Team:NTU-Taida/Modeling/Parameters

From 2012.igem.org

(Difference between revisions)
(Fatty Acid Reaction Absorption Model Model)
(Cell-Cell Communication Model)
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==Cell-Cell Communication Model==
==Cell-Cell Communication Model==
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width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;background:#F2F2F2; padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><b><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Parameter</span></b></p>
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<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" width="502" style="margin-left:.65pt;border-collapse:collapse;mso-table-layout-alt:fixed;
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width="260" style="width:194.85pt;border:solid #AAAAAA 1.0pt;border-left: none;background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><b><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Description&nbsp;</span></b></p>
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mso-yfti-tbllook:1184;mso-padding-alt:0cm 1.4pt 0cm 1.4pt">
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width="104" style="width:77.95pt;border:solid #AAAAAA 1.0pt;border-left: none;background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><b><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Value&nbsp;</span></b></p>
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  <tbody><tr style="mso-yfti-irow:0;mso-yfti-firstrow:yes;height:17.25pt">
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width="66" style="width:49.6pt;border:solid #AAAAAA 1.0pt;border-left:none; background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><b><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Reference</span></b></p>
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  <td width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;background:#F2F2F2;
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|- style="mso-yfti-irow:1;height:17.25pt"
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  padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">cd</span></p>
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  <p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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width="260" style="width:194.85pt;border-top:none;border-left:none; border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><i><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; background-position: initial initial; background-repeat: initial initial; ">E. coli</span></i><span class="apple-converted-space"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; background-position: initial initial; background-repeat: initial initial; ">&nbsp;</span><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; background-position: initial initial; background-repeat: initial initial; ">Cell Density</span><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; "></span></span></p>
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  新細明體;mso-font-kerning:0pt">Parameter<o:p></o:p></span></b></p>
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width="104" style="width:77.95pt;border-top:none;border-left:none; border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">0.1</span></p>
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  </td>
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width="66" style="width:49.6pt;border-top:none;border-left:none;border-bottom: solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;background:#F9F9F9; padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><span lang="EN-US">&nbsp;</span></p>
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  <td width="260" style="width:194.85pt;border:solid #AAAAAA 1.0pt;border-left:
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|- style="mso-yfti-irow:2;height:17.25pt"
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  none;background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">D<sub>FA</sub></span></p>
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  <p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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width="260" style="width:194.85pt;border-top:none;border-left:none; border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">FA </span><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; background-position: initial initial; background-repeat: initial initial; ">Diffusion Constant</span><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; "></span></p>
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  新細明體;mso-font-kerning:0pt">Description&nbsp;<o:p></o:p></span></b></p>
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width="104" style="width:77.95pt;border-top:none;border-left:none; border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">6.46* 10^-10m^2 /s</span></p>
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  </td>
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width="66" style="width:49.6pt;border-top:none;border-left:none;border-bottom: solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;background:#F9F9F9; padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" |
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  <td width="104" style="width:77.95pt;border:solid #AAAAAA 1.0pt;border-left:
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|- style="mso-yfti-irow:3;height:17.25pt"
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  none;background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">D<sub>AHL</sub></span></p>
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  <p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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width="260" style="width:194.85pt;border-top:none;border-left:none; border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">AHL Diffusion Constant</span></p>
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  新細明體;mso-font-kerning:0pt">Value&nbsp;<o:p></o:p></span></b></p>
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width="104" style="width:77.95pt;border-top:none;border-left:none; border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">4.9e-6 cm2/s</span></p>
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  </td>
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width="66" style="width:49.6pt;border-top:none;border-left:none;border-bottom: solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;background:#F9F9F9; padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">[9]</span></p>
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  <td width="66" style="width:49.6pt;border:solid #AAAAAA 1.0pt;border-left:none;
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|- style="mso-yfti-irow:4;mso-yfti-lastrow:yes;height:17.25pt"
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  background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">γAHL,ext</span></p>
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  <p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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width="260" style="width:194.85pt;border-top:none;border-left:none; border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">AHL cell-external degradation</span></p>
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  新細明體;mso-font-kerning:0pt">Reference<o:p></o:p></span></b></p>
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width="104" style="width:77.95pt;border-top:none;border-left:none; border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt; background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">8.0225e-006/s</span></p>
