Team:NTU-Taida/Modeling/Parameters

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(Single-Cell/ System analysis Model)
(Cell-Cell Communication Model)
 
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==Single-Cell/ System analysis Model==
==Single-Cell/ System analysis Model==
<html>
<html>
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    <table>
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    <table class='table table-bordered table-condensed table-hover'>
       <thead>
       <thead>
         <tr>
         <tr>
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       <tbody>
       <tbody>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\alpha_{TetR} \) </td>
-
            \{\alpha_{TetR}\}
+
           <td> TetR max. production rate </td>
-
          </td>
+
           <td> \(0.8~\mu \text{M}\cdot\text{min}^{-1} \) </td>
-
           <td>
+
           <td> [5] </td>
-
            TetR max. production rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.8 &#206;&#188;M/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [5]
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-
 
+
-
          </td>
+
         </tr>
         </tr>
-
         <tr>
+
         <tr>  
-
           <td>
+
           <td> \(\alpha_{FadR} \) </td>
-
           
+
           <td> FadR max. production rate </td>
-
            &#206;&#177;<sub>FadR</sub>
+
           <td> \(100~\mu\text{M}\cdot\text{min}^{-1} \)</td>
-
 
+
           <td> a. </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            FadR max. production rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            100 &#206;&#188;M/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            a.
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\alpha_{GLP-1} \) </td>
-
           
+
           <td> GLP-1 max. production rate </td>
-
            &#206;&#177;<sub>GLP-1</sub>
+
           <td> \(1.23~\mu\text{M}\cdot\text{min}^{-1} \)</td>
-
 
+
           <td> a. </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            GLP-1 max. production rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            1.23 &#206;&#188;M/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            a.
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\alpha_{LacI} \) </td>
-
           
+
           <td> LacI max. production rate </td>
-
            &#206;&#177;<sub>LacI</sub>
+
           <td> \(0.8~\mu\text{M}\cdot\text{min}^{-1} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LacI max. production rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.8 &#206;&#188;M/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(k_{s1} \)</td>
-
           
+
           <td> AHL <sub>i</sub> production rate </td>
-
            k<sub>s1</sub>
+
           <td> \(0.01~\text{min}^{-1} \)</td>
-
 
+
           <td> [2] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            AHL<sub>i</sub> production rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.01 1/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [2]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\rho_R \) </td>
-
           
+
           <td> LuxR-AHL dimerization rate </td>
-
            &#207;<sub>R</sub>
+
           <td> \(0.5~\mu\text{M}^{-3}\cdot \text{min}^{-1} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LuxR-AHL dimerization rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.5 1/(&#206;&#188;M<sup>3</sup>*min)
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\beta_{TetR} \) </td>
-
           
+
           <td> TetR repression coefficient </td>
-
            &#206;&#178;<sub>TetR</sub>
+
           <td> \(0.13~\mu\text{M} \)</td>
-
 
+
           <td> a. </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            TetR repression coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.13 &#206;&#188;M
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            a.
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\beta_{FA} \) </td>
-
           
+
           <td> FA repression coefficient </td>
-
            &#206;&#178;<sub>FA</sub>
+
           <td> \(10~\mu\text{M} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            FA repression coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            10 &#206;&#188;M
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\beta_{FadR} \) </td>
-
           
+
           <td> FadR repression coefficient </td>
-
            &#206;&#178;<sub>FadR</sub>
+
           <td> \(0.13~\mu\text{M} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            FadR repression coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.13 &#206;&#188;M
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\beta_{LacI} \) </td>
-
           
+
           <td> LacI repression coefficient </td>
-
            &#206;&#178;<sub>LacI</sub>
+
           <td> \(0.8~\mu\text{M} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LacI repression coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.8 &#206;&#188;M
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\beta_R \) </td>
-
           
+
           <td> LuxR-AHL repression coefficient </td>
-
            &#206;&#178;<sub>R</sub>
+
           <td> \(0.01~\mu\text{M} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LuxR-AHL repression coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.01 &#206;&#188;M
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\gamma_{TetR} \) </td>
-
           
+
           <td> TetR degradation rate </td>
-
            &#206;&#179;<sub>TetR</sub>
+
           <td> \(0.0692~\text{min}^{-1} \)</td>
-
 
+
           <td> a. </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            TetR degradation rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.0692 1/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            a.
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\gamma_{LacI} \) </td>
-
           
