Team:MIT tmodel

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<a href="http://2010.igem.org/wiki/images/7/79/Dynamical_Equations.png" class="thickbox" title="Updated differential equations for AHL/Fluorescence propagation."><img width=100% src= "http://2010.igem.org/wiki/images/7/79/Dynamical_Equations.png"></a>
<a href="http://2010.igem.org/wiki/images/7/79/Dynamical_Equations.png" class="thickbox" title="Updated differential equations for AHL/Fluorescence propagation."><img width=100% src= "http://2010.igem.org/wiki/images/7/79/Dynamical_Equations.png"></a>
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<div class="bodybaby">Modeling Parameters</div><br>
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<table style="background:#f0f0f0;"><tr><td style="text-align:center;"><strong>Parameter</strong></td>
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<td style="text-align:center;"><strong>Value</strong></td>
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<td style="text-align:center;"><strong>Description</strong></td>
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<td style="text-align:center;"><strong>Reference</strong></td>
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C<sub>1<sub> </td><td>Normalized to 1 </td><td>p15A origin with copy number ~12 </td><td><a href="http://wolfson.huji.ac.il/expression/vector/origin.html">Link</a> Origin of Replication  </td>
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C<sub>2<sub></td><td>1.25</td><td>ColE1 origin with copy number ~15</td><td><a href="http://wolfson.huji.ac.il/expression/vector/origin.html">Link</a> Origin of Replication </td>
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<tr><td> g<sub>luxI<sub> </td><td> 1.67 x 10<sup>-2</sup>  min<sup>-1<sup> </td><td> Degradation rate of LuxI protein </td><td> <a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347">Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants</a></td>
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g<sub>GFP<sub> </td><td> 2.14 x 10<sup>-4</sup> min<sup>-1<sup> </td><td> Degradation rate of GFP protein </td><td> <a href="http://partsregistry.org/Part:BBa_E0040"> Registry of Standard Biological Parts:BBa_E0040</a>    </td>
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g<sub>AHL<sub> </td><td> 1 x 10<sup>-2</sup> min<sup>-1<sup> </td><td>Degradation rate of AHL molecule </td><td><a href="http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html">A synthetic multicellular system for programmed pattern formation</a> </td>
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D<sub>A<sub> </td><td> 0.23s<sup>-1<sup></td><td> Diffusion coefficient of AHL </td><td> <a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347">Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants</a> </td>
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k<sub>Rp<sub> </td><td> 9.6 x 10<sup>-1</sup> min<sup>-1<sup> </td><td> Rate of Lux protein translation </td><td><a  href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347">Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants</a></td>
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g<sub>luxR<sub> </td><td> 2.31 x 10<sup>-2</sup> min<sup>-1<sup> </td><td> Degration rate of LuxR protein </td><td><a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347">Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants</a></td>
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n<sub>LuxR<sub> </td><td> 1.6 </td><td>Hill coefficient of LuxR </td><td><a  href="http://2008.igem.org/team:kuleuven iGEM 2008 KULeuven">KULeuven 2008</a></td>
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n<sub>lacI<sub> </td><td> 2</td><td> Hill coefficient of lacI </td><td><a  href="http://2009.igem.org/Team:Aberdeen_Scotland/parameters">Aberdeen 2009</a>  </td>
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n<sub>cI<sub> </td><td> 2 </td><td> Hill coefficient of cI</td><td><a href="http://2009.igem.org/Team:Aberdeen_Scotland/parameters">Aberdeen 2009</a></td>
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k<sub>M<sub> </td><td>700 </td><td>Dissociation constant </td><td> Unknown(varies) </td>
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g<sub>mCherry<sub> </td><td> .04 hr<sup>-1</sup>  </td><td>Degradation rate of mCherry protein </td><td> <a href="http://biomaps.rutgers.edu/Ting_Lu.pdfEmergent">Pattern Formation in a Synthetic Bacterial Population</a>      </td>
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l<sub>n<sub></td><td>  0.5-1 x 10<sup>-7</sup> cm2/s  </td><td> Leakiness of all proteins estimated as approximately equal to that of GFP </td><td><a href="http://www.ncbi.nlm.nih.gov/pubmed/10233100">Diffusion of green fluorescent protein in the aqueous-phase lumen of endoplasmic reticulum</a></td>
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k<sub>cells<sub></td><td> .15 hr<sup>-1</sup> </td><td> Rate of cell growth</td><td><a  href="http://biomaps.rutgers.edu/Ting_Lu.pdfEmergent">Pattern Formation in a Synthetic Bacterial Population</a>    </td>
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Latest revision as of 02:25, 28 October 2010

Bacteria
fluorescence propagation model
propagation differential equations
To view our preliminary differential equations and learn more about the background behind AHL diffusion dynamics, please click here. To learn about our modelling effort in mammalian cells, please click here.


Modeling Parameters

Parameter Value Description Reference
C1 Normalized to 1 p15A origin with copy number ~12 Link Origin of Replication
C21.25ColE1 origin with copy number ~15Link Origin of Replication
gluxI 1.67 x 10-2 min-1 Degradation rate of LuxI protein Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants
gGFP 2.14 x 10-4 min-1 Degradation rate of GFP protein Registry of Standard Biological Parts:BBa_E0040
gAHL 1 x 10-2 min-1 Degradation rate of AHL molecule A synthetic multicellular system for programmed pattern formation
DA 0.23s-1 Diffusion coefficient of AHL Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants
kRp 9.6 x 10-1 min-1 Rate of Lux protein translation Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants
gluxR 2.31 x 10-2 min-1 Degration rate of LuxR protein Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants
nLuxR 1.6 Hill coefficient of LuxR KULeuven 2008
nlacI 2 Hill coefficient of lacI Aberdeen 2009
ncI 2 Hill coefficient of cIAberdeen 2009
kM 700 Dissociation constant Unknown(varies)
gmCherry .04 hr-1 Degradation rate of mCherry protein Pattern Formation in a Synthetic Bacterial Population
ln 0.5-1 x 10-7 cm2/s Leakiness of all proteins estimated as approximately equal to that of GFP Diffusion of green fluorescent protein in the aqueous-phase lumen of endoplasmic reticulum
kcells .15 hr-1 Rate of cell growthPattern Formation in a Synthetic Bacterial Population