Team:Paris/Analysis

This page presents the principal analytic results derived from the models, corresponding to the genetic networks we have designed (FIFO, oscillations, ...), as well as representative simulations' results. This has led us to propose some modifications of the initial system, in order to obtain an improved oscillating system.

= FIFO behaviour = Here are the network and simulations corresponding to the FIFO aspect :

As explained here, the FIFO circuit is made of a main regulator (FlhDC) that activates an intermediary regulator (FliA) and the three output genes Z1, Z2, and Z3 that are activated by the combined effect of the two regulators.

The simulation on the right, based on parameter values found in Shiraz Kalir et al. (2004) directly repoduced a FIFO behaviour: the output genes are inactivated in the same order they are activated.

Go further into
 * the model
 * the mathematical analysis and the simulations ?

= Oscillations = The first attempt for an oscillation circuit is implemented as a simple negative feedback loop connecting one output of the FIFO circuit to the input regulator :

From the simulations performed with parameters found in the literature, we conclude that the system reaches a steady state and is far from oscillating ! We evaluate the role of key interactions of the core system by successively simulating altered forms of the system. Curves below display simulations of 3 simple variants of the model, none of which producing sustained oscillations. Moreover, a mathematical analysis confirms that the core system cannot produce oscillations. These three alternatives are implemented using the programming environment for modeling biochemical systems BIOCHAM (see code).

{|
 * - style="background: #ffffff; text-align: center;"

''Read more about:
 * the description of the two proposed improvements
 * the analysis of these improvements
 * the outcome of our analysis