE 544)This course provides the essential mathematicaltools and analytical techniques for the analysis ofcontinuous-time and discrete-time systems. Basicsignal and system characteristics — linearity, time-invariance, convolution and correlation — are firstexamined from the time domain perspective. Wethen proceed to study a family of transforms -Fourier Series, Fourier Integral Transform, LaplaceTransform, Discrete Time Fourier Transform (DTFT),Discrete Fourier Transform (DFT) and z-Transform— which take the study of these systems to a deep-er level and introduce useful properties which thetime perspective alone does not reveal. Basic appli-cations in information processing, communicationand control fill out the mathematically derivedresults. A greater portion of the syllabus in EE581/681 is allotted to continuous time signals/sys-

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tems than to discrete time signals/systems, becausethe latter are taken up in detail in other informationprocessing courses, particularly EE 582/682. A goalof the presentation in EE 581/681 is to impart theessential unity of all the transforms and the almostperfect correspondence of approach in continuous-time and discrete-time contexts. The studentbecomes a well-equipped practitioner who knows theway around the entire territory. This course is a use-ful prerequisite or co-requisite to EE 582/682 andall other courses in the information processing area.

3 credits

EE 582/682 Introduction to Digital Signal Processing(Formerly ECE 551)The representation and processing of signals andsystems in the discrete or digital domain is the pre-ferred mode in today’s computer and informationdriven technologies. DSP provides the core buildingblock from cell phones to modems, HDTV to videoconferencing, or from speech recognition to MP3audio. This classes covers the fundamental conceptsand mathematics including representation andanalysis of discrete time signals and systems, Z-Transforms, Discrete-Time Fourier Transform(DTFT), and the Discrete Fourier Transform (DFT),sampling and windowing techniques pertaining todiscrete time processing of continuous signals,analysis and design of recursive (IIR) and non-recursive (FIR) digital filters, and applications of theFast Fourier Transform (FFT) to convolution, spec-tral analysis, and audio processing. Prerequisite: EE581/681 or equivalent. 3 credits

EE 583/683 Digital Signal Processing II(Formerly ECE 552)This follow-up course to EE 582/682 examines sev-eral widely used advanced signal processingmethods. Topics include computational complexityconsiderations in DSP algorithm development; multi-rate signal processing; filterbanks and wavelets, andtheir application in audio and image processing (e.g.MPEG standards). Topic coverage is weighted towardthe interests of the students enrolled. 3 credits

EE 584/684 Introduction to Image Processing(Formerly ECE 542)This course covers basic image processing princi-ples and techniques with a brief introduction tomachine vision. Students acquire theoretical andworking knowledge of image processing approachesincluding image representation, transform methods,image filtering, multi resolution representation,edge detection, texture characterization, and motionanalysis. This course demonstrates application ofthese methods to image enhancement, imagerestoration, and image compression, with emphasison image quality metrics based on human visualperception. Selected areas in machine visioninclude image segmentation, elementary techniquesin pattern recognition, and object representation.Numerous examples show how to apply these tech-niques. Prerequisite: EE 582/682. 3 credits

EE 585/685 Introduction to Digital Video Processing(Formerly ECE 543)This course introduces digital video processing formultimedia systems. It begins with video capture,

image formation, analog and digital video signalsand standards, and spatio-temporal sampling.Subsequent topics include motion estimation, seg-mentation and tracking, video filtering and videostandards conversion. Students are familiarizedwith video compression techniques and standards(JPEG, MPEG2, H.261, H.263), and model-basedvideo quality estimation. Students will gain workingknowledge of these video techniques through classprojects. Familiarity with digital signal processingand transform methods is desirable. Prerequisite:EE 584/684. 3 credits

EE 586/686 Adaptive and Statistical Signal Processing(Formerly ECE 554)The field of adaptive filters and systems constitutesan important part of statistical signal processing.An adaptive system alters or adjusts its definingparameters in such a way that it improves per-formance through contact with the environment.Adaptive filters are currently applied in suchdiverse fields as communications, control, radar,seismology, and biomedical electronics. This coursewill cover the theory and applications of adaptivelinear systems. Topics include Wiener filters, leastsquares, steepest descent, LMS, RLS, Newton’smethod, FIR and IIR adaptive structures, andKalman filters. Applications covered include noisecanceling, signal enhancement, adaptive control,adaptive beam-forming, system identification, andadaptive equalization. The theory also lays thefoundation for study in nonlinear signal processingwith neural networks and will be introduced in thelater half of the class. This course should be ofinterest to electrical and computer engineers spe-cializing in signal processing and the informationsciences. This course should also be taken as back-ground for additional classes offered in artificialneural networks, connectionist models, andmachine learning. Prerequisites: EE 582/6821 plusan undergraduate level course in probability and statistics. 3 credits

EE 590/690 Digital Communication I(Formerly ECE 526)Communications system models for various modula-tion and demodulation band limited base-bandsystems. Optimum detection, source encoding/decoding. Waveform communications and signalspace representation. Pre-requisite: undergraduatecourse in digital or analog communications.

