Team:KULeuven/Model/Filter

From 2008.igem.org

(Difference between revisions)
(Simulations)
Line 103: Line 103:
[[Image:Sim_filter_1.png|800px|center|filter]]
[[Image:Sim_filter_1.png|800px|center|filter]]
 +
Discussion of the simulation:
 +
 +
1. AND gate of the filter
 +
 +
  ribokey --> T7 --> |
 +
    |                | --> lactonase
 +
    |--------------> |
 +
 +
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 ===
=== Sensitivity Analysis ===
[[Image:Sens Filter.png|center]]
[[Image:Sens Filter.png|center]]

Revision as of 10:21, 14 August 2008

  dock/undock dropdown  

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 --> T7 --> |
   |                | --> lactonase
   |--------------> |

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