Biological Acquisition Unit

Team Members:Fred AveryNy ‘Jaa BoboGene CouncilSalvatore Giorgi

Advisors:Dr. HelfertyDr. Pillapakkam

Outline of Presentation

• Mission Overviewo Objectiveo Theoryo Background / Previous Researcho Biological Analysiso Success Criteria

• Designo Project Overviewo Design Processo Electrical Systemo Physical Modelo Software Flow Charto Power Systemo Componentso Filter Systemo Optical Systemo Design Complianceo Testing / Testing Equipmento Biological Analysis / Chemical Analysiso Shared Can Logistics

• Managemento Scheduleo Team Memberso Advisorso Part List / Budget Outlineo Conclusion

Mission Overview

Objective• Measure the earth’s magnetic field as a function

of altitude. • Measure flight dynamics of the rocket.• Capture biological samples in the atmosphere. • Identify types and concentration of samples as

function of altitude. • Measure UV intensity as function of altitude• Identify UV damaged DNA in samples.

Theory• Two accelerometers and one gyroscopes will be used

to measure the rocket’s flight dynamics (roll, pitch, and yaw).

• The magnetometer will measure the strength and direction of the earth’s magnetic field as a function of altitude.

• The filtration system will combine passive and active collection techniques to gather organic and inorganic material suspended in the atmosphere.

• Spectrometer measures properties of light over a specific electromagnetic spectrum, specifically intensity of wavelengths between 200 and 850 nm.

Background• Biological aerosol defined as airborne solid particles

(dead or alive) that are or were derived from living organisms, including microorganisms and fragments of living things.

• Includes bacteria, fungi, viruses, unicellular organisms

• Potential roles of micro-organisms• Act as cloud condensation nuclei and to

participate in radiative forcing.• Many airborne micro-organisms likely metabolize

chemical components of aerosols thereby modifying atmospheric chemistry.

• Some researchers suggest that a self contained ecosystem might exists at high altitudes.

Previous Research• Types of species found at high altitudes: bacterial

species Bacillus subtilis and Bacillus endophyticus, and the fungal genus Penicillium.

• Size of particles: biological aerosol particles range from 0.2 to 5 μm.

• DNA photolyase, a FAD-containing flavoprotein, uses light to drive an electron transfer reaction between the protein and a DNA lesion. The mechanism by which this transferred electron repairs the DNA is currently unknown.

Success Criteria• Acquire specimens in middle atmosphere

o Collect a statistically significant sample to compare to previous studies.• Type of samples and their concentration• Determine altitude where samples were collected

• Spectrometero Accurately measure and record UV intensityo Correlate UV damaged DNA in samples with UV intensity

• Accelerometers and Gyroscopeo Accurately and precisely measure flight conditions

• Velocity• Spin Rates• Gravitational Force

• Magnetometero Study magnetic field in middle atmosphere.o Compare experimental magnetic field to actual values .

System Overview

Project Overview

Design ProcessDesign Sensing Circuit• Schematics• Placement on

plates• Software flow

Acquire Material (Sensing Circuit)• XY-Axis accelerometer• Z-Axis accelerometer• Gyroscope• Voltage Regulators• Microprocessors• Magnetometer• Spectrometer• Servo Motors

Acquire Material (Passive System)• Filters• Filter Canister• Ball valves• Tubing

Assemble Design• Construct plates• Secure components

on plates• Mount Cosine

Corrector

Test Components• Sensors• Processors• Filter System• Spectrometer

Test System• Pressure• Vibration• Spin• Sterilization• Data Storage

Electrical System Block Diagram

Physical Model

Software Flow ChartInitialize System

Write sensor data

Sample Sensors (I2C, SPI, USB, and analog pins)

Initialize System

Start timer for opening valve (36 sec)

First Timer

Finished

Open Valve

Start timer for closing valve (300 sec)

Second Timer

Finished

Close Valve

Start timer for shutting down system (900 sec)

Interrupt from Timer

Write sensor data

Shut Down System

Main Microprocessor

Second Microprocessor

PowerBasic System Requirements• Main Microprocessor – 90 mA @ 3.3 V

• Second Microprocessor - 90 mA @ 3.3 V

• Magnetometer – 0.9 mA @ 3.3 V

• Gyroscope – 3.5 mA @ 5 V

• XY-axis accelerometer – 15 mA @ 6 V

• Z axis accelerometer – 2.5 mA @ 6 V

• Spectrometer – 0.6 A @ 5 V

Sources• Voltage regulators will be

used to maintain the proper amount of power for each sensor

• Five 9 V batteries will power system

ComponentsMagnetometer• Power: 2.5 to 3.3 V• Field Range: +/- 8 Gauss• Current: 0.9 mA• Bandwidth: 10 kHz• Weight: 50 mg• I2C interface

