IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full System/Modelling

 Specifications Design Modelling Implementation Testing/Validation  

Model variables and parameters
Full derivation of the above equations.

SBML Model
[[Media:IGEM_IMPERIAL_FullSystem_Model.sbml]]

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.


 * Assumption on the Chemostat:
 * It assumes that the prey molecule generator and the predator molecule generator populations are stable (the cell populations have reached steady-state).
 * the degradation of the molecules is mainly due to the wash-out of the chemostat.


 * 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 concentration of the heterodimer is in equilibrium with the concentration of AHL
 * LuxR is constitutively produced and reaches steady state before AHL production begins. [LuxR] in the prey can be considered constant
 * The degradation rate of luxR and AHL-lactonase is due to the growth dilution which, in this case, is controlled by the chemostat
 * AHL is diffusing freely throughout the system

Characterization

 * Characterization of the parameters a, ao shall be done using the  Prey Generator Test Contstruct
 * Characterization of the parameters c, c0 shall be done using the  Predator Generator Sensing Test Construct
 * Characterization of the parameters b, b0 shall be done using the  Predator Generator Killing Test Construct
 * The growth dilution can be controlled by the chemostat washout.

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