3 credits

EE 591/691 Digital Communication II (Formerly ECE 527)Channel noise and capacity. Typical random and fad-ing channels, optimum filters and signal design.Probability of error in noisy band limited channelsfor different modulations. Optimal design of BFSK,BPSK, QPSK, m-QAM, CPM modulators and demodu-lators via MAP and ML techniques. Phase lock loopsand Costas detectors. Energy-bandwidth tradeoffs indigital modulation. Pre-requisite: EE 590/690 or per-mission, and statistics with probability. 3 credits

EE 592/692 Digital Communication Systems(Formerly ECE 529)Convolutional and RS coding, Viterbi decoding.

Multi-path fading and its effects on performance anddiversity signaling. Synchronization architectures.Spread spectrum. Channel equalization. Pre-requi-site: EE591/691 or equivalent or permission.

3 credits

EE 593/693 Analytical Techniques in Statistical SignalProcessing and Communications(Formerly ECE 525)Development of the mathematical techniques need-ed to analyze systems involving random variablesand/or stochastic processes with particular applica-tion to communications and instrumentation. Topicsinclude Bayes Theorem (discrete and continuousforms), Tchebycheff inequality, Chernoff Bound,Central Limit Theorem, stationary processes andlinear systems, mean square estimation, Poissonprocess, Gaussian process, Markoff process, andseries representations. MATLAB and the MATLABStatistics Tool Box are used in this course. 3 credits

EE 599/699 Reciprocity Course(Formerly ECE 595)OGI students admitted to a degree program have theopportunity to take classes at other OregonUniversity System schools under the Joint CampusAgreement or Reciprocity Agreement. Contact theDepartment of Graduate Education for details.Courses taken under these agreements are listed as 599/699. Variable and repetitive credit

EE 601 Prequalifying Ph.D. Research(Formerly ECE 600)Supervised research participation. Pre-qualifyingPh.D. research prior to passing qualifying examination. Variable and repetitive credit

EE 603 Ph.D. Dissertation(Formerly ECE 800)Research toward the dissertation for the Ph.D. degree.


APPLIED MATHMATICS

MATH 510/610 Multivariate Calculus and Differential Equations(Formerly CSE 555a)This course reviews essential mathematical meth-ods required for the analysis of continuous timeprocesses in science and engineering, focusing onmultivariate differential and integral calculus andthe solution of ordinary differential equations.Calculus topics include: continuity and convergence,Taylor’s theorem, gradients and directional deriva-tives, chain rules, and implicit functions. In thesecond half of the course, the fundamentals of ordi-nary differential equations are examined.Differential equations topics include: exact, numeri-cal and power series solution methods, systems ofcoupled ODEs, qualitative analysis of autonomousand nonautonomous linear and non-linear systems,linearization of non-linear systems, and Lyapunovstability analysis. An introduction will also be pro-vided to the topics of bifurcations and chaos.

3 credits

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MATH 511/611 Introduction to DiscreteNumerical Methods(Formerly ESE 500)This course provides an introduction to discretenumerical methods. Lectures cover the theory andapplication of methods for the numerical solution ofinitial-value, boundary-value and mixed initial-boundary-value problems by finite differences,weighted residuals, numerical integration and finiteelements. Prerequisite: Calculus. 3 credits

MATH 513/613 Linear AlgebraThis course covers the fundamentals of linear alge-bra. Major topics include: vector spaces andsubspaces, linear transformations and linear opera-tors, orthogonal bases and orthogonal projections,and the properties of eigenvalues and eigenvectors.Particular emphasis will be given to: similaritytransformations to canonical forms such as theJordan form, canonical operator representationssuch as the Spectral Factorization and the SingularValue Decomposition, and the interpretation of allmatrix results as an application of general operatortheory to the particular class of finite-dimensionallinear operators. Properties of determinants,Moore-Penrose pseudoinverse, and solutions to sys-tems of linear equations will also be studied in detail.