Gyroscope• Power: 5 V• Range: +/- 20,000 °/sec• Current: 3.5 mA• Bandwidth: 2 kHz• Weight: 0.5 g• Output voltage

proportional to spin

ComponentsXY-axis Accelerometer• Power: 3.0 to 3.6 V• Range: +/- 37 g• Current: 15 mA• Bandwidth: 400 kHz• Serial Peripheral Interface

(SPI)

Z-axis Accelerometer• Power: 3.3 to 5 V• Range: +/- 70 g• Current: 2.5 mA• Bandwidth: 22 kHz• Output voltage

proportional to acceleration

Flash Memory: 512KRAM Memory: 128KOperating Voltage: 3.3VOperating Frequency: 80 MHzTypical Operating Current: 90 mAI/O Pins: 83Analog Inputs: 16Analog Input Voltage Range: 0V to 3.3VDC Current Per Pin: +/- 18 mAUSB 2.0 Full Speed OTG controllerI2C and SPI interfaces

ComponentsPrimary Microprocessor

Flash Memory: 128KRAM Memory: 16KOperating Voltage: 3.3VOperating Frequency: 80 MHzTypical Operating Current: 90 mAAnalog Input Voltage Range: 0V to 3.3VI/O Pins: 42DC Current Per Pin: +/- 18 mA

ComponentsSecond Microprocessor

Ethernet ShieldOnboard microSD card readerCommunicates with SD card using the SPI busWill connect with our primary processorOperating Voltage: 5 V

Filter SystemDesign• Connects to two ports: Static and

Dynamico Dynamic port draws in sampleso Air flow exits through the static

port• Contains four filters in series

o Filters are decreasing in size from 5 to 0.2 μm

• Filter system terminates with NPT connector at each end

Testing• All parts must be autoclave-able• Two filter systems will be

constructedo One will be included one

rocketo Other kept on groundo Results compared

Mass Flow Rate• The mass flow rate is

expected to be about 5.3×10-6 kg/s

• Particle sizes ranging from 0.2 to 5 µm

Exposure Time• System will open at 30 km

and close at 30 km

• Based on previous data we estimate the filter system will be open for 5 min

Filtration System

Optical SystemGrating Specifications• Groove Density: 600 mm-1

• Spectral Range: 650 nm• Blaze Wavelength: 300 nm• Best Efficiency (>30%):

200 – 575 nm

Optical Resolution• Goal of approximately 1.0 nm• Resolution = Dispersion * Pixel Resolution

• Dispersion = Spectral Range / Detector Elements• Detector Elements = 2048• Pixel Resolution determined by entrance slit size

• Entrance Slit of 25 microns was chosen which results in a 4.2 pixel resolution

• Resolution = (650 nm / 2048 pix)*4.2 = 1.33 nm

Optical SystemOptical Bench1) Fiber optics connector2) Fixed entrance slit of 25

microns3) Longpass absorbing filter4) Collimating Mirror5) Grating with Groove Density of

600 lines/mm6) Focusing Mirror7) Detector collection lens8) 2048 element Linear CCD

Array9) Longpass order-sorting filter10)UV detector lens

The Longpass absorbing filter(3) is not included in our system.

Optical System

• Numerical Aperture (NA) of lens must match that of fiber optics cable, which is 0.22.

• Calculated using: NA = (nD) / 2f)• n = index of refraction• f = focal length

Cosine Corrector• Couples to optical fiber for

spectral intensity measurements• Wavelength Range: 200 - 1100

nm• Field of View: 180°• Diffusing Material:

Polytetrafluoroethylene (PTFE)

Design Compliance• Final mass must be 6.55 lbs

o Total weight of sensors and spectrometer is less than 3 lbs

o Projected filtration system weight is less than 2 lbso More weight will be added once we are able to fully

assemble the system• Payload Activation

o G-switch

• Center of Masso Solid Works projection shows this constraint will be meto Once additional weight is added this must be

recalculated

TestingMechanical• Drag Force

• Test to see if filtration system can withstand air flow

• Low Pressure• Simulate depressurization of

canister• Test to see if entire system

functions at low pressures• Stability

• Make sure entire canister functions under range of spin rates and impulses

• Determine structural integrity of plates and sensor mounting

Biological• Test to see if filtration system can

be properly sterilized• Test to see if filtration tube can

be completely sealed • Determine if filters can remain

sterilized for one week

Electrical• Sensors

• Test accuracy• Functioning Properly

• Data• Test processor is properly

handling incoming data• SD Card / Reader properly

storing• Power

• Test to see if entire system is fully powered during flight

Optical• Measure light of known

intensity

Testing EquipmentThe following testing equipment will be used• Vibration Table

• The table at Temple will not match expected impulses• Air Foil• Vacuum Pump

• Supplied by the Biology Department• Spin Table

• Neither Temple nor Drexel University own a spin table that will spin at 5 Hz

• We will construct our own table which will operate between 0 and 5 Hz and support a 20 lbs canister

• Autoclave• Supplied by the Biology Department• Will not kill any DNA present in our filter system

• Mock Canister• Will be built to simulate the optical port in canister• Fluorescent light and Sun light will be measured

Biological Analysis• DAPI (type of microorganisms)

o DAPI (6-diamidino-2-phenylindole) is a stain used in fluorescence microscopy. DAPI passes through cell membranes therefore it can be used to stain both live and fixed cells.

