Team:Paris/Analysis/Construction2

From 2008.igem.org

Revision as of 23:21, 25 October 2008 by Felipe (Talk | contribs)

Model Construction


Description

  • We chose to use a chemostat. We want to impose to our model the fact that the rate of production has to be proportional to the existing population and to the amount of available resources.
  • We assume a logistic model for the population kinetics in the chemostat (reference).
  • To archieve synchronization we use QS. Explain the principle?

Kinetics

  • Following standard assumptions, We use a logistic equation for representing cell growth [Garcia-Ojalvor--ref]. This captures the fact that at low population density, the concentration of cells in the chemostat (c) increase exponentialy with a growth rate αcell and at high population density, the population reaches a maximum concentration cmax. As a consequence, the concentration of cells in the medium can be expressed in terms of a production (positive) term and degradation (negative) terms, as follows:


Population evolution full 2.jpg,


where...

  • To model the quorum sensing dynamics, we consider the production of HSL as:

eqHSL 1,

the transport of HSL is given by:

HSLext sum 2.jpg,

where...

when in...:

HSLext final 2.jpg,          where     Cell number volume.jpg;

and the activation of envZ depends of the concentration of HSL according to:

eqHSL 3.


Parameters Search

manly from literature but also from S0 analysis.

Parameters
 
Chemostat Parameter Meaning Original Value Normalized Value Unit Source
figure / equations of Chemostat αcell Growth rate 0.0198 1 min-1 wet-lab
cmax Carrying capacity for cell growth 0.1 0.1 µm3 [3]
Drenewal Dilution rate 0.00198 0.1 min-1 wet-lab ([3])
d Death rate 0.0099 0.5 min-1 wet-lab
 
Quorum Sensing Parameter Meaning Original Value Normalized Value Unit Source
figure / equations of Quorum Sensing γHSL Degradation rate 0.0053 0.2690 min-1 wet-lab
γHSLext

Degradation rate 0.0106 0.5380 min-1 [6]
βHSL Production rate 0.3168 16 min-1
η Diffusion rate 10 505 min-1 [2]
nHSL Hill coefficient   4   [3]
θHSL Hill characteristic concentration for the second operator   0.5 c.u [3]