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Prof Liu Xiang YangProf Liu Xiang YangPhysics, NUS

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Course Home Pagehttp://www.physics.nus.edu.sg/~Biophysics/pc3267/indexa.htmlP d  Password: pc3267Please familiarize yourselves with the information there  especially with respect to the tutorials and other there, especially with respect to the tutorials and other matters

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Wh i bi h i i t t?Why is biophysics important? 

Many breakthroughs in biology are based on biophysicalprinciples and techniques Biophysical techniquesprinciples and techniques. Biophysical techniquescontinue to play an important role in biological andbiomedical science:X‐ray, NMR images, Electron microscopy, AFM,S i b iScanning probe microscopy, …To explore physical principles and underlyingmechanisms of many phenomena and problemsassociated with life sciences.To assist you to construct the overall picture that at firstsight appears to consist of many disconnected facts.To establish “physics” thinking ‐ “Does this hypothesismake sense given what is known about the dynamics ofmake sense, given what is known about the dynamics ofthis biological system?”, “Can I obtain a betterunderstanding based on exact physical principles?”

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Virus and cellus a d ceHIV, SARS

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C Vi l t iCase: Viral protein

Low pH

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Case: SNARE proteinThe protein works like a nanomachine.The mechanism is pH  the process is driven by a 

Case: SNARE protein

The mechanism is pH, the process is driven by a hydrophilic/hydrophobic force 

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Fusion peptide

Physics can be applied to examine y ppmembrane fusion

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Ai f thiAim of this course

By delivering general knowledgeconcerning the basic principles andi t f h i i lif i thimportance of physics in life sciences, theaim is to establish the interconnectednessof knowledge between human life andof knowledge between human life andactivity and basic physics.To establish the essential knowledge andTo establish the essential knowledge andpractical skills in modern life sciences.

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Course OutlineBio‐molecular thermodynamics/statistics

First law of thermodynamics; molecular interpretation f  h d    of thermodynamic quantities; 

Second law of thermodynamics in biological systems; Statistical complications in modeling macromolecular Statistical complications in modeling macromolecular structure; Molecular mechanics; bonding and non‐bonding g gpotentials; stabilizing interactions in macromolecules. 

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C O liCourse OutlineBiophysical description of Biophysical description of MacromoleculesPhysical and structural characteristics of yproteins and amino acidsPhysical environment in the cell Physical and symmetry relationships between molecules

l l   h l    d  Molecular physical interactions and  macromolecular structures

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What is to be gained at the end of the Course?

You would be able to obtain essential knowledge of bio‐physical principles which play a very important part in many fields of life sciences.It will help you take other advanced modules in life sciences related subjects.You should be equipped with the basic q ppknowledge/skills to carry out life sciences related research

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Reference Texts: CompulsoryReference Texts: Compulsory

Principles of Physical Biochemistry, K. Van Holde , W. Johnson , Pui Shing Ho, , J , g ,Prentice‐Hall, ISBN: 0‐13‐720459‐0 Biological Physics, Philip g y , pNelson, W.H. Freeman and CompanyISBN: 0‐7167‐4372‐87 7 437

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f lReference Texts: Supplementary

Biophysics, An Introduction, C. Sybesma, Kluwer Academic Publishers, ISBN: 0‐7923‐0029‐7

Biophysics, Roland Glaser, Springer, ISBN: 3‐540‐6 8867088‐2

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Biophysics Teaching Web: http://www.physics.nus.edu.sg/%7EBiophysics/

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Module Structure/AssessmentModule Structure/Assessment

Biophysics IIBiophysics IIp y(PC3267)

p y(PC3267)

~ 26 Lectures,(2.5 hrs/wk)

~ 26 Lectures,(2.5 hrs/wk)

15 hours Experiments

(20%)

15 hours Experiments

(20%)( )( )

~5 Tutorials~5 Tutorials 1 Test (10%)1 Test (10%)5 Tutorials(10%)

5 Tutorials(10%)

Short projectShort projectFinal Exam (50%)Final Exam (50%) (10%)(10%)

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Term paper/presentatione pape /p ese tat o

To provide the opportunity for you to get in touch with  some get in touch with  some frontiers in biophysics.Team spirit: Several (~3) p ( 3)students to work together as a Team

lActive‐learningPresentation skill

Teamwork

Scripps Res. Inst.

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Project/presentation (cont )Project/presentation (cont.)

Group size: 3 studentsChoose a topic and submit an abstract (~100 words) to 

Topic:To be chosen by yourself from the  ( )

me  by Feb. 8,  2008Carry out readings on this topic, and write a 10‐15 page 

yourself from the list provided in the web.S  th   b f  

p 5 p gessay and prepare the presentation.Deadline of submission: A il   

See the web for more details

April 11, 2008

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Expt  Arrangements3 experiments.Start at the end of Jan (to be announced). J ( )

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& i lTerm Test & Final Exam          Test:  Test – Tue, Mar 4, 2008

Venue: S1A‐0212

Duration: 1 hour (8:15‐9: 15am).  

EXAM

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Official Lecture Time

1.5 times a week

T  F i  8    S ATue, Fri., 8:00‐9:30 am, S1A‐0212

Format: Lecturing, and misc/videog

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L A ti l D i L tLearn Actively During Lectures

T  t   d t d th  Try to understand the key concepts during the lecture itself, as details can be filled in afterwards

Please do not hesitate to stop me to ask questions if things are not clear to you, or if I am going too fastast

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Taking NotesJust jot down key points, or something that strikes you

Slides will be made available on the web a few days before each lecture (which you may want to print out beforehand)beforehand)

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ExpectationsPl  b   l f  l     i i      Please be punctual for lectures, as missing even a small portion might make it harder to follow at a later stage

Attendance is very important, as slides will deliberately be kept brief, and only elaborated y p , yupon in the lectures

Students should take the initiative to read up Students should take the initiative to read up further on the lecture material to enhance their understanding 

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Contact InformationContact Information

Prof. Dr. Xiang Yang LIUTel: 6516 2812Email: phyliuxy@nus edu sgEmail: phyliuxy@nus.edu.sgOffice: S13, M01‐4

Teaching Assistant (experiment): Dr.Office: S11‐02‐03,  Lab: S7‐01‐17Tel: 6516 6598 (office)Email: phyclc@nus.edu.sg