3 credits

MATH 517/617 Probability and Statistics(Formerly CSE 544a and CSE 544b)This course provides an introduction to probability,statistical inference and statistical analysis. Theaims of the course are to provide scientists andengineers with a comprehensive introduction toessential concepts in probability and statistics, andfor students to gain proficiency in applying theseconcepts to data analysis. Topics include explorato-ry data analysis, sampling distribution theory,confidence intervals, hypothesis testing, maximumlikelihood estimation, linear regression, goodness-of-fit, ANOVA, and parametric and non-parametrictests. The primary analysis tool for this course is Excel. 3 credits

MATH 519/619 Engineering Optimization(Formerly CSE 5556 and CSE 556b and ECE 555)This course introduces advanced numerical opti-mization methods for quantitative work in scienceand engineering. The course will cover importanttraditional methods for constrained and uncon-strained multivariate optimization, including linesearch methods and gradient-based techniques, aswell as linear, quadratic and dynamic programming.In addition, more heuristic techniques such asgenetic algorithms, differential evolution and simu-lated annealing will also be presented. The primaryprogramming tool for this course is Matlab. Someknowledge of linear algebra and multivariate calcu-lus is required, as is a basic grasp of probability and statistics. 3 credits

MATH 521/621 Random Processes and SimulationThis course provides an introduction to randomprocesses and their application in science and engi-neering. The approach is non-theoretical, where keyresults are explained heuristically and the focus is

on application of the concepts. Topics includePoisson and Gaussian processes, Markov chains,spectral analysis, and Monte Carlo simulation. Theprimary analysis tool for this course is Matlab.

3 credits

MATH 523/623 Combinatorics and Graph TheoryDiscrete mathematical models based on combina-torics and graph theory have a wealth ofapplications, to computer science, communications,transportation, genetics, experimental design,scheduling, and so on. This course is an introductionto the tools of combinatorics from an applied pointof view. Topics covered include counting techniques,generating functions and recurrence relations, mod-eling using graphs, digraphs and weighted graphs,graph properties and algorithms. 3 credits

MATH 525/625 Partial Differential EquationsThis course addresses the most common of thePartial Differential Equations used in science andengineering, namely second order linear equations.Topics covered are complex variable theory, areview of Linear Algebra (including vector spaces,matrices, and eigenvectors), Fourier Series, Fourierand Laplace Transforms, and Elliptic, Parabolic andHyperbolic equations. The use of Separation ofVariables in solving these types of equations will bea focus as will Boundary Conditions of the first, sec-ond and third kinds. Sturm-Liouville theory forexpansion and solutions in the Cartesian and Polarcoordinate systems will also be discussed. 3 credits

MATH 527/627 Applied Functional Analysis(Formerly ECE 580-AFA)This course aims to make the guiding ideas of RealAnalysis, Complex Analysis and formal FunctionalAnalysis accessible to students, researchers andpractitioners in applied engineering areas. Basicalgebraic, geometric and measure structures aredefined, including: Group, Ring, Field, Vector Space,Inner Product Space, Topological Space, MetricSpace, Measure Space, Probability Space, NormedLinear Space, Banach Space, Hilbert Space. Westudy the distinctive properties of mappingsbetween mathematical objects of these sorts, rang-ing from the simplest set correspondences, throughthe basic real and complex functions, up to the high-ly structured class of Hilbert Space operators, withparticular emphasis on generalized FourierAnalysis. Knowledge of this material greatlyenhances one’s ability to read sophisticated techni-cal material and to conduct one’s own advancedwork in any highly mathematical area. 3 credits

MANAGEMENT IN SCIENCEAND TECHNOLOGY

MST 502 Independent StudyIndependent study allows a student to work one-on-one with a faculty member on selected topic(s) ofinterest. Registering for independent study requirespre-approval from the faculty member and the stu-dent’s academic department.


MST 506 — Special Topics (Formerly MST 58X)Special topics courses are offered in areas of par-ticular relevance to the research interests of facultyor in response to industry needs. Special Topiccourses are subject to change and are offered intermittently.

