1. Modeling the Chemical Reactions Involved in Biological Digital Inverters Rick Corley Mentor: Geo Homsy

2. High level goal: Program biological cells Implement digital gates using gene/protein interactions in cells Potential applications: –“smart” drugs/medicine –agriculture –embedded systems Cellular Computing

3. Contributions Described a detailed model of a biological inverter –the most basic logic circuit Simulated and analyzed the model Result: –evidence that system may work in Biology

4. An Inverter A Logic Gate Takes one input, true or false Outputs the opposite TrueFalse True

5. A Biological Inverter Proteins are the inputs and outputs –a high concentration represents true –a low concentration represents false The input represses the creation of the output

6. Biological Inversion Promoter Operator DNA RNA Polymerase Repressor Protein Promoter Operator DNA RNA Polymerase False -> True True -> False

7. The Simulation Model Select chemical reactions for circuit Model reactions with differential equations Use real-life kinetic constants ( -phage virus)

8. input output The Transfer Curve Describes “steady- state” behavior Gives the output for a certain input Has a point where the output equals the input

9. Our Transfer Curve Upper bound = 4258 Flip Point =24.6

10. Dynamic Behavior Simulation shows: –lack of input protein X results in high concentrations of output protein Y –X suppresses the creation of Y –The recovery time is very long Y X2X2 X time

11. Conclusion design and analysis of a more detailed model better understanding of the characteristics of a realistic biological inverter actual system may be realized in biological cells