Endy:Chassis engineering/VM2.0: Difference between revisions
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__NOTOC__ | __NOTOC__ | ||
<showhide><h1>VM2.0 regulation design considerations</h1>__HIDER__ | |||
<hide> | |||
[[Image:BC-VM20Regulation.png|thumb|right|500px|Regulation scheme for VM2.0]] | [[Image:BC-VM20Regulation.png|thumb|right|500px|Regulation scheme for VM2.0]] | ||
#Stability | #Stability | ||
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What are the metrics for each of the design considerations? | What are the metrics for each of the design considerations? | ||
</hide></showhide> | |||
<br style="clear:both" /> | <br style="clear:both" /> | ||
==Model== | ==Reduced Model== | ||
[[Image:BC-VM20RegulationReduced Model.jpg|thumb|400px|right|Reduced network for VM2.0]] | |||
*Two species, RNAP (activator) and repressor | |||
*Continuous differential equations | *Continuous differential equations | ||
*MATLAB | *MATLAB | ||
*Dimensionless variables, lumped parameters. | *Dimensionless variables, lumped parameters. | ||
*Parameterized for T7 RNAP, "typical" repressor | *Parameterized for T7 RNAP, "typical" repressor | ||
< | <br> | ||
<math> | <math> | ||
\dot{[u]} = \frac{a_{0}+a_{1}[u]}{1+[u]+[v]^{n}}-[u]\qquad(1) | \dot{[u]} = \frac{a_{0}+a_{1}[u]}{1+[u]+[v]^{n}}-[u]\qquad(1) | ||
| Line 40: | Line 44: | ||
<math>[v]</math> = dimensionless concentration of repressor | <math>[v]</math> = dimensionless concentration of repressor | ||
<br> | <br> | ||
</ | <br style="clear:both" /> | ||
<showhide><h2>Species</h2>__HIDER__ | |||
<hide> | |||
#T7 RNAP | #T7 RNAP | ||
#Repressor | #Repressor | ||
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===Model analysis notes=== | ===Model analysis notes=== | ||
*A cooperative autogene network can exhibit bistability or monostability depending on parameter values ([http://web.mit.edu/biophysics/sbio/ 7.81]). Does this apply if there is no cooperativity? | *A cooperative autogene network can exhibit bistability or monostability depending on parameter values ([http://web.mit.edu/biophysics/sbio/ 7.81]). Does this apply if there is no cooperativity? | ||
</hide></showhide> | |||
Revision as of 20:41, 14 March 2007
<showhide>
VM2.0 regulation design considerations
__HIDER__
<hide>
- 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)
- Noise
- Self-booting/controlled
- Ability to turn on or off
- Portability
- Tunable
- Pros and cons of DNA copy number, promoter strength, repressor affinities etc.
- Efficient
- Minimizing levels of repressor needed
- Minimizing consumption of small molecules
What are the metrics for each of the design considerations?
</hide></showhide>
Reduced Model
- Two species, RNAP (activator) and repressor
- Continuous differential equations
- MATLAB
- Dimensionless variables, lumped parameters.
- Parameterized for T7 RNAP, "typical" repressor
[math]\displaystyle{
\dot{[u]} = \frac{a_{0}+a_{1}[u]}{1+[u]+[v]^{n}}-[u]\qquad(1)
}[/math]
[math]\displaystyle{
\dot{[v]} = \frac{a_{0}+a_{1}[u]}{1+[u]+[v]^{n}}-[v]\qquad(2)
}[/math]
[math]\displaystyle{ [u] }[/math] = dimensionless concentration of T7 RNAP
[math]\displaystyle{ [v] }[/math] = dimensionless concentration of repressor
<showhide>
Species
__HIDER__
<hide>
- T7 RNAP
- Repressor
- Ribosomes
- Repressible T7 promoter
- T7RNAP-promoter complex
- Repressor-promoter complex
- T7 RNAP mRNA
- Repressor mRNA
- Elongating T7 RNAP
- Elongating Ribosomes
- 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?
</hide></showhide>
