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Team:KULeuven/Model/Inverter
From 2008.igem.org
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=== Simulations === | === Simulations === | ||
| + | Remark: simulation is not from latest version. | ||
[[Image:Sim_inverter_1.png|800px|center|filter]] | [[Image:Sim_inverter_1.png|800px|center|filter]] | ||
Revision as of 09:20, 17 August 2008
dock/undock dropdown
Contents |
Inverter
Position in the system
The inverter part receives its input from the filter, T7. The inverter's function is to produce HSL when no light is present, so a low T7 input gives rise to a high HSL output and vice versa. A high output of HSL will be used in the cell death part to produce CcdB, meaning that the cell will start a timer and eventually die off if no light remains present.
Describing the system
ODE's
Parameters
| Name | Value | Comments | Reference |
|---|---|---|---|
| Degradation Rates | |||
| dLuxI | 0.00231 s-1 | ||
| dRNA_LuxI | 0.0025 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dLuxI_antimRNA | 0.00125 s-1 | ||
| dLacI | 0.00231 s-1 | [http://www.biophysj.org/cgi/content/full/89/6/3873?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=89&firstpage=3873&resourcetype=HWCIT link] | |
| dLacI (closed mRNA) | 0.0046209812 s-1 | estimate: because this mRNA isn't translated, it degrades faster | |
| dLacI (open mRNA) | 0.0023104906 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dLacI_mRNA (open complex) | 0.0023104906 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dHSL | 1.02E-6 s-1 | [http://aem.asm.org/cgi/content/abstract/71/3/1291 link] | |
| Dissociation Rates | |||
| KmRNA_LuxI:antisense_mRNA | 4.22E14 | Complex of LuxI mRNA with antisense mRNA | |
| Transcription Rates | |||
| kmRNA_LacI | 0.0011 s-1 | ||
| kmRNA_LuxI | 0.0025 s-1 | ||
| Hill Cooperativity | |||
| KLuxI | 1.0E-10 s-1 | ||
| nLuxI | 2.0 | ||
| kmaxT7 | 0.044 s-1 | [http://www.jbc.org/cgi/content/full/279/5/3239#FIG2 link] | |
| nT7 | 1 | ||
| Translation Rates | |||
| kLuxI | 0.167 s-1 | RBs is B0032 (efficiency 0.3) | |
| kLacI | 0.167 s-1 | RBS is situated in the keylock | |
| kT7 | 182 s-1 | ||
| Equilibrium Constants | |||
| KmRNA_LacI | 0.015 | equilibrium between open and closed mRNA LacI | |
| KmRNA_LacI_Key | 0.0212 /M | equilibrium between closed mRNA LacI and complex of mRNA with keymRNA | |
| Reaction Rates | |||
| kLuxI:HSL | 0.0167 s-1 | [http://www.pnas.org/content/93/18/9505.full.pdf+html link Vmax] | |
Models
CellDesigner (SBML file)
Matlab (SBML file)
Remark: not yet up to date to latest (final) version
Simulations
Remark: simulation is not from latest version.
Sensitivity Analysis
