Team:Paris/Modeling/Molecular Reactions

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{{Paris/Header|Molecular Reactions}}
{{Paris/Header|Molecular Reactions}}
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We show here the elementary reactions that served us as basis. They intend to be "exhaustive" in the sense that every step of the [[Team:Paris/Modeling/Protocol_Of_Characterization|system]] is described. Each of these reactions has to be "mathematically interpreted", in a [[Team:Paris/Modeling/FromMolReactToNLOde|model]] which accounts for the observable phenomena, and, in the same time, allows us to well estimate [[Team:Paris/Modeling/Protocol_Of_Characterisation|experimentally]] all the involved parameters.
We show here the elementary reactions that served us as basis. They intend to be "exhaustive" in the sense that every step of the [[Team:Paris/Modeling/Protocol_Of_Characterization|system]] is described. Each of these reactions has to be "mathematically interpreted", in a [[Team:Paris/Modeling/FromMolReactToNLOde|model]] which accounts for the observable phenomena, and, in the same time, allows us to well estimate [[Team:Paris/Modeling/Protocol_Of_Characterisation|experimentally]] all the involved parameters.
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[[Team:Paris/Modeling/Workflow_Example| <Back to "Workflow on an Example"]]|
 
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{{Paris/Navig|Team:Paris/Modeling/Workflow_Example}}
{{Paris/Navig|Team:Paris/Modeling/Workflow_Example}}

Latest revision as of 03:39, 30 October 2008

Molecular Reactions


We show here the elementary reactions that served us as basis. They intend to be "exhaustive" in the sense that every step of the system is described. Each of these reactions has to be "mathematically interpreted", in a model which accounts for the observable phenomena, and, in the same time, allows us to well estimate experimentally all the involved parameters.


The system we are studying is the "Core System with three genes of interest" that we can represent in the scheme below (with all alternatives pFlhDC or pTet and TetR or envZ or OmpR*)

↓ Core System ↑


core system

The "core systeme"
* Every interactions are modelised by a ƒX function
* The detailed example FP1 = ƒ5([FlhDC],[FliA]) is surrounded in red


Complexation Reactions

The double triangle (><) is a symbol for complexations :
Compl.jpg means n1 molecules of FlhDC complexed with a pFliA promoter

↓ Complexation Reactions ↑


Equa Complex.jpg
 On the Example :

How given amounts of FlhDC and FliA would produce FP1 ?

  • FlhDC and FliA bind to pFliL :

DCiLcompl.jpg

AiLcompl.jpg

Production Reactions

The double triangle (><) is a symbol for complexations :
Compl.jpg means n1 molecules of FlhDC complexed with a pFliA promoter

↓ Production Reactions ↑


Prod React.jpg
 On the Example :

How given amounts of FlhDC and FliA would produce FP1 ?

  • FlhDC><pFliL and FliA><pFliL causes "production" of FP1 :



BFP1.jpg

Degradation/Dilution Reactions

↓ Degradation/Dilution Reactions ↑


D React.jpg
 On the Example :

How given amounts of FlhDC and FliA would produce FP1 ?

  • FP1 disappears because of its degradation and dilution :

DFP1.jpg

For complete PDF with all Reactions and Numbered References : complete list of reactions and equations



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