MST 507HC Seminar for Healthcare ManagementA Healthcare Management student participationseminar and a topical paper or product. 2 credits

MST 509 Commercialization Practicum(Formerly MST 543)Student teams produce assessments and plans forbringing new technologies to market. The teamsevaluate the commercial potential of real technolo-gies, including those under development at OHSU.Wherever possible, industry advisors will mentorstudents in their area of expertise within the design,management and product manufacturing process.Each team’s final paper, which may include marketresearch, a design for a manufacturable product,profiles of desired management teams, licensingplans, tech-marketing feasibility and/or preliminarystartup business plan, will be submitted to the insti-tution that originated the technology. M.S. inManagement students may be able to extend work from this practicum into their MST 550Capstone project. 3 credits

MST 510 Principles and Trends inTechnology ManagementThis course is about how companies choose,acquire, and develop the technologies that they useto develop, manufacture, deliver and support theirproducts. We look at these practices both from thevendor and buyer points of view, and also considerinternal technology development for internal use.Other topics addressed include profitably managingtechnology cycles, standards, technology forecast-ing, and the technology startup company. Relatedtopics such as competitive analysis, managingresearchers, and maintaining an innovative organi-zational atmosphere are dealt with in MST 573 andMST 514. The format includes lectures, discussions,guest speakers, and team and homework projects.

3 credits

MST 511 Quality ManagementThe course covers total quality management (TQM)from the managerial vantage point, that is, behav-ioral and operational management aspects,excluding sophisticated statistical analysis, of TQM.Classroom discussion, based on the participants’experiences and assigned readings from the text-book and cases, is the primary source of learning.Lectures are used, but generally as a basis for afacilitated discussion led by the instructor. The lim-itations of TQM also are discussed, given theinherent risks of excessive optimism associated withany social trend or perceived panacea. 3 credits

MST 512 Project ManagementThis is an introductory course that addresses thefield of project management from a managementperspective rather than an engineering or mathe-

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matical perspective. Accordingly, we will adopt thelife cycle of a project and structure this course inthree segments: Project Initiation, ProjectImplementation, and Project Conclusion. Class willbe conducted in the setting of a seminar/workshopenvironment with guest speakers on real life project experiences. 1 of the 4 credits is dedicatedto Effective Presentation Skills. 4 credits

MST 513 Operations Management and Practices This course will introduce the study of businessprocess management in the operation of a firm. Wewill utilize a systems view with an emphasis on theunderstanding of current process performance aswell as learning practices to enable higher levels ofperformance. The course will engage students fromthe perspective of a typical vice president of opera-tions, in order to ensure a comprehensive view ofoperations from strategic through daily control.

3 credits

MST 514 Issues in R & D ManagementParticipants examine issues in managing R&D andtechnological innovation in an environment ofincreasing time- and competence-based competi-tion, a competition that is simultaneously global andlocal in both markets and technology, where competitors draw on an existing technology basethat supports incremental innovation through radi-cal innovation, and where quality is a given.Particular attention is given to R&D managementissues in integrating technology into business strat-egy and operations, managing internal developmentand external sourcing of technology, seeking competitive advantage through collaborative advantage, and building new technical competenceas a part of every project. Key trends, new concep-tual frameworks, management tools and techniques,and best practices in R&D management are exam-ined through presentation, interactive classdiscussions, selected readings, case studies, and anumber of invited speakers from both small andlarge companies. 3 credits

MST 515 Supply Chain ManagementSupply Chain Management (SCM) denotes a totalsystem approach to the management of all of thoseactivities involved in physically moving raw materi-als, inventory and finished goods inventory frompoint of origin to point of consumption. SCM is a sys-tem approach to managing the entire flow ofinformation, materials, products and funds to andfrom suppliers and end-customers. 3 credits

MST 516 Global Logistics and Financial ManagementThe course emphasizes operations and logistics infirms that source, produce, distribute and market inmultiple nations. The management of logistics insuch firms differs from its domestic counterpartalong several key dimensions. First, the companymust be able to identify and analyze factors that dif-fer across nations and that influence theeffectiveness of the logistics function. In addition,because of the distances involved, transportationand distribution are of greater significance. Finally,these geographically dispersed facilities and mar-kets must be integrated and managed to enhance the

strategy of the business unit. Therefore, some ses-sions will focus on cross-national decisions andothers on managing across nations. 3 credits

MST 517 Supply Chain Management: Advanced ModelingThis course will introduce optimization in supplychain modeling. The emphasis will be mainly onlarge-scale real-world supply chain distribution net-work design. The major skills taught are problemdefinition, model formulation, and solution analysis.There will be use of commercial software such asSAILS and GSCM for large mixed-integer program-ming. Students will also be introduced to GAMS forhands-on mathematical modeling. Other topics ofthe course will be focused on how to manage finan-cial uncertainty under market chaos using realoptions methodology with Crystal Ball Monte Carlo-based software. 3 credits

