IGEM:IMPERIAL/2006/project/Oscillator/project browser/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.

 var sc_project=1999441; var sc_invisible=1; var sc_partition=18; var sc_security="18996820";

 

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.)

Model description of the killing of the prey molecule by the predator

 * mathematical description of the killing of the prey:
 * $$\frac{d[AHL]}{dt} = \frac{b * [aiiA] * [AHL]}{(b0 + [AHL])} - e * [AHL]$$

Dynamical and sensitivity analysis

 * Template__HIDER__
 * analyze model in order to show how the part could fulfill its specifications
 * insert graph and charts
 * We have decoupled the predator into sensing and killing parts
 * For detail modelling, please refer to the modelling section in subparts.
 * Predator Sensing
 * Predator Killing

Characterization

 * To characterize the part, we have to measure the production rate and aiiA enzyme activity seperately
 * For details characterization, please refer to subparts