• BRDU (type of microorganisms)o Bromodeoxyuridine (5-bromo-2-deoxyuridine) is a synthetic nucleoside

that is used for detecting actively dividing cells.• Genetic Sequencing (type of microorganisms)

o Determines the number of nucleotides in sample’s DNA: adenine, guanine, cytosine, and thymine

• Scanning Electron Microscope (concentration of microorganisms)o Scans the sample and re-generates image to be analyzed, i.e.

structural analysis of microbes

Chemical Analysis• A research team at Temple University is working to

understand the unknown mechanism of DNA repair by DNA photolyase.

• Group studies this mechanism byo Use of ultra fast laser and biochemical techniques o Exploring the details of substrate binding using fluorescence reporter, two

photon excitation techniques, and single molecule microscopy• Once samples are identified through biological analysis

they will be handed over for chemical analysis• Team proposes to compare samples to similarly

damaged DNA found in extreme terrestrial environments

Shared Can Logistics• Sharing canister with Drexel University• Communication has been opened up between the teams

o Both teams expect to use half the canister space and weight

• Drexel’s proposed experiments will not effect ours• Close proximity will allow us to integrate entire canister prior

to flight• Drexel’s team will be using vibration table at Temple

Management

ScheduleDecember January

Goals: Finalize Software Construct Spin Test PlatformConstruct Filtration System Spin Tests

Machine canister plates Sterilization TestsConstruct Payload Construct Spin Test Platform 

Vibration Tests Spectrometer Tests Build mock canister

Important Dates:

December 1: CDR Teleconference

January 1: Final Down Select - Flights Awarded

Team MembersFred Avery (ME)• Filtration System• Center of gravity testing• Mass Flow Rates• Spin rate testing platform

Ny ‘Jaa Bobo (EE)• Hardware

• Magnetometer• Accelerometers• Gyroscope

• Power

Gene Council (EE)• Hardware

• Magnetometer• Accelerometers • Gyroscope

• Programming

Salvatore Giorgi (ECE)• Team Leader• Spectrometer• Microprocessor

• Data Acquisition• Filtration System

Parts List / BudgetParts Manufacture Cost Quantity

Payload Canister - $7,000 1

Pic32 chipKIT Max Digilent $49.50 1

chipKIT Uno32 Digilent $29.95 1

Magnetometer Sparkfun $19.95 1

G-Switch Digikey $12.95 1

SD card 2 GB SanDisk $27.99 1

Arduino Ethernet Shield Sparkfun $39.95 1

Filter Paper Millipore Supplied by Bio Department 4 types

Filter canister Millipore $388.00 1 pack = 8 canisters

Parts List / BudgetParts Manufacture Cost Quantity

Gyroscope Analog Devices $90.00 1

XY-axis accelerometer Analog Devices $99.00 1

Z-axis accelerometer Analog Devices $75.90 1

Spectrometer Ocean Optics $3334.00 1

Fiber Optics Cable Ocean Optics $184.00 1

Cosine Corrector Ocean Optics $150.00 1

Spectroscopy Operating Software Ocean Optics $199.00 1

PolypropyleneBall Valve Cole-Parmer $8.00 4

Standard Servo motor Parallax $12.99 2

AdvisorsElectrical

Dr. John HelfertyDepartment of Electrical and

Computer Engineering

MechanicalDr. Shriram Pillapakkam

Department of Mechanical Engineering

BiologicalDr. Erik CordesDepartment of Biology

ChemicalDr. Robert StanleyDepartment of Chemistry

Conclusion• Concerns

o Properly counting samples as function of altitudeo Properly sterilizing and maintaining sterilization of the filtration systemo Autoclave does not kill DNAo Correcting for any stray light that might enter our cosine corrector

• Major Riskso Failure of filter system leading to depressurization of canister

• Recently Finishedo Spectrometer design completedo Ordered second microprocessor, ethernet shield, and spectrometer

• Future Planso Purchase and machine plateso Write library for USB interfaceo Order ball valves and tubing for filter systemo Test servo motors available in lab with ball valveso Continue programming processoro Construct spin test platform and mock canistero Begin tests