MST 520 Managing Organizational Relationships This course develops participants’ ability to under-stand and influence human behavior withintechnology-intensive organizations. By studying andapplying four theory-based frames (structural,human resource, political, and symbolic), studentslearn to identify and fill gaps in their current understanding of challenging organizational situa-tions. The course also analyzes the influenceprocesses and network of relationships required formanaging research scientists, engineers, andother professionals, both as individuals and inteams, in a fast-changing environment. Self-assessment, networking, and developmentalrelationships are explored as means of devel-oping influence and impact. 4 credits

MST 521 Human Resource Management in Science and TechnologyThis course focuses on the development, implemen-tation, and evaluation of human resourcemanagement (HRM) systems, and the relationshipbetween an organization’s HRM practices and theorganization’s effectiveness and competitive suc-cess. Specifically, the course addresses the choicesan organization must make in three HRM policyareas: organization of work and employee influence;personnel flows and development; and measurementand rewards. We consider the perspectives of boththe line manager and the HRM specialist in examin-ing these three policy areas. The course alsoincludes a limited overview of employment law, witha particular focus on recent cases and changes inemployment legislation. 3 credits

MST 522 Change Leadership for BuildingEffective OrganizationsThis course focuses on designing effective organiza-tions and managing change in organizations in whichengineering, manufacturing, and/or scientific tech-nologies are critical. Tools for assessing the need forreorganization and implementing structural changesare emphasized. The course pays special attentionto organizing for lateral coordination and integra-tion, as this is a required capability in technology-intensive organizations. Students are invitedto consider the relationship between organizational

theory and practice. A range of theoretical perspec-tives is reviewed, and students are encouraged tocompile their own approach by combining those pre-sented. Extensive use is made of cases and actualexamples drawn from the readings and from courseparticipants’ experiences. Taking MST 520 first is recommended. 3 credits

MST 523 New Product DevelopmentTechnology integration and creating innovative envi-ronments have been critical to developing profitableproducts in today’s technology oriented companies.The course will review cases and published articlesaddressing key issues in new product development.Topics such as disruptive technologies, technologyintegration, concurrent engineering, and managingtechnological innovation will be covered. Studentswill form teams and develop a plan for a new product. The plan will include risk assessments in areas such as manufacturing, design, test, etc.The team will make several presentations through-out the course. 4 credits

MST 524 eBusiness: Strategy and RoadmapSuccessful companies are pursuing focused e-busi-ness strategies that build new kinds of enterprises.These enterprises are (re)designed to attract,serve and retain customers, manage suppliers,inform and empower employees better than everbefore. The course will provide students with apractical understanding of what it takes to developthe “digital enterprise”. The first part will addressthe issue of developing a robust business modelthat capitalizes on the new opportunities. The sec-ond part will cover the e-business architecture andapplications (like customer relationship manage-ment, supply chain management, selling chainmanagement), and how to develop and implementthe e-business strategy. Cases and articles will beutilized to illustrate the successful strategies andtechniques used by leading companies. TakingMST573 and MST530 previously is highly recom-mended. 4 credits

MST 530 Strategic Management and PlanningThis course focuses on the analysis of fast-changing(“hyper-velocity”) competitive environments and onthe decision-making process leading to the formula-tion and implementation of strategy. The classexplores using time, knowledge, and technology ascompetitive advantages, managing strategic change,and developing strategic plans for a future that cannot be known with certainty. Several differentmodels for strategy formulation such as game theo-ry, portfolio analysis, the “Five-Forces”, and“Competing on the Edge” will be examined. As theultimate test of strategy in the business world isrunning a company, class teams will play acomputer simulation of operating a multi-productbusiness in a dynamic, competitive environment.Prerequisites: MST 572, MST 573, MST 520 orinstructor permission. 4 credits

MST 531 Software CommercializationThis course investigates the rapidly changing soft-ware industry, and how to work in and run acommercial software company. The course provides

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real-world perspective on the current issuesinvolved in creating and commercializing software.Because the business models for hardware and soft-ware companies are quite different, the coursefocuses on the special problems of marketing, entre-preneurship, globalization, and alliancesexperienced by software firms. Special attention isgiven to the creation of value, standardization, andcompetitive strategy for high-volume software mar-kets. The course includes lectures, discussions,speakers, assignments and class presentations.