+
           <td> LacI degradation rate </td>
-
            &#206;&#179;<sub>LacI</sub>
+
           <td> \(0.0231~\text{min}^{-1} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LacI degradation rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.0231 1/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\gamma_{GLP-1} \) </td>
-
           
+
           <td> GLP-1 degradation rate </td>
-
            &#206;&#179;<sub>GLP-1</sub>
+
           <td> \(0.0731~\text{min}^{-1} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            GLP-1 degradation rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.0731/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\gamma_{LuxI} \) </td>
-
           
+
           <td> LuxI degradation rate </td>
-
            &#206;&#179;<sub>LuxI</sub>
+
           <td> \(0.0167~\text{min}^{-1} \)</td>
-
 
+
           <td> [3] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LuxI degradation rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.0167 1/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [3]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(k_{s0} \) </td>
-
           
+
           <td> AHL<sub>i</sub> degradation rate </td>
-
            k<sub>s0</sub>
+
           <td> \(1~\text{min}^{-1} \)</td>
-
 
+
           <td> [2] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            AHL<sub>i</sub> degradation rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            1 1/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [2]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(k_{se} \) </td>
-
           
+
           <td> AHL<sub>e</sub> degradation rate </td>
-
            k<sub>se</sub>
+
           <td> \(1~\text{min}^{-1} \)</td>
-
 
+
           <td> [2] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            AHL<sub>e</sub> degradation rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            1 1/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [2]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\gamma_R \) </td>
-
           
+
           <td> LuxR-AHL degradation rate </td>
-
            &#206;&#179;<sub>R</sub>
+
           <td> \(0.0231~\text{min}^{-1} \)</td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LuxR-AHL degradation rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.0231 1/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\gamma_{RFP} \) </td>
-
           
+
           <td> RFP degradation rate </td>
-
            &#206;&#179;<sub>RFP</sub>
+
           <td> \(0.0041~\text{min}^{-1} \)</td>
-
 
+
           <td> [4] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            RFP degradation rate
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            0.0041 1/min
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [4]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(n_1\) </td>
-
           
+
           <td> FadR cooperativity coefficient </td>
-
            n<sub>1</sub>
+
           <td> \(3\) </td>
-
 
+
           <td> a. </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            FadR cooperativity coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            3
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            a.
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(n_2\) </td>
-
           
+
           <td> FA cooperativity coefficient </td>
-
            n<sub>2</sub>
+
           <td> \(2\) </td>
-
 
+
           <td> a. </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            FA cooperativity coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            2
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            a.
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(n_3\) </td>
-
           
+
           <td> LuxR-AHL cooperativity coefficient </td>
-
            n<sub>3</sub>
+
           <td> \(3\) </td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LuxR-AHL cooperativity coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            3
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(n_5\) </td>
-
           
+
           <td> TetR cooperativity coefficient </td>
-
            n<sub>5</sub>
+
           <td> \(2\) </td>
-
 
+
           <td> [2] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            TetR cooperativity coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            2
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [2]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(n_6\) </td>
-
           
+
           <td> LacI cooperativity coefficient </td>
-
            n<sub>6</sub>
+
           <td> \(4\) </td>
-
 
+
           <td> [1] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            LacI cooperativity coefficient
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            4
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [1]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\eta\) </td>
-
           
+
           <td> AHL Diffusion rate across the cell membrane </td>
-
            &#206;&#183;
+
           <td> \(2\) </td>
-
 
+
           <td> [2] </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            AHL Diffusion rate across the cell membrane
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            2
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [2]
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
         <tr>
         <tr>
-
           <td>
+
           <td> \(\eta\)<sub>ext</sub> </td>
-
           
+
           <td> Average diffusion rate for all cells </td>
-
            &#206;&#183;<sub>ext</sub>
+
           <td> \(1\) </td>
-
 
+
           <td> [2]<b></b> </td>
-
          </td>
+
-
           <td>
+
-
           
+
-
            Average diffusion rate for all cells
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            1
+
-
 
+
-
          </td>
+
-
           <td>
+
-
           
+
-
            [2]<b></b>
+
-
 
+
-
          </td>
+
         </tr>
         </tr>
       </tbody>
       </tbody>
     </table>
     </table>
-
 
