Team:Grenoble/Modeling/Notebook/August
From 2012.igem.org
August
Week 31 • Week 32 • Week 33 • Week 34 • Week 35Week 31: July 30th to August 5th
Goal
 Know if there is a basal production of Cya
 Determine modeling for the receptor
Conclusion

There is no wild type in the experiments, but thanks to the glucose we can say that there is no basal production of Gfp/Cya (it is the same because they are regulated by the same promotor.
The problem with the receptor model is that we have a lot of equations and thus too much parameters (16). After a meeting with our advisors we decided to simplify the equations and chose a different model.
For the deterministic model of the receptor, we chose to model reactions of the receptor behavior by a series of complexations. We got the inspiration from iGEM Imperial College 2010. The graphs obtained weren't satisfying so we decided to review the parameters values.
Week 32: August 6th to 12th
Goal
 Parameters research for the receptor model
 Script and simulation for the stochastic model
 Comparaison between the systems with the amplification loop and without. However without the loop we don't consider the degradation.
Conclusion

The script for the stochastic model and its optimisation is done but there are problems because of parameters.
We can have a better result with the amplificationn loop if we amplify CRP. However we face a new problem : the system could be always turned on.
Week 33: August 13th to 19th
Goal
 End of the script for the stochastic and analysis
 Beginning of the equilibrium analysis to answer the question : Is the system always turned on ?
 Set a new deterministic model for the receptor
Conclusion

The script is definitely done but the parameters are not fixed. Thus we can't make simulations and analyse the results.
We learnt how to use isoclines.
For the receptor we chose a phenomenological extension of GoldbeterKoshland biochemical switch model[1].
The system is now much simple. We have 2 equations and 8 parameters.
[1] Alejandra C.Ventura, JacquesA. Sepulchre, Sofia D.Merajver. A Hidden Feedback in Signaling Cascades Is Revealed. PLOS Computational Biology, 2008, 4, 3, e1000041.
Week 34: August 20th to 26th
Goal
 End of the stochastic
 Redaction of the stochastic part
 Equilibrium analysis
 Determine which parameters we should modify to get better results
Conclusion
For the stochastic part we are still waiting on parameters. Concerning the redaction of the stochastic part, we can't progress seeing that we can't analyse our results yet.
It seems that we reach the wanted equilibriums only if the basal production of Ca is zero. We modified the ODE to make them be always right.
Week 35: August 27th to September 02nd
Goal
 Check the receptor modell
 End of stochastic and redaction for the wiki
 Equilibrium analysis on a simplified model to compute the threshold under which the equilibrium point changes
Conclusion

The receptor model and the stochastic model are checked. All the equilibrium analysis are done. We should work with more CRP and a little arabinose. For the receptor script we have a problem with the curve of AC evolution : it decreases at high dipeptide concentration.We're thinking about the origin of the problem.