July

Week 27: July 02nd to 08th

• Building of a complete deterministic model for the amplifier considering the enzymatic reaction
• Check of the Grenoble section & putting it on-line

Everything has been done.

Week 28: July 09th to 15th

• Research for quorum sensing parameters
• ODEs' comparaison with and without amplification

Some quorum sensing parameters have been found but there are still some numerical instabilities. We had to reconsider our solving method.
After comparaison we could notice that the amplification isn't better with the loop. We decided to reconsider the model.

Week 29: July 16th to 22th

• Research of parameters for ODE's
• Integration of arabinose in our model

All the parameters have not been found but Arabinose has been integrated in the system. We have to work with a few arabinose else the system will always be turned on. The integration of arabinose enabled us to have a better control on cya.

Week 30: July 23rd to 29th

• Fit theoretical graphs with biological graphs and analyse the biological results
• Set the deterministic model for Rsma/rsmy network

We realized that we didn't have to take the growth of the bacteria in consideration. Indeed the bacteria grows as long as there is some glucose in the system, but the system can't turn on when there is some glucose.Thus, when the system runs, the bacteria isn't growing. Concerning the graphs, we tried to obtain better theorical graphs but, because of the basal parameters, we didn't succeded.
We have set the ODEs for the RsmA/rsmY network but, after a crisis meeting with the biologists about how we should manage the last month, we decided to give a higher priority to the receptor and the amplification loop. We can reconsider RsmA/rsmY later if we still have time.