Team:PKU Beijing/Modeling/Stochastic

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(New page: {{PKU_Beijing/Header}} {{PKU_Beijing/Sidebar_Modeling}} {{PKU_Beijing/Header2}} Modeling > Stochastic Model We have ...)
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We have successfully conduct ODE model for both T3 design and P2 design. However, there's a inborn defect. The ODE models regard memory as a switch, only two state - 0 and 1. Actually, the memory is continous. Besides that, since the number of molecules in cell is not large enough, which means the circuit itself has a stochastic property. For these reasons, we conduct a stochastic model. Since ODE model for P2 is not as good as the one for T3, we will only conduct stochastic model for the T3 design.
We have successfully conduct ODE model for both T3 design and P2 design. However, there's a inborn defect. The ODE models regard memory as a switch, only two state - 0 and 1. Actually, the memory is continous. Besides that, since the number of molecules in cell is not large enough, which means the circuit itself has a stochastic property. For these reasons, we conduct a stochastic model. Since ODE model for P2 is not as good as the one for T3, we will only conduct stochastic model for the T3 design.
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==='''Equations'''===
+
==='''Construction'''===
 +
 
 +
New model needs new equations. In stochastic model, the equations should represent more elementary reactions. So we split the 13 equations in our deterministic model into 29 more elementary ones. Here we'll demonstrate these equations, without much explaination. If you're confused by some equations, please visit [[Team:PKU_Beijing/Modeling/ODE|ODE]] page, on which there're detailed explainations for each equation we used.
 +
 
 +
{|cellpadding=5
 +
|Equations||Remark
 +
|-
 +
|d[tRNA]/dt=||Synthesis of tRNA
 +
|-
 +
| ||Degradation of tRNA
 +
|-
 +
| ||Transformation from tRNA to Aa-tRNA
 +
|-
 +
| ||Degradation of Aa-tRNA (Aa-tRNA->tRNA)
 +
|-
 +
| ||Dilution of Aa-tRNA
 +
|-
 +
| ||Transcription of T7RNAP
 +
|-
 +
| ||Degradation of T7RNAP
 +
|-
 +
| ||AND Gate 1
 +
|-
 +
| ||Degradation of T7RNAP protein
 +
|-
 +
| ||Transcription of trigger CI
 +
|-
 +
| ||Transcription of Bistable CI
 +
|-
 +
| ||Degradation of trigger CI mRNA
 +
|-
 +
| ||Degradation of bistable CI mRNA
 +
|-
 +
| ||Translation of trigger CI mRNA
 +
|-
 +
| ||Translation of bistable CI mRNA
 +
|-
 +
| ||Degradation of CI protein
 +
|-
 +
| ||Transcription of CI434
 +
|-
 +
| ||Degradation of CI434 mRNA
 +
|-
 +
| ||Translation of CI434 mRNA
 +
|-
 +
| ||Degradation of CI434 mRNA
 +
|-
 +
| ||Transcription of T3
 +
|-
 +
| ||Degradation of T3 mRNA
 +
|-
 +
| ||AND Gate 2
 +
|-
 +
| ||Degradation of T3
 +
|-
 +
| ||Transcription of GFP - OR Gate
 +
|-
 +
| ||Transcription of GFP - AND Gate - OR Gate
 +
|-
 +
| ||Degradation of GFP mRNA
 +
|-
 +
| ||Translation of GFP mRNA
 +
|-
 +
| ||Degradation of GFP
 +
|}
==='''Parameters'''===
==='''Parameters'''===
-
==='''Result'''
+
==='''Result'''===
{{PKU_Beijing/Foot}}
{{PKU_Beijing/Foot}}
__NOTOC__
__NOTOC__

Revision as of 07:01, 20 October 2009

Modeling

Modeling Home
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Parameters
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Stochastic Model
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Modeling > Stochastic Model

We have successfully conduct ODE model for both T3 design and P2 design. However, there's a inborn defect. The ODE models regard memory as a switch, only two state - 0 and 1. Actually, the memory is continous. Besides that, since the number of molecules in cell is not large enough, which means the circuit itself has a stochastic property. For these reasons, we conduct a stochastic model. Since ODE model for P2 is not as good as the one for T3, we will only conduct stochastic model for the T3 design.

Construction

New model needs new equations. In stochastic model, the equations should represent more elementary reactions. So we split the 13 equations in our deterministic model into 29 more elementary ones. Here we'll demonstrate these equations, without much explaination. If you're confused by some equations, please visit ODE page, on which there're detailed explainations for each equation we used.

EquationsRemark
d[tRNA]/dt=Synthesis of tRNA
Degradation of tRNA
Transformation from tRNA to Aa-tRNA
Degradation of Aa-tRNA (Aa-tRNA->tRNA)
Dilution of Aa-tRNA
Transcription of T7RNAP
Degradation of T7RNAP
AND Gate 1
Degradation of T7RNAP protein
Transcription of trigger CI
Transcription of Bistable CI
Degradation of trigger CI mRNA
Degradation of bistable CI mRNA
Translation of trigger CI mRNA
Translation of bistable CI mRNA
Degradation of CI protein
Transcription of CI434
Degradation of CI434 mRNA
Translation of CI434 mRNA
Degradation of CI434 mRNA
Transcription of T3
Degradation of T3 mRNA
AND Gate 2
Degradation of T3
Transcription of GFP - OR Gate
Transcription of GFP - AND Gate - OR Gate
Degradation of GFP mRNA
Translation of GFP mRNA
Degradation of GFP

Parameters

Result



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