Team:Paris/Modeling/FromMolReactToNLOde

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(Mathematical Interpretation and Simulation of the Molecular Reactions)
 
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{{Paris/Header|From Molecular Reactions to Non-Linear ODEs}}
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== Idea and Assumptions ==
== Idea and Assumptions ==
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We will here propose a Mathematical Modeling of the <span style="color:#0000FF;">elementary molecular reactions</span>. The idea of the ''Characterization Approach'' is that this modelization must both accounts for <span style="color:#0000FF;">every small steps</span> of the system and allow the <span style="color:#0000FF;">experimental characterizations</span>.
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We will here propose a Mathematical Modeling of the [[Team:Paris/Modeling/Molecular_Reactions|elementary molecular reactions]]. The idea of the ''Characterization Approach'' is that this modelization must both accounts for [[Team:Paris/Modeling/Protocol_Of_Characterization|every small steps]] of the system and allow the [[Team:Paris/Modeling/Protocol_Of_Characterization|experimental characterizations]].
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{{Paris/Toggle|precisions|Team:Paris/Modeling/More_From2Ode_Intro}}
 
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Therefore, the following equations do not describe properly what ''really'' happens in the cells. For exemple, we know that the transcription factor FlhD-FlhC is actually an ''hexamere FlhD<sub>4</sub>C<sub>2</sub>''. But, as we will surely not get access to the ''dissociation constant'' of the ''hexamerisation'', we just treat it as an ''abstract'' inducer protein "''FlhDC''", with an order (''n'') in its ''complexation caracterization'' probably around 2*4 = 8 (but perhaps completly different ! ; the estimation of the error by the <span style="color:#0000FF;">parameter finder program</span> would tell us if it stays consistent).
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Therefore, the following equations do not describe properly what ''really'' happens in the cells. For exemple, we know that the transcription factor FlhD-FlhC is actually an ''hexamere FlhD<sub>4</sub>C<sub>2</sub>''. But, as we will surely not get access to the ''dissociation constant'' of the ''hexamerisation'', we just treat it as an ''abstract'' inducer protein "''FlhDC''", with an order (''n'') in its ''complexation caracterization'' probably around 2*4 = 8 (but perhaps completly different ! ; the estimation of the error by the [[Team:Paris/Modeling/Implementation#Parameters_Finder_Programs|Parameters Finder Programs]] would tell us if it stays consistent).
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== Mathematical Interpretation and Simulation of the Molecular Reactions ==
== Mathematical Interpretation and Simulation of the Molecular Reactions ==
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First, we consider the '''complexation phenomenon'''. We show, under the <span style="color:#0000FF;">quasi steady-state hypothesis</span>, how it leads to <span style="color:#0000FF;">Non-Linear interactions</span> like "Hill functions".
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First, we consider the '''complexation phenomenon'''. We show, under the ''quasi steady-state hypothesis'', how it leads to ''Non-Linear interactions'' like "Hill functions".
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{{Paris/Toggle|precisions|Team:Paris/Modeling/More_From2Ode_M}}
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{{Paris/Toggle|developments|Team:Paris/Modeling/More_From2Ode_M|250px}}
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Then, we apply these results to the <span style="color:#0000FF;">Molecular Reactions</span> of our system. That gives all the theoretical calculation of the complexations, and finally, with the <span style="color:#0000FF;">previous assumptions</span>, we get the <span style="color:#0000FF;">equations of the full system of ODEs</span>.
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Then, we apply these results to the ''Molecular Reactions'' of our system. That gives all the theoretical calculation of the complexations, and finally, with the ''previous assumptions'', we get the ''equations of the full system of ODEs''.
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[[Image:compl.jpg|110px]] means ''n<sub>1</sub>'' molecules of ''FlhDC'' complexed with a ''pFliA'' promoter<br><br>
[[Image:compl.jpg|110px]] means ''n<sub>1</sub>'' molecules of ''FlhDC'' complexed with a ''pFliA'' promoter<br><br>
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<html><iframe height="300" width="650" src="https://static.igem.org/mediawiki/2008/4/46/Complexations_QSS.pdf"></iframe></html>
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{{Paris/Toggle2|Complexation Steady-State|Team:Paris/Modeling/Compl_SS}}
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| width="25%" | '''On the Example :''' <br>
| width="25%" | '''On the Example :''' <br>
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[[Image:compl.jpg|110px]] means ''n<sub>1</sub>'' molecules of ''FlhDC'' complexed with a ''pFliA'' promoter<br><br>
[[Image:compl.jpg|110px]] means ''n<sub>1</sub>'' molecules of ''FlhDC'' complexed with a ''pFliA'' promoter<br><br>
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<html><iframe height="300" width="650" src="https://static.igem.org/mediawiki/2008/a/a2/Temporal_ODEs.pdf"></iframe></html>
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{{Paris/Toggle2|ODEs of the Global System|Team:Paris/Modeling/ODEs}}
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| width="25%" | '''On the Example :''' <br>
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Latest revision as of 03:39, 30 October 2008

From Molecular Reactions to Non-Linear ODEs


Idea and Assumptions

We will here propose a Mathematical Modeling of the elementary molecular reactions. The idea of the Characterization Approach is that this modelization must both accounts for every small steps of the system and allow the experimental characterizations.



Therefore, the following equations do not describe properly what really happens in the cells. For exemple, we know that the transcription factor FlhD-FlhC is actually an hexamere FlhD4C2. But, as we will surely not get access to the dissociation constant of the hexamerisation, we just treat it as an abstract inducer protein "FlhDC", with an order (n) in its complexation caracterization probably around 2*4 = 8 (but perhaps completly different ! ; the estimation of the error by the Parameters Finder Programs would tell us if it stays consistent).



Mathematical Interpretation and Simulation of the Molecular Reactions

First, we consider the complexation phenomenon. We show, under the quasi steady-state hypothesis, how it leads to Non-Linear interactions like "Hill functions".


Then, we apply these results to the Molecular Reactions of our system. That gives all the theoretical calculation of the complexations, and finally, with the previous assumptions, we get the equations of the full system of ODEs.

Complexation Steady-State

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

↓ Complexation Steady-State ↑


Compl SS.jpg
On the Example :

How given amounts of FlhDC and FliA would produce FP1 ?

  • FlhDC and FliA bind to pFliL

following "Hill functions" :
DCiLcomplEq.jpg

AiLcomplEq.jpg

Equations of the Full System

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

↓ ODEs of the Global System ↑


Equa ODEs.jpg
On the Example :

How given amounts of FlhDC and FliA would produce FP1 ?

  • FlhDC><pFliL and FliA><pFliL causes "production" of FP1, diluted along times :


bFP1dot.jpg the outlined parameters are necessary and enough to fully characterize ƒ5

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