Team:KULeuven/Model/Filter

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==== Matlab ([https://static.igem.org/mediawiki/2008/c/ce/Filter_Matlab.zip SBML file])====
==== Matlab ([https://static.igem.org/mediawiki/2008/c/ce/Filter_Matlab.zip SBML file])====
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Matlab diagram for the filter system:
 
[[Image:Filter_Matlab.jpg|center]]
[[Image:Filter_Matlab.jpg|center]]
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=== Simulations ===
=== Simulations ===

Revision as of 09:19, 17 August 2008

  dock/undock dropdown  

Pictogram filter.png

Contents

Filter

Position in the system

todo

Describing the system

Filter BioBrick.jpg

ODE's

Parameters

Parameter values Filter
Name Value Comments Reference
Degradation rates
dpT7_tag 0.00155 s-1 tag added to speed up degradation of otherwise too stable T7 polymerase link
dmRNA_RIBOKEY 0.00462 s-1 link
dclosed_mRNA_T7 0.00462 s-1 link
dopen_mRNA_T7 0.00231 s-1 link
dopen_mRNA_T7_complex 0.00231 s-1 link
Equilibrium constants
Keq_1 0,015 [M] closed and open mRNA
Keq_2 0.0212 [M] closed and key (binded with ribokey) complex mRNA
Transcription rates
kmRNA_RIBOKEY Input dependent
kmRNA_T7 0,0011 s-1

Remark: The key-lock system can be enhanced to 0.3%-14% (todo: Jonas/Dries)

Models

CellDesigner (SBML file)

filter

Matlab (SBML file)

Filter Matlab.jpg

Simulations

filter

Discussion of the simulation:

1. AND gate of the filter

Filter 1.PNG

In the simulation we can clearly see this series of events:

  • when dark blue(ribokey) starts to increase, red (T7) also starts to increase, giving rise to an increasing amount of lactonase (blue) = AND-GATE.
  • when dark blue(ribokey) starts to decrease, red (T7) also starts to decrease, but much slower. The lactonase also starts to decrease, as it should be.

The short lifetime of the ribokey compared to the lifetime of the T7-protein, guarantees that the AND-GATE always works perfectly fine: when there's no more input, the ribokey will rapidly decrease (and disappear) and makes sure that the AND-GATE is not activated anymore, even when the T7-protein is slowly decreasing.


2. Filtering in practice

  • First Lightpulse: 300s
    • small peak of lactonase
    • no influence on the timer
  • Second Lightpulse: 1000s
    • medium peak of lactonase
    • influences the timer by levelling the timing capabilities, but it doesn't reset the timer
  • Third Lightpulse: 5000s
    • huge peak of lactonase
    • reset of the timer: amount of complex goes to zero

Sensitivity Analysis

Sens Filter.png