Team:MIT tmodel

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	<dt><b>Bacteria</b></dt>
	<dd>
		<ul>
                        <li><a href="https://2010.igem.org/Team:MIT_toggle">Overview</a></li>
                        <li><a href="https://2010.igem.org/Team:MIT_tmodel">Modelling</a></li>
			<li><a href="https://2010.igem.org/Team:MIT_tconst">Toggle Construction</a></li>
			<li><a href="https://2010.igem.org/Team:MIT_composite">Characterization</a></li>
		</ul>
	</dd>
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	<dt><b>Phage</b></dt>

	<dd>
		<ul>
<li><a href="https://2010.igem.org/Team:MIT_phage">Introduction</a></li>
<li><a href="https://2010.igem.org/Team:MIT_phage_background">Background</a></li>
<li><a href="https://2010.igem.org/Team:MIT_phage_design">Design</a></li>
<li><a href="https://2010.igem.org/Team:MIT_phage_construction">Construction</a></li>
<li><a href="https://2010.igem.org/Team:MIT_phage_results">Results</a></li>
<li><a href="https://2010.igem.org/Team:MIT_phage_context">Context</a></li>

		</ul>
	</dd>
	<dt><b>Mammalian</b></dt>

	<dd>
		<ul>
                        <li><a href="https://2010.igem.org/Team:MIT_mammalian">Overview</a></li>
			<li><a href="https://2010.igem.org/Team:MIT_mammalian_Standard">New Mammalian Standard </a></li>
                        <li><a href="https://2010.igem.org/Team:MIT_mammalian_Circuit">Circuit Design</a></li>
			<li><a href="https://2010.igem.org/Team:MIT_mammalian_Mechanosensation"> Mechanosensation</a></li>
			<li><a href="https://2010.igem.org/Team:MIT_mammalian_Bone"> Bone Formation</a></li>
			<li><a href="https://2010.igem.org/Team:MIT_mammalian_Switch"> Synthetic Switch</a></li>

		</ul>
	</dd>
	
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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 width=45% src= "https://static.igem.org/mediawiki/2010/c/c3/AYBallin.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>
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<tr><td>

<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>
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<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>

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<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>
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<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>
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