3 credits

MST 540 International Management in Science and TechnologyTopics in this course include trends in the conduct ofinternational business, the international businessenvironment, the operation of multinational enter-prises, international technology transfer, and thespecial considerations associated with managing onthe international level. 3 credits

MST 541 Leadership and Communication SkillsThis course helps students develop interpersonalcommunication and negotiation skills for effectiveleadership. The focus is on personal skill buildingthrough effectively influencing in-class workinggroups. We explore nine leadership styles to discov-er where and when each is most effective. Studentsdiscover and assess their negotiations skills basedon five standard negotiation styles. Effective inter-personal communication is the core competencyfrom which we build the skills of personal influence,coaching, conflict resolution, personal awareness,and leadership. Personal reflection and learning arerequired for maximum skill development. 3 credits

MST 542 Business Ethics and CorporateSocial ResponsibilityThis course focuses on ethical dilemmas, socialissues and responsibilities, and government regula-tions and influences. First, the course examinesdifferent frameworks for individual decision makingin an organizational setting. Next, the impact oforganizational policies and practices, and the wordsand actions of managers on the behavior of individ-uals within those organizations is examined. Finally,the course focuses on the relationship betweenorganizations and the societies in which they oper-ate. We consider the perspectives of keystakeholders, including government regulators,community representatives, customers, employees,managers, and stockholders, and examine differentviews on corporate social responsibility. 3 credits

MST 544 Strategic AlliancesThis course explores a model of implementingstrategic alliances, business partnering and jointventures. The course examines best practices instrategic alliance formation and implementation dis-tilled from approximately 40 differenthigh-performance international and domesticstrategic alliances. It offers a well-articulatedframework, which is applicable across a broadrange of alliance types. The objective of this courseis to provide each student with an opportunity tolearn practical, effective methods for forming,

implementing and executing high-performancestrategic alliances. 3 credits

MST 549 Applied Business ForecastingThis web-based course emphasizes generating andimplementing business forecasts. It is designed forstudents who want to know how forecasts are actu-ally developed and utilized, emphasizing modernstatistical methods that are widely used to generatebusiness forecasts. Specific applications to businessinclude forecasting sales, production, inventory,macroeconomic factors such as interest rates andexchange rates, and other aspects of both short- andlong-term business planning. Topics include a statis-tical review, data considerations, model selection,moving averages and exponential smoothing,regression analysis, time-series decomposition,Box-Jenkins (ARIMA) models, optimal forecast com-bination, and forecast implementation. Anybodyseeking to enhance his or her understanding of busi-ness forecasting from an applied perspective wouldbenefit from taking this course. Knowledge of basicstatistics and regression analysis is highly recom-mended, but not required. 4 credits

MST 550 Capstone Project: Business PlanThe course objective is to provide students with anopportunity to demonstrate, through an integrativeproject, knowledge gained from other course worktaken in the MST program. Business plans are use-ful in a variety of ways, including a bid for equity ordebt financing by startup companies, and requestsfor additional financing by existing companies. Thecommon theme in these situations is the undertak-ing to convince others to commit resources to bringnew or additional products or services to market ina profitable manner. Business plans are also usefulplanning documents, aiding managers in theirefforts to develop viable strategies and communi-cate them to other stakeholders in the enterprise. Inthis Capstone course students will plan, research,prepare and present a business plan in teams of 3 to5 members. Presentation of the plan will be in bothwritten and oral form. Prerequisites: MST 571, MST572, MST 573, MST 512, MST 520, MST 530 andinstructor approval. 4 credits

MST 560 The Organization, Financing, and History ofHealth Care Delivery in the United States (Formerly MST 583)This course provides a historical context for the cur-rent system: the current economic drivers, politicalpressures, ethical issues, and the roles of insuranceand pharmaceutical companies. 4 credits

MST 561 Managerial and Financial Accounting forHealth Care Professionals (Formerly MST 581)This is a practical course that addresses the financ-ing of health care, budgeting, and metrics assessingthe value-added use of funds. It also includes anunderstanding of the health care revenue cycle andcommon tools for managing service/product lines.

4 credits

MST 562 Health Care Program ManagementFocusing on managing and developing a health care

program, this course will have more detailed empha-sis on business planning, program design, scheduling,and resource management (e.g. human resources,capital equipment, software infrastructure).