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  </td>
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width="66" style="width:49.6pt;border-top:none;border-left:none;border-bottom: solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;background:#F9F9F9; padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt" | <p class="MsoNormal" align="center" style="text-align:center;mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Derived from 1
+
  </tr>
-
day half-life at pH 7&nbsp;<a href="http://2011.igem.org/Team:ETH_Zurich/Modeling/References#Ref7" title="Team:ETH Zurich/Modeling/References"><span style="color:black;
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<tr style="mso-yfti-irow:1;height:17.25pt">
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text-decoration:none;text-underline:none">[7]</span></a></span></p>
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">cd<o:p></o:p></span></p>
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----
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 +
  <p class="MsoNormal"><i><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; background-position: initial initial; background-repeat: initial initial; ">E.
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  coli</span></i><span class="apple-converted-space"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; background-position: initial initial; background-repeat: initial initial; ">&nbsp;</span></span><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; background-position: initial initial; background-repeat: initial initial; ">Cell Density</span><span lang="EN-US" style="font-size:
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  10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:新細明體;
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  mso-font-kerning:0pt"><o:p></o:p></span></p>
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  </td>
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">0.1<o:p></o:p></span></p>
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  </td>
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  <td width="66" style="width:49.6pt;border-top:none;border-left:none;border-bottom:
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  <p class="MsoNormal"><span lang="EN-US">&nbsp;</span></p>
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  </td>
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  </tr>
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<tr style="mso-yfti-irow:2;height:17.25pt">
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  <td width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none;
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  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">D<sub>FA</sub><o:p></o:p></span></p>
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  </td>
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  <td width="260" style="width:194.85pt;border-top:none;border-left:none;
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
  新細明體;mso-font-kerning:0pt">FA </span><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; background-position: initial initial; background-repeat: initial initial; ">Diffusion Constant</span><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;
 +
  mso-fareast-font-family:新細明體;mso-font-kerning:0pt"><o:p></o:p></span></p>
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  </td>
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  <td width="104" style="width:77.95pt;border-top:none;border-left:none;
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  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">6.46* 10^-10m^2 /s<o:p></o:p></span></p>
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  </td>
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  <td width="66" style="width:49.6pt;border-top:none;border-left:none;border-bottom:
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  </tr>
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<tr style="mso-yfti-irow:3;height:17.25pt">
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  <td width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none;
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  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">D<sub>AHL</sub><o:p></o:p></span></p>
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  </td>
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  <td width="260" style="width:194.85pt;border-top:none;border-left:none;
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  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
  新細明體;mso-font-kerning:0pt">AHL Diffusion Constant<o:p></o:p></span></p>
 +
  </td>
 +
  <td width="104" style="width:77.95pt;border-top:none;border-left:none;
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  border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">4.9e-6 cm2/s<o:p></o:p></span></p>
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  </td>
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  <td width="66" style="width:49.6pt;border-top:none;border-left:none;border-bottom:
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">[9]<o:p></o:p></span></p>
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  </td>
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  </tr>
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<tr style="mso-yfti-irow:4;mso-yfti-lastrow:yes;height:17.25pt">
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  <td width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none;
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  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">γAHL,ext<o:p></o:p></span></p>
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  </td>
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  <td width="260" style="width:194.85pt;border-top:none;border-left:none;
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">AHL cell-external degradation<o:p></o:p></span></p>
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  </td>
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  <td width="104" style="width:77.95pt;border-top:none;border-left:none;
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  border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;
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  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">8.0225e-006/s<o:p></o:p></span></p>
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  </td>
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  <td width="66" style="width:49.6pt;border-top:none;border-left:none;border-bottom:
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  <p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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  新細明體;mso-font-kerning:0pt">Derived from 1 day half-life at pH 7&nbsp;</span><span lang="EN-US"><a href="http://2011.igem.org/Team:ETH_Zurich/Modeling/References#Ref7" title="Team:ETH Zurich/Modeling/References"><span style="font-size:10.0pt;
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  font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:新細明體;color:windowtext;
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==Reference==
==Reference==

Revision as of 02:21, 27 September 2012

Contents

Single-Cell/ System analysis Model

Parameter

Description 

Value 

Reference

αTetR

TetR max. production rate

0.8 μM/min

[5]

αFadR

FadR max. production rate

100 μM/min

a.

