Modeling the Chemical Reactions Involved in Biological Digital Inverters

1
Modeling the Chemical Reactions Involved in
Biological Digital Inverters

• Rick Corley
• Mentor Geo Homsy

2
Cellular Computing

• High level goal Program biological cells
• Implement digital gates using gene/protein
  interactions in cells
• Potential applications
• smart drugs/medicine
• agriculture
• embedded systems

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

True
False
False
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
RNA Polymerase
Repressor Protein
DNA
Promoter
Operator
True -gt False
False -gt True
7
The Simulation Model

• Select chemical reactions for circuit
• Model reactions with differential equations
• Use real-life kinetic constants (l-phage virus)

8
The Transfer Curve

• Describes steady-state behavior
• Gives the output for a certain input
• Has a point where the output equals the input

output
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

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