4 credits

MST 563 The Regulation and Legislation of Health Care Delivery The course reviews how governmental and non-gov-ernmental organizations influence health caredelivery. Special emphasis is placed on current reg-ulatory and legislative initiatives. 4 credits

MST 564 Business Planning and Strategy in the HealthCare Industry The strategic management and planning of healthcare functional units, clinics and hospitals in today’sfast-changing technology intensive environments isextremely challenging. It will be shown that theplanning and management of strategy at all levels,not just the senior executives, is essential to theorganization. This class will focus on analyzing,planning, decision-making, formulation of strategyand implementation in a world where “growing”today’s organization into an essentially unknowablefuture is essential for long-term success. Theapproach uses a combination of lectures, materialsdrawn from a text, and illustrative case studies,combined with first-hand information provided byinvited speakers drawn from strategic decision mak-ers in the health care industry. 4 credits

MST 565 Human Resources in Health CareThis course focuses on the management of people inhealthcare organizations. This course is designed toprovide the knowledge and tools for healthcare man-agers to manage people in all aspects of their work:recruiting, hiring, motivating, and managing per-formance, conflict and change. In addition, aspectsof the external environment that affect how peopleare managed in the workplace, including employ-ment laws and regulations and labor unions will beexamined. The general objective of this course is toprovide the healthcare manager with current think-ing, theory, and best practices for the managementof people in healthcare organizations in order thats/he can be a better manager of people. 4 credits

MST 566 Health Care Information Systems ManagementThis course is aimed at health professionals, bothadministrators and health care providers, who moreand more find themselves needing to understandhow to manage the high technology systems, toolsand products that have become such an integralpart of the health delivery spectrum. Today’s healthpractitioner has to use technology to find medicalinformation and use accounting systems, personnelsystems, health insurance company systems, inven-tory systems, patient billing systems, purchasingsystems, as well as input and retrieve data. Thiscourse is focused on the business of health care andhow to understand, use and manage technology andsystems in a medical environment. Its overall goal isto give students a conceptual framework for under-standing how to use technology to reduce costs andimprove productivity, efficiency and effectiveness intheir current and future work situations. 4 credits

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MST 567 Health Care Technology — New Medical AdvancesHighlighting the role of technology and its influenceon treatment and health care delivery in the US, thiscourse includes the role of medical technology sup-pliers in shaping delivery as well as decision-makingand strategy for acquisition of new technology.

4 credits

MST 568 New Trends in Health Care Delivery This course will be continuously updated to respondto timely topics in health care (e.g. Compliance,Patients Rights, Patient Safety, health care and he Internet, B to B Internet transactions, etc.). Itwill be taught by a specialist in the appropriate fieldand will focus on practical knowledge needed by managers. 2-4 credits

MST 571 Managerial and Financial Accounting forScience and Technology(Formerly MST 501)The course focuses on understanding and evaluatingfinancial reports and information for use in makingdecisions, particularly as they pertain to managing inscience, technology, engineering, and manufacturing.

4 credits

MST 572 Financial Management for Science and Technology(Formerly MST 502)The course combines a survey of the relevantaspects of micro- and macroeconomics with an in-depth study of key concepts in the financialmanagement of a firm. Key topics include the finan-cial structure and financial analysis of the firm,working capital management and short- and long-term financing. Particular attention is paid tovaluation of investment alternatives through studyof risk and rates of return, bond and stock valuation,and capital budgeting. The course is designed toachieve a balance between understanding theoreti-cal foundations and techniques of practicalapplication. Prerequisite: MST 571. 4 credits

MST 573 Technology Marketing: Planning for Market(Formerly MST 503)The course is designed to provide an advancedunderstanding of the marketing process for technol-ogy-based products and organizations, fromopportunity identification to product introductionand market development. The course is articulatedaround three core areas: 1) how to create value forthe customers, 2) how customers and value changealong the technology adoption lifecycle, and 3) howto develop competitive advantage. Particularemphasis is placed on the front end of the market-ing process: understanding what customers valueand then developing strategies and offerings thatcapitalize on that knowledge. A wide range of topicsis explored: how to identify value opportunities, howdisruptive innovation becomes accepted by the mar-ket place, how values change along with time, howto segment and select markets, how to understandand outmaneuver competitors, how to develop amarketing strategy that creates strong competitiveadvantage, and, last but not least, how to priceproducts and go to market. 4 credits

MST 574 Going to Market: Delivering Value toCustomers and Shareholders (Formerly MST 504)The course will provide an understanding of thetools, mechanics and management of operationalmarketing implementation processes in high-tech-nology environments. Integrating lectures, classdiscussions, case studies, videos and individualpapers and team projects, the course emphasizesdeveloping the detailed implementation plan tobring products or services to market. The goal is toshow how to turn strategy into practice by imple-menting the marketing plan begun in MST 573,developing the specifics of a product or service’sbusiness model and persuasively outlining theblueprint of the business case. The course drillsdown into the operational specifics of pricing, promotion, sales, advertising and customer relation-ship management, e-business and web marketing,supply chain and distribution logistics, channelalliance building and implementation standards,metrics and controls. The course complements andcompletes the marketing knowledge and expertisegained through MST 573, which is a prerequisite.

