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Team:KULeuven/Model/Output
From 2008.igem.org
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates | ! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates | ||
|- | |- | ||
| - | | d<sub> | + | | d<sub>GFP</sub> |
| - | | | + | | d<sub>LVA</sub> = 2.814E-4 s<sup>-1</sup> |
| - | | | + | | LVA-tag reduces lifetime to 40 minutes |
| [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] | | [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] | ||
|- | |- | ||
| - | | d<sub> | + | | d<sub>mRNA_GFP</sub> |
| 0.0023 s<sup>-1</sup> | | 0.0023 s<sup>-1</sup> | ||
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates | ! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates | ||
|- | |- | ||
| - | | | + | | TetR_var_transcr_rate |
| - | + | | p(TetR) dependent | |
| + | | between 5E-5 and 0.0125 s<sup>-1</sup> ~ [aTc] | ||
| | | | ||
| - | |||
|- | |- | ||
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates | ! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates | ||
|- | |- | ||
| - | | k<sub> | + | | k<sub>B0032</sub> |
| 0.167 s<sup>-1</sup> | | 0.167 s<sup>-1</sup> | ||
| - | | | + | | translation rate for B0032 RBS (0.3 relative efficiency) |
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Revision as of 09:58, 27 August 2008
Contents |
Output
Position in the system
The output system is one of three modules directly linked to the input. The output system is a simple gene regulation, of which transcription is activated by tetR. The output signal is GFP (green fluorescent protein).
In the applied project of dealing with Crohn's disease this would be replaced by the drug necessary to cure the local inflammation. The drug concentration would be proportional to the amount of local inflammation sensed.
Describing the system
see also: Project:Output
ODE's
Parameters
| Name | Value | Comments | Reference |
|---|---|---|---|
| Degradation Rates | |||
| dGFP | dLVA = 2.814E-4 s-1 | LVA-tag reduces lifetime to 40 minutes | [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters link] |
| dmRNA_GFP | 0.0023 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| Transcription Rates | |||
| TetR_var_transcr_rate | p(TetR) dependent | between 5E-5 and 0.0125 s-1 ~ [aTc] | |
| Translation Rates | |||
| kB0032 | 0.167 s-1 | translation rate for B0032 RBS (0.3 relative efficiency) | |
Models
CellDesigner (SBML file)
Matlab (SBML file)
Simulations
Several simulations were conducted, the following two show the transient respons and eventual saturation of the output system to a low and a high step signal as input, respectively. We see that there is a great distinction in the number of CFP molecules between the two input signals.
Next figure shows the switching behaviour of the output system to an light signal turning off and on:
Sensitivity Analysis
