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

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!height="25pt" width="80pt"|Actual Part
!height="25pt" width="80pt"|Actual Part
!colspan="4"| Logo of the Part
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! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/intermediate_part| intermediate_part]]
! <bbpart>B0034</bbpart>
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/intermediate_part| intermediate_part]]
! <bbpart>C0062</bbpart>
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/intermediate_part| intermediate_part]]
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__NOTOC__
==Model assumptions and relevance==


*Modelling
*General assumptions on gene expression modelling:
*Modelling
**Quasi-steady state hypothesis on mRNA expression.
*Modelling
**Gene activation can be approximated by [http://en.wikipedia.org/wiki/Hill_equation 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==
 
'''[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Modelling Full derivation of the above equations.]'''
 
==Model description of the growth of the predator==
*mathematical description of the predator growth and death:
**<math>\frac{d[luxR]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [luxR]</math>
**<math>\frac{d[aiiA]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [aiiA]</math>
 
*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.)
 
{| border="1" width="100%"
| style="background:lightblue" colspan="5"| '''Variables'''
|- style="background:lightgrey"
!Name !! Description !! Initial Value !! Confidence !! Reference
|-
|width="100"| AHL || homoserine lactone acting as the prey-molecule || 0|| depends how good is the control of the prey positive feedback || links
|-
|width="100"| luxR || molecule acting as the sensing module for the predator || 0|| to be measured as we might have to deal with some leakage of the promoter || links
|-
|width="100"| aiiA || molecule acting as the killing module of the prey for the predator  || 0 || to be measured as we might have to deal with some leakage of the promoter || links
|}
 
{| border="1" width="100%"
| style="background:lightblue" colspan="5"| '''Parameters'''
|- style="background:lightgrey"
! Name !! Description !! Value !! Confidence !! Reference
|-
|width="100"| c || maximum synthesis rate of the pLux promoter || to be characterized || to be measured || links
|-
|width="100"| c0 || dissociation constant according to Hill eq || to be characterized|| to be measured || links
|-
|width="100"| gd || growth dilution  || to be characterized || to be measured || links
|}
 
==Characterization==
 
*Parameters c & c0 for characterization have to be extracted.
*gd[luxR] and gd[aiiA] can be controlled by the chemostat.

Latest revision as of 08:13, 29 October 2006

Super Parts Predator Construct
Actual Part
Sub Parts <bbpart>R0062</bbpart> <bbpart>B0034</bbpart> <bbpart>C0062</bbpart> <bbpart>I13504</bbpart>


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:
    • [math]\displaystyle{ \frac{d[luxR]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [luxR] }[/math]
    • [math]\displaystyle{ \frac{d[aiiA]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [aiiA] }[/math]
  • 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.)

Variables
Name Description Initial Value Confidence Reference
AHL homoserine lactone acting as the prey-molecule 0 depends how good is the control of the prey positive feedback links
luxR molecule acting as the sensing module for the predator 0 to be measured as we might have to deal with some leakage of the promoter links
aiiA molecule acting as the killing module of the prey for the predator 0 to be measured as we might have to deal with some leakage of the promoter links
Parameters
Name Description Value Confidence Reference
c maximum synthesis rate of the pLux promoter to be characterized to be measured links
c0 dissociation constant according to Hill eq to be characterized to be measured links
gd growth dilution to be characterized to be measured links

Characterization

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