4 credits

MST 577 Principles for Process TechnologyDevelopment & Introduction to Manufacturing This is a project-oriented course on the manage-ment procedures and key underlying concepts foreffective manufacturing technology planning, devel-opment, and introduction into volume production ina competitive environment. While emphasis will beon semiconductor technology and manufacturing,most principles and methodology are generallyapplicable to both hardware and software technolo-gy management. Issues of technology strategicplanning, process definition and characterization,decision-making, technology transfer, product defi-nition, yield improvement, and concurrentengineering principles will be explored to identifyeffective management approaches for shorteningtime to volume production, minimizing risks, andminimizing engineering effort. As part of the coursestudents will form teams assigned either to developa corporate procedure for the introduction of newproducts and manufacturing processes, each for aspecific company situation, applying the conceptslearned, or to carry out a case study of a specificcompany’s procedures. There are no prerequisitesfor the course, although some technical backgroundand/or experience in industry are desirable.

4 credits

MST 590 Effective Business Writing for ManagementTailored to meet the individual writing needs ofmanagement professionals, this course reviews andpractices standard conventions in grammar andpunctuation, and innovative stylistics using a highlyinteractive format. The course addresses both elec-tronic (email) and traditional (letter, summary,report) managerial writing tasks with the goal ofclearer, more concise business communication. Fornative speakers of English and bilinguals with anative-level of written English. 1 credit

MST 591 Effective Business Writing for Non-native SpeakersTailored to meet the individual writing needs of man-agement professionals, this course reviews andpractices the English grammar, punctuation, andstylistics that challenge the advanced-level non-native and bilingual speaker of English. Using a highly interactive format, this course addressesboth electronic and traditional managerial writingtasks with the goal of clearer, more concise businesscommunication. 1 credit

MST 599 Reciprocity Course(Formerly MST 595)OGI students admitted to a degree program have theopportunity to take classes at other OregonUniversity System schools under the Joint CampusAgreement or Reciprocity Agreement. See theDepartment of Graduate Education for details.Courses taken under these agreements are listed as 599/699. Variable and repetitive credit

OREGON MASTER OFSOFTWARE ENGINEERING

OMSE 511 Managing Software Development This course provides the knowledge and skills need-ed to plan, organize, lead and control softwareprojects. Topics include planning and estimating,measuring and controlling, and achieving results inenvironments that include a great deal of ambiguityand contradictory information. Quantitative meas-ures and risk management will be emphasized.Students will prepare project plans for real or hypo-thetical software projects; to include effort, cost andschedule estimates and risk management plans.Prerequisite: OMSE 500. 3 credits

OMSE 521 Using Metrics and Models to SupportQuantitative Decision Making This course provides the knowledge and skills need-ed to apply quantitative tools based on metrics andmodels of the software product and developmentprocess to make decisions under uncertainty.Topics covered will include measurement concepts,decision- making under uncertainty, and model andmetric development for the software developmententerprise. Prerequisite: OMSE 500. 3 credits

OMSE 531 Software Requirements Engineering This course covers the principles, tools and tech-niques for requirements elicitation, specificationand analysis. The focus is on understanding the roleof requirements in system development and mainte-nance, goals of the requirements phase, essentialdifficulties of specifying requirements for real sys-tems, and effective methods, tools and techniques.The course covers techniques for formally modelingand specifying software requirements with hands-onexperience as well as the role of prototyping in val-idating requirements. Prerequisite: OMSE 500.

3 credits

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OMSE 533 Software Design Techniques This course covers the principles of software designand a survey of design methods, techniques andtools. In-depth and hands-on study of at least onemethod such as object-oriented design as applied toa realistic industrial problem. It examines theeffects of design decisions on the functional andnonfunctional properties of the software (e.g., easeof understanding, maintainability, reuse) and howsoftware engineering principles are applied to makeappropriate trade-offs. Students also examine thedesign process and products in context, includingthe effect of design decisions on function, quality,cost and schedule. Prerequisite: OMSE 500. CSEstudents may not receive credit for both CSE519/619 and OMSE 533 because there is significantoverlap in content. 3 credits

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