Team:KULeuven/Model/Filter

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Pictogram filter.png

Contents

Filter

Position in the system

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 can be enhanced to 0.3%-14% (todo: Jonas/Dries)

Models

CellDesigner (SBML file)

filter

Matlab (SBML file)

Matlab diagram for the filter system:

Filter Matlab.jpg


Simulations

filter

Discussion of the simulation:

1. AND gate of the filter

 ribokey (dark blue) --> T7 (red)--> |
     |                               | --> lactonase (blue)
     |-----------------------------> |


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