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BioWire Progress Report Week Two

BioWire Progress Report Week Two. Orr Ashenberg, Patrick Bradley, Connie Cheng, Kang-Xing Jin, Paula Nunes, Danny Popper, Sasha Rush. What we did last week. Ordered BioBricks Experiments Miniprepped the BioBricks Modeling Photolithography. Modeling.

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BioWire Progress Report Week Two

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  1. BioWire Progress ReportWeek Two Orr Ashenberg, Patrick Bradley, Connie Cheng, Kang-Xing Jin, Paula Nunes, Danny Popper, Sasha Rush

  2. What we did last week • Ordered BioBricks • Experiments • Miniprepped the BioBricks • Modeling • Photolithography

  3. Modeling • Located parameters for all AHL rate constants • Updated the discrete model to use a faster algorithm • Constructed a parallel continuous model • Issues: Major discrepancies for constants in different papers.

  4. Photolithography • Went through microprinting process for mammalian cells in Kit’s lab. • In contact with member of Prof. Whitesides’ lab; we should be able to get a 50 μm line. • Also working on CAD design for our own masks and stamps.

  5. Update on the Weiss Circuit • They are working on the same PPG (propagating pulse generator) design as us. • They have simulations done, but no experimental data. • Their simulations show potential back-propagation and self-signaling.

  6. New Ideas • Have two signaling mechanisms to create circle or line oscillator • Lux with either Las or Rh1 • Would require two “routers” to receive the old signal and begin the new one. • Challenges: Designing another signaling pathway, crosstalk • Use one signaling pathway to create line oscillator • Bounce the pulse through the wire with delays on the ends • Use an intracellular lactonase • Allow for faster AHL degradation to reduce noise and potential back-propagation.

  7. Schedule (old) • Week 1 (6/6): Project Choice and Design • Week 2 (6/13): Test AHL receiver/sender • Week 3 (6/20): Test sender+receiver and repressor • Week 4 (6/27): More tests • Week 5 (7/4): Finish testing • Week 6 (7/11): Test cell signaling density; photolithography done • Week 7 (7/18): Construct IFFL (incoherent feed-forward loop) • Week 8 (7/25): Test it • Week 9 (8/1): “ • Week 10 (8/8): “ • Week 11 (8/15): “ • Week 12 (8/22): “

  8. Schedule (new) • Week 1 (6/6): Project Choice and Design • Week 2 (6/13): Got parts and set up tests • Week 3 (6/20): Get remaining parts; Test all • Week 4 (6/27): Tests we couldn’t get to last week • Week 5 (7/4): Finish testing • Week 6 (7/11): Test cell signaling density; photolithography done • Week 7 (7/18): Construct IFFL • Week 8 (7/25): Test it • Week 9 (8/1): “ • Week 10 (8/8): “ • Week 11 (8/15): “ • Week 12 (8/22): “

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