</html>
</html>
-
==Fatty Acid Reaction Absorption Model Model==
+
==Fatty Acid Reaction Absorption Model==
<html>
<html>
-
<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" width="502" style="margin-left:.65pt;border-collapse:collapse;mso-table-layout-alt:fixed;
+
<table class='table table-bordered table-condensed table-hover'>
-
mso-yfti-tbllook:1184;mso-padding-alt:0cm 1.4pt 0cm 1.4pt">
+
  <thead>
-
<tbody><tr style="mso-yfti-irow:0;mso-yfti-firstrow:yes;height:17.25pt">
+
    <tr>
-
  <td width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;background:#F2F2F2;
+
      <td> <b>Parameter</b> </td>
-
  padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> <b>Description</b> </td>
-
  <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:
+
      <td> <b>Value</b> </td>
-
  新細明體;mso-font-kerning:0pt">Parameter<o:p></o:p></span></b></p>
+
      <td> <b>Reference</b> </td>
-
  </td>
+
    </tr>
-
  <td width="260" style="width:194.85pt;border:solid #AAAAAA 1.0pt;border-left:
+
   </thead>
-
  none;background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
  <tbody>
-
  <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:
+
    <tr>
-
  新細明體;mso-font-kerning:0pt">Description&nbsp;<o:p></o:p></span></b></p>
+
      <td> \([E]_t \) </td>
-
  </td>
+
      <td> Total active enzyme </td>
-
  <td width="104" style="width:77.95pt;border:solid #AAAAAA 1.0pt;border-left:
+
      <td> \(50~\text{U}\text{mL}^{-1} \) </td>
-
  none;background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> [8][10][11] </td>
-
  <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:
+
    </tr>
-
  新細明體;mso-font-kerning:0pt">Value&nbsp;<o:p></o:p></span></b></p>
+
    <tr>
-
  </td>
+
      <td> \(K_m \) </td>
-
  <td width="66" style="width:49.6pt;border:solid #AAAAAA 1.0pt;border-left:none;
+
      <td> Reaction rate constant </td>
-
  background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> \(47.9\) </td>
-
  <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:
+
      <td> [6][7] </td>
-
  新細明體;mso-font-kerning:0pt">Reference<o:p></o:p></span></b></p>
+
    </tr>
-
   </td>
+
    <tr>
-
</tr>
+
      <td> \(D_{FA} \) </td>
-
<tr style="mso-yfti-irow:1;height:17.25pt">
+
      <td> FA Diffusion Constant </td>
-
  <td width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none;
+
      <td> \( 6.46 \times 10^{-10}~\text{m}^2\text{s}^{-1} \) </td>
-
  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> [9] </td>
-
  <p class="MsoNormal"><span lang="EN-US">[E]<sub>t</sub></span><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
    </tr>
-
  新細明體;mso-font-kerning:0pt"><o:p></o:p></span></p>
+
    <tr>
-
  </td>
+
      <td> \(d\) </td>
-
  <td width="260" style="width:194.85pt;border-top:none;border-left:none;
+
      <td> Thickness of the unstirred water layer </td>
-
  border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;
+
      <td> \( 190~\mu\text{m} \) </td>
-
  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> [9] </td>
-
  <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:
+
    </tr>
-
  新細明體;mso-font-kerning:0pt">Total active enzyme<o:p></o:p></span></p>
+
    <tr>
-
  </td>
+
      <td> \( K_{cat}\)</td>
-
  <td width="104" style="width:77.95pt;border-top:none;border-left:none;
+
      <td> Catalytic Rate constant </td>
-
  border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;
+
      <td> \(1.3\times10^{-5}\text{min}^{-1}\) </td>
-
  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> [6][7] </td>
-
  <p class="MsoNormal"><span lang="EN-US">50 uM</span><span lang="EN-US" style="font-size:
+
    </tr>
-
  10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:新細明體;
+
  </tbody>
-
  mso-font-kerning:0pt"><o:p></o:p></span></p>
+
</table>
-
  </td>
+
 
