IGEM:IMPERIAL/2006/project/Oscillator/project browser/Test Sensing Predator Construct/Modelling

 Specifications Design Modelling Implementation Testing/Validation  

Model assumptions and relevance

 * General assumptions on gene expression modelling:
 * Quasi-steady state hypothesis on mRNA expression.
 * Gene activation can be approximated by Hill equations.


 * Assumptions linked to the quorum sensing:
 * As a first approximation, we assume that luxR and AHL molecules form a heterodimer (even if it has been found that the complex formed is more complicated).
 * The degradation rate of luxR and aiiA is mainly due to the growth dilution.

Model description of the oscillator
Full derivation of the above equations.

Model description of the growth of the predator

 * mathematical description of the predator growth and death:
 * $$\frac{d[luxR]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [luxR]$$
 * $$\frac{d[aiiA]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [aiiA]$$


 * insert a graphical representation if possible (e.g. CellDesigner display)
 * link to SBML file or matlab.

Model variables and parameters for the growth of the predator
(list all the variables and parameters of the model in a table, specifying if their values are known, unknown, to be measured.)

Characterization

 * Parameters c & c0 for characterization have to be extracted.
 * gd[luxR] and gd[aiiA] can be controlled by the chemostat.