# Team:Paris/Modeling/hill approach

(Difference between revisions)
 Revision as of 13:58, 19 August 2008 (view source)Hugo (Talk | contribs) (→What kind of Mathematical Simulation ?)← Older edit Revision as of 10:46, 3 September 2008 (view source)Hugo (Talk | contribs) (→What kind of Mathematical Simulation ?)Newer edit → Line 5: Line 5: We decided to use mostly Ordinary Differential Equation approach, at least for the study of the Oscillations and of the FIFO. For the Synchronisation module, we will probably use Probabilistic Differential Equations, in order to introduce the differences between the cells. We decided to use mostly Ordinary Differential Equation approach, at least for the study of the Oscillations and of the FIFO. For the Synchronisation module, we will probably use Probabilistic Differential Equations, in order to introduce the differences between the cells. - We assume in this section that the concentrations of the products of complexation reactions are at steady-states, desceibed as ''hill function'' (see [[Team:Paris/Modeling/Programs|precision on hill functions]]). + We assume in this section that the concentrations of the products of complexation reactions are at steady-states, described as ''hill function'' (see [[Team:Paris/Modeling/Programs|precision on hill functions]]). ==Bio-Chemical General Assumptions== ==Bio-Chemical General Assumptions==

# Hill functions approach

## What kind of Mathematical Simulation ?

We decided to use mostly Ordinary Differential Equation approach, at least for the study of the Oscillations and of the FIFO. For the Synchronisation module, we will probably use Probabilistic Differential Equations, in order to introduce the differences between the cells.

We assume in this section that the concentrations of the products of complexation reactions are at steady-states, described as hill function (see precision on hill functions).

## Bio-Chemical General Assumptions

We know that the following equations do not describe properly what really happens in the cells. For exemple, we know that the transcription factor flhD-flhC is actually an hexamere FlhD4C2. But, as we will surely not get access to the dissociation constant of the hexamerisation, we just treat it as an abstract inducer protein "FlhDC", with an order in its Hill function probably between 3 and 6 (but perhaps completly different; the estimation of the error by the 'findparam' program will tell us if we are right to do so).

For the moment, at each part of our modelisation, we reduce the expression of a gene at its transcription. The translation process is not taken into acount (see however considerations on RBS).

To see more details about the modelisation and the values of the involved constants, see the bibliography.