Team:KULeuven/Model/Filter

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Pictogram filter.png

Contents

Filter

Position in the system

The filter is positioned immediately after the input, because its job is to filter out possible noise signals or background signals that aren't caused by the "desease". It is the starting piece of the whole system, situated before the invertimer- and the reset-subsystem.

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 [http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation link]
dmRNA_RIBOKEY 0.00462 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dclosed_mRNA_T7 0.00462 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dopen_mRNA_T7 0.00231 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dopen_mRNA_T7_complex 0.00231 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf 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 has been enhanced to 0.3%-14% (todo: new parameters will be added in a new overview)

Models

CellDesigner (SBML file)

filter

Matlab (SBML file)

Filter Matlab.jpg

Simulations

filter
Filter 1.PNG

1. AND gate of the filter

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
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