-
  <td 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;
+
</html>
-
  padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
-
  <p class="MsoNormal"><span lang="EN-US">[8]<o:p></o:p></span></p>
+
-
  </td>
+
-
</tr>
+
-
<tr style="mso-yfti-irow:2;height:17.25pt">
+
-
  <td 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"><span lang="EN-US">K<sub>m</sub></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>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">Reaction rate constant<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">47.9<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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"><span lang="EN-US">[6][7]<o:p></o:p></span></p>
+
-
  </td>
+
-
</tr>
+
-
<tr style="mso-yfti-irow:3;height:17.25pt">
+
-
  <td 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"><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">D<sub>FA</sub><o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">FA Diffusion Constant<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">6.46*10<sub>­</sub><sup>-10</sup>m<sup>2</sup>/s<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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"><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">&nbsp;</span></p>
+
-
  </td>
+
-
</tr>
+
-
<tr style="mso-yfti-irow:4;height:17.25pt">
+
-
  <td 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"><span lang="EN-US">d</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>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">Thickness of the unstirred water layer<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">190 um<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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"><span lang="EN-US">[9]<o:p></o:p></span></p>
+
-
  </td>
+
-
</tr>
+
-
<tr style="mso-yfti-irow:5;mso-yfti-lastrow:yes;height:17.25pt">
+
-
  <td 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"><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">Kcat/ molecular weight<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">Catalytic Rate constant<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">1.8*10^-3<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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"><span lang="EN-US">[6][7]<o:p></o:p></span></p>
+
-
  </td>
+
-
</tr>
+
-
</tbody></table></html>
+
==Cell-Cell Communication Model==
==Cell-Cell Communication Model==
<html>
<html>
-
<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" width="502" style="margin-left:.65pt;border-collapse:collapse;mso-table-layout-alt:fixed;
+
 
-
mso-yfti-tbllook:1184;mso-padding-alt:0cm 1.4pt 0cm 1.4pt">
+
<table class='table table-bordered table-condensed table-hover'>
-
<tbody><tr style="mso-yfti-irow:0;mso-yfti-firstrow:yes;height:17.25pt">
+
  <thead>
-
  <td width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;background:#F2F2F2;
+
    <tr>
-
  padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> <b>Parameter</b> </td>
-
  <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:
+
      <td> <b>Description</b> </td>
-
  新細明體;mso-font-kerning:0pt">Parameter<o:p></o:p></span></b></p>
+
      <td> <b>Value</b> </td>
-
  </td>
+
      <td> <b>Reference</b> </td>
-
  <td width="260" style="width:194.85pt;border:solid #AAAAAA 1.0pt;border-left:
+
    </tr>
-
  none;background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
   </thead>
-
  <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:
+
  <tbody>
-
  新細明體;mso-font-kerning:0pt">Description&nbsp;<o:p></o:p></span></b></p>
+
    <tr>
-
  </td>
+
      <td> \( cd \) </td>
-
  <td width="104" style="width:77.95pt;border:solid #AAAAAA 1.0pt;border-left:
+
      <td> Relative E. coli Cell Density </td>
-
  none;background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> \( 0.1 \) </td>
-
  <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:
+
      <td> </td>
-
  新細明體;mso-font-kerning:0pt">Value&nbsp;<o:p></o:p></span></b></p>
+
    </tr>
-
  </td>
+
    <tr>
-
  <td width="66" style="width:49.6pt;border:solid #AAAAAA 1.0pt;border-left:none;
+
      <td> \( D_{FA} \)</td>
-
  background:#F2F2F2;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> FA Diffusion Constant</td>
-
  <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:
+
      <td> \( 6.46 \times 10^{-10}\text{m}^2\text{s}^{-1} \)</td>
-
  新細明體;mso-font-kerning:0pt">Reference<o:p></o:p></span></b></p>
+
      <td> [9]</td>
-
   </td>
+
    </tr>
-
</tr>
+
    <tr>
-
<tr style="mso-yfti-irow:1;height:17.25pt">
+
      <td> \(D_{AHL} \)</td>
-
  <td width="72" style="width:54.0pt;border:solid #AAAAAA 1.0pt;border-top:none;
+
      <td> AHL Diffusion Constant</td>
-
  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> \( 4.9\times10^{-6}~\text{cm}^2\text{s}^{-1} \)</td>
-
  <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:
+
      <td> [9]</td>  
-
  新細明體;mso-font-kerning:0pt">cd<o:p></o:p></span></p>
+
    </tr>
-
  </td>
+
    <tr>
-
  <td width="260" style="width:194.85pt;border-top:none;border-left:none;
+
      <td> \( \gamma_{AHL,ext} \)</td>
-
  border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;
+
      <td> AHL cell-external degradation</td>
-
  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
      <td> \( 8.0225\times10^{6}~\text{s}^{-1} \)</td>
-
  <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.
+
      <td> Derived from 1 day half-life at pH 7 [7]</td>
-
  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:
+
    </tr>
-
  10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:新細明體;
+
  </tbody>
-
  mso-font-kerning:0pt"><o:p></o:p></span></p>
+
</table>
-
  </td>
+
 
