Endy:Chassis engineering/VM2.0

VM2.0 regulation design considerations

Regulation scheme for VM2.0

1. Stability
   • Noise
     • analytical stability analysis on very simple model or Routh-Hurwitz analysis for full model
     • parameter sensitivity analysis
   • Response time
     • Better to have this fast or slow (slow response time averages out short time scale fluctuations)
2. Self-booting/controlled
   • Ability to turn on or off
   • Portability
3. Tunable
   • Pros and cons of DNA copy number, promoter strength, repressor affinities etc.
4. Efficient
   • Minimizing levels of repressor needed
   • Minimizing consumption of small molecules

What are the metrics for each of the design considerations?

Model

Continuous differential equation model in MATLAB

Species

1. T7 RNAP
2. Repressor
3. Ribosomes
4. Repressible T7 promoter
5. T7RNAP-promoter complex
6. Repressor-promoter complex
7. T7 RNAP mRNA
8. Repressor mRNA
9. Elongating T7 RNAP
10. Elongating Ribosomes
11. etc.

Model analysis notes

• A cooperative autogene network can exhibit bistability or monostability depending on parameter values (7.81). Does this apply if there is no cooperativity?