Team:KULeuven/Model/Reset

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=== Simulation ===
=== Simulation ===
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Remark: up to date with latest version?
The number lactonase genes is held constant during the entire simulation. For the first 15.000 seconds the number of mRNA Ribokey is equal to 0.015 and the number of pT7 molecules to 0.4, then for 15000 s these numbers are set on 6 and 3 respectively (based on the results of the model of the filter) after which they are reduced back to 0.015 and 0.4. <br>
The number lactonase genes is held constant during the entire simulation. For the first 15.000 seconds the number of mRNA Ribokey is equal to 0.015 and the number of pT7 molecules to 0.4, then for 15000 s these numbers are set on 6 and 3 respectively (based on the results of the model of the filter) after which they are reduced back to 0.015 and 0.4. <br>
We see that an increase in the number of mRNA Ribokey and pT7(due to an increase in light intensity) will lead to a much higher number of lactonase molecules.
We see that an increase in the number of mRNA Ribokey and pT7(due to an increase in light intensity) will lead to a much higher number of lactonase molecules.
[[Image:Sim_lactonaseproduction_1.png|700px|center]]
[[Image:Sim_lactonaseproduction_1.png|700px|center]]

Revision as of 09:22, 17 August 2008

  dock/undock dropdown  

Logo reset.jpg

Contents

Pulse Generator

Position in the system

Describing the system

Pulse Generator BioBrick.jpg

ODE's

Parameters

Parameter values (Pulse Generator)
Name Value Comments Reference
Degradation rates
dRNA_cI 0.00462 s-1
dcI 7.0E-4 s-1 link
dRNA_Lac 0.00231 s-1
dLac 2.888E-4 s-1
dRNA_Ribokey:cI 0.00231 s-1
Dissociation constants
KRibokey:cI 0.00212 kass/kdiss for the Ribokey cI complex
KcI 0.00337 binding cI on cI-Promotor link
Transcription rates
kRNA_cI 0.025 s-1 maximal transcription rate RNA cI (no cI repressor present)
kRNA_Lac 0.025 s-1
Translation rates
kcI 0.167 s-1
kLac 0.167 s-1 RBS is B0032 (efficiency 0.3) link
Hill cooperativity
ncI 2.0 link

Models

CellDesigner (SBML file)

Pulse Generator

Matlab

Pulse Generator Matlab.jpg

Constant Lactonase Production

Pictogram lactonaseproduction.png

Position in the system

The Constant Lactonase Production-system is directly linked to the Filter.

When the filter indicates that the input is zero (there is no light), the system will (ideally) produce no lactonase. As soon as the output of the filter is one, the system starts producing lactonase and remains doing this untill the light goes off again.

Describing the system

Modeling Reset.PNG

ODE's

Parameters

Parameter values Constant Lactonase Production
Name Value Comments Reference
Degradation Constants
dlactonase 2.888E-4 s-1
dclosed_mRNA_lactonase 0.0046209812 s-1 link
dopen_mRNA_lactonase 0.0023104906 s-1 link
dopen_mRNA_lactonase_complex 0.0023104906 s-1 link
Transcription Rates
kmRNA_lactonase 0.03 s-1
Translation Rates
klactonase 0.1666667 s-1 RBS is B0032 (efficiency of 0.3)
Equilibrium constants
Keq_1 0.015 closed and open mRNA
Keq_2 0.0212 M closed and key (binded with ribokey) complex mRNA
Association/Dissociation/Reaction Rates
kass (closed mRNA lactonase + mRNA Ribokey) 2.12 s-1
kdiss (closed mRNA lactonase + mRNA Ribokey) 100 s-1
k (open mRNA lactonase) 1.5 s-1
k (closed mRNA lactonase) 100 s-1

Models

CellDesigner (SBML file)

LactonaseProduction CellDesigner.png

Matlab (SBML file)

Remark: not yet up to date to latest (final) version

LactonaseProduction Matlab.jpg

Simulation

Remark: up to date with latest version?

The number lactonase genes is held constant during the entire simulation. For the first 15.000 seconds the number of mRNA Ribokey is equal to 0.015 and the number of pT7 molecules to 0.4, then for 15000 s these numbers are set on 6 and 3 respectively (based on the results of the model of the filter) after which they are reduced back to 0.015 and 0.4.
We see that an increase in the number of mRNA Ribokey and pT7(due to an increase in light intensity) will lead to a much higher number of lactonase molecules.

Sim lactonaseproduction 1.png