αGLP-1

GLP-1 max. production rate

1.23 μM/min

a.

αLacI

LacI max. production rate

0.8 μM/min

[1]

ks1

AHLi production rate

0.01 1/min

[2]

ρR

LuxR-AHL dimerization rate

0.5 1/(μM3*min)

[1]

βTetR

TetR repression coefficient

0.13 μM

a.

βFA

FA repression coefficient

10 μM

[1]

βFadR

FadR repression coefficient

0.13 μM

[1]

βLacI

LacI repression coefficient

0.8 μM

[1]

βR

LuxR-AHL repression coefficient

0.01 μM

[1]

γTetR

TetR degradation rate

0.0692 1/min

a.

γLacI

LacI degradation rate

0.0231 1/min

[1]

γGLP-1

GLP-1 degradation rate

0.0731/min

[1]

γLuxI

LuxI degradation rate

0.0167 1/min

[3]

ks0

AHLi degradation rate

1 1/min

[2]

kse

AHLe degradation rate

1 1/min

[2]

γR

LuxR-AHL degradation rate

0.0231 1/min

[1]

γRFP

RFP degradation rate

0.0041 1/min

[4]

n1

FadR cooperativity coefficient

3

a.

n2

FA cooperativity coefficient

2

a.

n3

LuxR-AHL cooperativity coefficient

3

[1]

n5

TetR cooperativity coefficient

2

[2]

n6

LacI cooperativity coefficient

4

[1]

η

AHL Diffusion rate across the cell membrane

2

[2]

ηext

Average diffusion rate for all cells

1

[2]

Fatty Acid Reaction Absorption Model Model

Parameter

Description 

Value 

Reference

[E]t

Total active enzyme

50 uM

[8]

Km

Reaction rate constant

47.9

[6][7]

DFA

FA Diffusion Constant

6.46*10­-10m2/s

 

d

Thickness of the unstirred water layer

190 um

[9]

Kcat/ molecular weight

Catalytic Rate constant

1.8*10^-3

[6][7]

Cell-Cell Communication Model

Parameter

Description 

Value 

Reference

cd

E. coli Cell Density

0.1

 

DFA

FA Diffusion Constant

6.46* 10^-10m^2 /s

DAHL

AHL Diffusion Constant

4.9e-6 cm2/s

[9]

γAHL,ext

AHL cell-external degradation

8.0225e-006/s

Derived from 1 day half-life at pH 7 [7]

Reference

Source

[1]

Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A synthetic multicellular system for programmed pattern formation, Nature Vol. 434, 2005

[2]

Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004

[3]

MIT igem 2010

[4]

Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott, Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts, Cytometry Part A, Volume 71A Issue 10, 2007

[5]

Wilfried Weber, Markus Rimann, Manuela Spielmann, Bettina Keller, Marie Daoud-El Baba, Dominique Aubel, Cornelia C Weber & Martin Fussenegger, Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology, volume 22, number 11, 2004

[6]

Sulaiman Al-Zuhair, Masitah Hasan, K.B. Ramachandran, Kinetics of the enzymatic hydrolysis of palm oil by lipase, Process Biochemistry

Volume 38, Issue 8, 2003

[7]

Ho-Shing Wu, Ming-Ju Tsai, Kinetics of tributyrin hydrolysis by lipase, Enzyme and Microbial Technology, Volume 35, Issues 6–7, 2004

[8]

Bengt Borgstrom, Luminal Digestion of Fats, Handbook of Physiology, The Gastrointestinal System, Intestinal Absorption and Secretion, 1991

[9]

Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake of short- and medium-chain fatty acids and alcohols, Journal of Lipid Research, 1973