Team:Paris/Analysis/Math+Sim
From 2008.igem.org
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* In addition to the previous FIFO system, we will add a negative feedback on FlhDC promoter to observe oscillations. Thus, we obtained the following network and the corresponding equations : | * In addition to the previous FIFO system, we will add a negative feedback on FlhDC promoter to observe oscillations. Thus, we obtained the following network and the corresponding equations : | ||
- | [[Image: | + | [[Image:Core_system.jpg|400px|center]] |
<br> | <br> | ||
[[Image:eqn_flhDC.jpg|center]] | [[Image:eqn_flhDC.jpg|center]] |
Revision as of 15:54, 26 October 2008
Mathematical analysis and simulations
FIFO
where CFP, YFP, and RFP will be denoted below as respectively Z1,Z2 and Z3.
We have implemented this system using Matlab (see the corresponding codes)
Indeed, we may see that there is a LIFO behavior rather than the FIFO we expect...
Oscillations
If you want more details about the way we have built them, you can go to the model construction page. If one tries to draw simulations of this system, he will obtain this kind of results : In a nutshell : It does not work !
Finally, the logical continuation of the process will be to try to improve the biological system in order to find oscillations. This will be described in the part below, as well as in the section System Improvements. System analysisSimulations of the core system displayed above reveal that it does not exhibit an oscillatory behavior. In this section we use the model of the core system to try to figure out the contribution of some key characteristics of the network topology on the dynamic of the system. This analysis is done by successively simulating altered forms of the system.
This analysis shows that the core system and its altered variants cannot oscillate. In the next section, we examine more significant topology improvements of the core system. |