Team:Michigan/Project/Modeling/Model2.html

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*A= NifA protein
*A= NifA protein
*A2i= NifA complex, where i=1 is a dimer, i=4 is a tetramer, and i=6 is a hexamer
*A2i= NifA complex, where i=1 is a dimer, i=4 is a tetramer, and i=6 is a hexamer
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<div align='center'> [[Image: Table2.png]]</div>
 
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We ran some Ninfa Index simulations on the i=1 model (the other models were too complex to run the simulations on [my MacBook lacks computing power]):
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<div align='center'> [[Image: Table2.png]]</div>
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Overall, we see smaller indices than the ones we saw in  Model 1.  Nonetheless,we see that the clock has at least some chance of oscillating.
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<br> When we decrease the randomization range of kf to in between 0 and 10 for trial 2, we see an almost threefold decrease in the Ninfa index.
[https://2008.igem.org/Team:Michigan/Project/Modeling Back to Modeling]
[https://2008.igem.org/Team:Michigan/Project/Modeling Back to Modeling]
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Revision as of 02:30, 30 October 2008


Michigan iGEM website header.jpg

HOME THE TEAM THE PROJECT REGISTRY PARTS NOTEBOOK


Sequestillator Model 2: A More Complicated Model

While Model 1 gave us some important results (mainly: need a low Kd for oscillations to occur) , we decided to look at more complete model that accounted for some of the dimerizations the proteins undergo:

Model2Equations.png

Parameters

  • a= production of NifA
  • kf= binding rate of NifA and NifL
  • kr= dissociation rate of NifA/NifL complex
  • any d= degradation rate of that species
  • kb:rate of complex formation (i.e. dimerization, formation of tetramers/hexamers)
  • kb2: dissociation rate of such complexes given above
  • m= represents how many subunits of NifA bind to NifHp (i.e., if we modeled NifA as a dimer [so 'i'=2], we would say m=3, since 2*3=6 (NifA is a hexamer).
  • tmax: Maximal transcription rate
  • tl: translation rate

Functions

  • We model the production function of mRNA as a Hill-like, sigmoidal function

Variables

  • mL=NifL mRNA
  • L=NifL protein
  • L2= NifL dimer
  • A= NifA protein
  • A2i= NifA complex, where i=1 is a dimer, i=4 is a tetramer, and i=6 is a hexamer

We ran some Ninfa Index simulations on the i=1 model (the other models were too complex to run the simulations on [my MacBook lacks computing power]):

Table2.png

Overall, we see smaller indices than the ones we saw in Model 1. Nonetheless,we see that the clock has at least some chance of oscillating.
When we decrease the randomization range of kf to in between 0 and 10 for trial 2, we see an almost threefold decrease in the Ninfa index.


Back to Modeling