-
  <td width="104" style="width:77.95pt;border-top:none;border-left:none;
+
 
-
  border-bottom:solid #AAAAAA 1.0pt;border-right:solid #AAAAAA 1.0pt;
+
</html>
-
  background:#F9F9F9;padding:0cm 1.4pt 0cm 1.4pt;height:17.25pt">
+
-
  <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">0.1<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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"><span lang="EN-US">&nbsp;</span></p>
+
-
  </td>
+
-
</tr>
+
-
<tr style="mso-yfti-irow:2;height:17.25pt">
+
-
  <td 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"><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">D<sub>FA</sub><o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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: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>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">6.46* 10^-10m^2 /s<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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"></td>
+
-
</tr>
+
-
<tr style="mso-yfti-irow:3;height:17.25pt">
+
-
  <td 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"><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">D<sub>AHL</sub><o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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: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;
+
-
  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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">4.9e-6 cm2/s<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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"><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">[9]<o:p></o:p></span></p>
+
-
  </td>
+
-
</tr>
+
-
<tr style="mso-yfti-irow:4;mso-yfti-lastrow:yes;height:17.25pt">
+
-
  <td 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"><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">γAHL,ext<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">AHL cell-external degradation<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
+
-
  新細明體;mso-font-kerning:0pt">8.0225e-006/s<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td 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"><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">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;
+
-
  font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:新細明體;color:windowtext;
+
-
  mso-font-kerning:0pt;text-decoration:none;text-underline:none">[7]</span></a></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>
+
-
  </td>
+
-
</tr>
+
-
</tbody></table></html>
+
==Reference==
==Reference==
<html>
<html>
-
<table class="MsoNormalTable" border="1" cellspacing="0" cellpadding="0" width="90%" style="width:90.0%;background:#F9F9F9;border-collapse:collapse;border:none;
+
 
