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Biological Acquisition Unit

Biological Acquisition Unit. Team Members : Fred Avery Ny ‘ Jaa Bobo Gene Council Salvatore Giorgi Advisors: Dr. Helferty Dr. Pillapakkam. Outline of Presentation . Mission Overview O bjective Theory Background / Previous R esearch Biological Analysis Success Criteria Design

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Biological Acquisition Unit

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  1. Biological Acquisition Unit Team Members: Fred Avery Ny ‘JaaBobo Gene Council Salvatore Giorgi Advisors: Dr. Helferty Dr. Pillapakkam

  2. Outline of Presentation • Mission Overview • Objective • Theory • Background / Previous Research • Biological Analysis • Success Criteria • Design • Project Overview • Design Process • Electrical System • Physical Model • Software Flow Chart • Power System • Components • Filter System • Optical System • Design Compliance • Testing / Testing Equipment • Biological Analysis / Chemical Analysis • Shared Can Logistics • Management • Schedule • Team Members • Advisors • Part List / Budget Outline • Conclusion

  3. Mission Overview

  4. 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.

  5. 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.

  6. 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.

  7. Previous Research • Types of species found at high altitudes: bacterial species Bacillus subtilisandBacillus 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.

  8. Success Criteria • Acquire specimens in middle atmosphere • Collect a statistically significant sample to compare to previous studies. • Type of samples and their concentration • Determine altitude where samples were collected • Spectrometer • Accurately measure and record UV intensity • Correlate UV damaged DNA in samples with UV intensity • Accelerometers and Gyroscope • Accurately and precisely measure flight conditions • Velocity • Spin Rates • Gravitational Force • Magnetometer • Study magnetic field in middle atmosphere. • Compare experimental magnetic field to actual values .

  9. System Overview

  10. Project Overview

  11. Design Process • 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 • Design Sensing Circuit • Schematics • Placement on plates • Software flow • Test System • Pressure • Vibration • Spin • Sterilization • Data Storage • Test Components • Sensors • Processors • Filter System • Spectrometer • Assemble Design • Construct plates • Secure components on plates • Mount Cosine Corrector

  12. Electrical System Block Diagram

  13. Physical Model

  14. Software Flow Chart Initialize System Initialize System Start timer for shutting down system (900 sec) Start timer for opening valve (36 sec) First Timer Finished Sample Sensors (I2C, SPI, USB, and analog pins) Open Valve Interrupt from Timer Start timer for closing valve (300 sec) Write sensor data Second Timer Finished Write sensor data Close Valve Shut Down System Second Microprocessor Main Microprocessor

  15. Power • Basic System Requirements • Main Microprocessor – 90 mA @ 3.3 V • Second Microprocessor - 90mA @ 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

  16. Components • Magnetometer • 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

  17. Components • XY-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

  18. Components Flash Memory: 512K RAM Memory: 128K Operating Voltage: 3.3V Operating Frequency: 80 MHz Typical Operating Current: 90 mA I/O Pins: 83 Analog Inputs: 16 Analog Input Voltage Range: 0V to 3.3V DC Current Per Pin: +/- 18 mA USB 2.0 Full Speed OTG controller I2C and SPI interfaces Primary Microprocessor

  19. Components Second Microprocessor Flash Memory: 128K RAM Memory: 16K Operating Voltage: 3.3V Operating Frequency: 80 MHz Typical Operating Current: 90 mA Analog Input Voltage Range: 0V to 3.3V I/O Pins: 42 DC Current Per Pin: +/- 18 mA Ethernet Shield Onboard microSD card readerCommunicates with SD card using the SPI bus Will connect with our primary processor Operating Voltage: 5 V

  20. Filter System Testing • All parts must be autoclave-able • Two filter systems will be constructed • One will be included one rocket • Other kept on ground • Results compared Design • Connects to two ports: Static and Dynamic • Dynamic port draws in samples • Air flow exits through the static port • Contains four filters in series • Filters are decreasing in size from 5 to 0.2 μm • Filter system terminates with NPT connector at each end • 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

  21. Filtration System

  22. Optical System • Grating 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

  23. Optical System Optical Bench Fiber optics connector Fixed entrance slit of 25 microns Longpass absorbing filter Collimating Mirror Grating with Groove Density of 600 lines/mm Focusing Mirror Detector collection lens 2048 element Linear CCD Array Longpassorder-sorting filter UV detector lens The Longpass absorbing filter (3) is not included in our system.

  24. Optical System • Cosine Corrector • Couples to optical fiber for spectral intensity measurements • Wavelength Range: 200 - 1100 nm • Field of View: 180° • Diffusing Material: Polytetrafluoroethylene (PTFE) • 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

  25. Design Compliance • Final mass must be 6.55 lbs • Total weight of sensors and spectrometer is less than 3 lbs • Projected filtration system weight is less than 2 lbs • More weight will be added once we are able to fully assemble the system • Payload Activation • G-switch • Center of Mass • Solid Works projection shows this constraint will be met • Once additional weight is added this must be recalculated

  26. Testing • 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 • Mechanical • 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 • 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

  27. Testing Equipment • The 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

  28. Biological Analysis • DAPI (type of microorganisms) • 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) • Bromodeoxyuridine (5-bromo-2-deoxyuridine) is a synthetic nucleoside that is used for detecting actively dividing cells. • Genetic Sequencing (type of microorganisms) • Determines the number of nucleotides in sample’s DNA: adenine, guanine, cytosine, and thymine • Scanning Electron Microscope (concentration of microorganisms) • Scans the sample and re-generates image to be analyzed, i.e. structural analysis of microbes

  29. 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 by • Use of ultra fast laser and biochemical techniques • 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

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

  31. Management

  32. Schedule

  33. Team Members Fred Avery (ME) • Filtration System • Center of gravity testing • Mass Flow Rates • Spin rate testing platform • Ny ‘JaaBobo (EE) • Hardware • Magnetometer • Accelerometers • Gyroscope • Power • Salvatore Giorgi (ECE) • Team Leader • Spectrometer • Microprocessor • Data Acquisition • Filtration System • Gene Council (EE) • Hardware • Magnetometer • Accelerometers • Gyroscope • Programming

  34. Parts List / Budget

  35. Parts List / Budget

  36. Advisors Electrical Dr. John Helferty Department of Electrical and Computer Engineering Mechanical Dr. ShriramPillapakkam Department of Mechanical Engineering Biological Dr. Erik Cordes Department of Biology Chemical Dr. Robert Stanley Department of Chemistry

  37. Conclusion • Concerns • Properly counting samples as function of altitude • Properly sterilizing and maintaining sterilization of the filtration system • Autoclave does not kill DNA • Correcting for any stray light that might enter our cosine corrector • Major Risks • Failure of filter system leading to depressurization of canister • Recently Finished • Spectrometer design completed • Ordered second microprocessor, ethernet shield, and spectrometer • Future Plans • Purchase and machine plates • Write library for USB interface • Order ball valves and tubing for filter system • Test servo motors available in lab with ball valves • Continue programming processor • Construct spin test platform and mock canister • Begin tests

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