Team:MIT tmodel

From 2010.igem.org

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Latest revision as of 02:25, 28 October 2010

Bacteria

Phage

Mammalian

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
C₂	1.25	ColE1 origin with copy number ~15	Link Origin of Replication
g_luxI	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
g_GFP	2.14 x 10^-4 min^-1	Degradation rate of GFP protein	Registry of Standard Biological Parts:BBa_E0040
g_AHL	1 x 10^-2 min^-1	Degradation rate of AHL molecule	A synthetic multicellular system for programmed pattern formation
D_A	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
k_Rp	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
g_luxR	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
n_LuxR	1.6	Hill coefficient of LuxR	KULeuven 2008
n_lacI	2	Hill coefficient of lacI	Aberdeen 2009
n_cI	2	Hill coefficient of cI	Aberdeen 2009
k_M	700	Dissociation constant	Unknown(varies)
g_mCherry	.04 hr^-1	Degradation rate of mCherry protein	Pattern Formation in a Synthetic Bacterial Population
l_n	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
k_cells	.15 hr^-1	Rate of cell growth	Pattern Formation in a Synthetic Bacterial Population

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 <tr><td><div class="bodybaby">fluorescence propagation model</div></td>
 <tr><td>
-<a href="https://static.igem.org/mediawiki/2010/c/c3/AYBallin.gif" class="thickbox" title="Point source propagation model."><img src= "https://static.igem.org/mediawiki/2010/c/c3/AYBallin.gif"></a>
+<a href="https://static.igem.org/mediawiki/2010/c/c3/AYBallin.gif" class="thickbox" title="Point source propagation model."><img width=45% src= "https://static.igem.org/mediawiki/2010/c/c3/AYBallin.gif"></a>
-<a href="https://static.igem.org/mediawiki/2010/9/90/W.gif" class="thickbox" title="Angular wave model."><img src= "https://static.igem.org/mediawiki/2010/9/90/W.gif"></a>
+<a href="https://static.igem.org/mediawiki/2010/d/de/LuxGif.gif" class="thickbox" title="MIT fluorescence model."><img width=45% src= "https://static.igem.org/mediawiki/2010/d/de/LuxGif.gif"></a>
 </tr></td>
 <tr><td>
-<a href="https://static.igem.org/mediawiki/2010/d/de/LuxGif.gif" class="thickbox" title="Point source propagation model."><img src= "https://static.igem.org/mediawiki/2010/d/de/LuxGif.gif"></a>
-<a href="https://static.igem.org/mediawiki/2010/3/3a/Diagonal.gif" class="thickbox" title="Diagonal  model."><img src= "https://static.igem.org/mediawiki/2010/3/3a/Diagonal.gif"></a>
+<a href="https://static.igem.org/mediawiki/2010/3/3a/Diagonal.gif" class="thickbox" title="Diagonal model."><img width=45% src= "https://static.igem.org/mediawiki/2010/3/3a/Diagonal.gif"></a>
+<a href="https://static.igem.org/mediawiki/2010/9/90/W.gif" class="thickbox" title="Angular wave model."><img width=45% src= "https://static.igem.org/mediawiki/2010/9/90/W.gif"></a>
 </tr></td>
-https://static.igem.org/mediawiki/2010/d/de/LuxGif.gif
+<tr><td><div class="bodybaby">propagation differential equations</div></td>
+<tr><td>
+<b class="bolded" id="model">
+To view our preliminary differential equations and learn more about the background behind AHL diffusion dynamics, please click <a href="https://static.igem.org/mediawiki/2010/c/c1/Summary.pdf">here</a>. To learn about our modelling effort in mammalian cells, please click <a href="https://static.igem.org/mediawiki/2010/e/e0/Mammalian_Full_Toggle.pdf">here</a>.</b>
+<br><br><br>
-https://2010.igem.org/Image:W.gif
+<a href="https://static.igem.org/mediawiki/2010/7/79/Dynamical_Equations.png" class="thickbox" title="Updated differential equations for AHL/Fluorescence propagation."><img width=100% src= "https://static.igem.org/mediawiki/2010/7/79/Dynamical_Equations.png"></a>
-Image:Diagonal.gif
+</td><tr><td>
-Image:LuxMIT.gif
-<tr><td><div class="bodybaby">propagation differential equations</div></td>
+<div class="bodybaby">Modeling Parameters</div><br>
+<table style="background:#f0f0f0;"><tr><td style="text-align:center;"><strong>Parameter</strong></td>
+<td style="text-align:center;"><strong>Value</strong></td>
+<td style="text-align:center;"><strong>Description</strong></td>
+<td style="text-align:center;"><strong>Reference</strong></td>
+<tr><td>
+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>
+<tr><td>
+ 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>
+<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>
+<tr><td>
+ 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>
+<tr><td>
+ 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>
+<tr><td>
+ 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>
+<tr><td>
+ 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>
+<tr><td>
+ 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>
+<tr><td>
+ n<sub>LuxR<sub> </td><td> 1.6 </td><td>Hill coefficient of LuxR </td><td><a  href="https://2008.igem.org/team:kuleuven iGEM 2008 KULeuven">KULeuven 2008</a></td>
+<tr><td>
+ n<sub>lacI<sub> </td><td> 2</td><td> Hill coefficient of lacI </td><td><a  href="https://2009.igem.org/Team:Aberdeen_Scotland/parameters">Aberdeen 2009</a>  </td>
+<tr><td>
+ n<sub>cI<sub> </td><td> 2 </td><td> Hill coefficient of cI</td><td><a href="https://2009.igem.org/Team:Aberdeen_Scotland/parameters">Aberdeen 2009</a></td>
+<tr><td>
+ k<sub>M<sub> </td><td>700 </td><td>Dissociation constant </td><td> Unknown(varies) </td>
+<tr><td>
+ 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>
+<tr><td>
+ 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>
+<tr><td>
+ 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>
+</table>
+</td>
 </table>