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Team:KULeuven/Model/Filter
From 2008.igem.org
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Contents |
Filter
Position in the system
Describing the system
ODE's
Parameters
| 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)
Matlab (SBML file)
Matlab diagram for the filter system:
Simulations
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