-
mso-border-alt:solid #AAAAAA .75pt;mso-yfti-tbllook:1184">
+
   [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 <br>
-
<tbody><tr>
+
   [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 <br>
-
   <td width="21" nowrap="" style="width:15.95pt;border:solid #AAAAAA 1.0pt;
+
   [3] MIT igem 2010 <br>
-
  mso-border-alt:solid #AAAAAA .75pt;background:#F2F2F2;padding:2.4pt 2.4pt 2.4pt 2.4pt"></td>
+
   [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 <br>
-
  <td style="border:solid #AAAAAA 1.0pt;border-left:none;mso-border-left-alt:
+
   [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 <br>
-
  solid #AAAAAA .75pt;mso-border-alt:solid #AAAAAA .75pt;background:#F2F2F2;
+
   [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 <br>
-
  padding:2.4pt 2.4pt 2.4pt 2.4pt">
+
   [7] Ho-Shing Wu, Ming-Ju Tsai, Kinetics of tributyrin hydrolysis by lipase, Enzyme and Microbial Technology, Volume 35, Issues 6–7, 2004 <br>
-
  <p class="MsoNormal" align="center" style="text-align:center;line-height:14.25pt;
+
   [8] Bengt Borgstrom, Luminal Digestion of Fats, Handbook of Physiology, The Gastrointestinal System, Intestinal Absorption and Secretion, 1991 <br>
-
  mso-pagination:widow-orphan"><b><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">Source<o:p></o:p></span></b></p>
+
   [9] Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake of short- and medium-chain fatty acids and alcohols, Journal of Lipid Research, 1973 <br>
-
  </td>
+
   [10] J Keller, P Layer, Human pancreatic exocrine response to nutrients in health and disease, Gut, 2005 <br>
-
</tr>
+
  [11] M Lingumsky, E Granot, D Branski, H Stankiewicz, R Goldstein, Isolated lipase and colipase deficiency in two brothers, Gut, 1990 <br>
-
<tr>
+
-
  <td style="border:solid #AAAAAA 1.0pt;border-top:none;mso-border-top-alt:
+
-
  solid #AAAAAA .75pt;mso-border-alt:solid #AAAAAA .75pt;padding:2.4pt 2.4pt 2.4pt 2.4pt">
+
-
  <p class="MsoNormal" align="center" style="text-align:center;line-height:14.25pt;
+
-
  mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">[1]<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td style="border-top:none;border-left:none;border-bottom:solid #AAAAAA 1.0pt;
+
-
  border-right:solid #AAAAAA 1.0pt;mso-border-top-alt:solid #AAAAAA .75pt;
+
-
  mso-border-left-alt:solid #AAAAAA .75pt;mso-border-alt:solid #AAAAAA .75pt;
+
-
  padding:2.4pt 2.4pt 2.4pt 2.4pt">
+
-
  <p class="MsoNormal" style="line-height:14.25pt;mso-pagination:widow-orphan"><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">Subhayu Basu, Yoram
+
-
  Gerchman, Cynthia H. Collins, Frances H. Arnold &amp; Ron Weiss.<b>A
+
-
  synthetic multicellular system for programmed pattern formation</b>,&nbsp;Nature
+
-
  Vol. 434, 2005<o:p></o:p></span></p>
+
-
   </td>
+
-
</tr>
+
-
<tr>
+
-
  <td style="border:solid #AAAAAA 1.0pt;border-top:none;mso-border-top-alt:
+
-
  solid #AAAAAA .75pt;mso-border-alt:solid #AAAAAA .75pt;padding:2.4pt 2.4pt 2.4pt 2.4pt">
+
-
  <p class="MsoNormal" align="center" style="text-align:center;line-height:14.25pt;
+
-
  mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">[2]<o:p></o:p></span></p>
+
-
  </td>
+
-
  <td style="border-top:none;border-left:none;border-bottom:solid #AAAAAA 1.0pt;
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Garcia-Ojalvo, Michael B. Elowitz,
+
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  and Steven H. Strogatz<b>. Modeling a synthetic multicellular clock:
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  Repressilators coupled by quorum sensing</b>,&nbsp;PNAS vol. 101 no. 30, 2004<o:p></o:p></span></p>
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  mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">[3]<o:p></o:p></span></p>
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">MIT igem 2010<o:p></o:p></span></p>
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+
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Michael Halter, Alex Tona,
+
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  Kiran Bhadriraju, Anne L. Plant, John T. Elliott,<b> Automated Live Cell
+
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  Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts</b>,
+
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  Cytometry Part A, Volume 71A Issue 10, 2007<o:p></o:p></span></p>
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  mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">[5]<o:p></o:p></span></p>
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+
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Wilfried Weber, Markus
+
-
  Rimann, Manuela Spielmann, Bettina Keller, Marie Daoud-El Baba, Dominique
+
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  Aubel, Cornelia C Weber &amp; Martin Fussenegger,&nbsp;<b>Gas-inducible
+
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  transgene expression in mammalian cells and mice, Nature Biotechnology</b>, volume
+
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  22, number 11, 2004<o:p></o:p></span></p>
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Sulaiman Al-Zuhair,
+
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  Masitah Hasan, K.B. Ramachandran, <b>Kinetics of the enzymatic hydrolysis of
+
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  palm oil by lipase</b>, Process Biochemistry<o:p></o:p></span></p>
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  <p class="MsoNormal" style="line-height:14.25pt;mso-pagination:widow-orphan"><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Volume 38, Issue 8, 2003<o:p></o:p></span></p>
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+
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Ho-Shing Wu, Ming-Ju Tsai,
+
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  <b>Kinetics of tributyrin hydrolysis by
+
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  lipase</b>, Enzyme and Microbial Technology, Volume 35, Issues 6–7, 2004<o:p></o:p></span></p>
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  mso-pagination:widow-orphan"><span lang="EN-US" style="font-size: 10pt; font-family: Arial, sans-serif; ">[8]<o:p></o:p></span></p>
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+
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Bengt Borgstrom,<b> Luminal Digestion of Fats,</b> Handbook
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  of Physiology, The Gastrointestinal System, Intestinal Absorption and
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  Secretion</span>, 1991<o:p></o:p></p>
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Sallee VL,</span><span lang="EN-US" style="font-size:10.0pt;mso-fareast-font-family:新細明體;mso-font-kerning:
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  0pt">&nbsp;</span><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;sans-serif&quot;;
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  mso-fareast-font-family:新細明體;mso-font-kerning:0pt">Dietschy JM.</span>, <b>Determinants of intestinal mucosal uptake
+
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  of short- and medium-chain fatty acids and alcohols, </b>Journal of Lipid
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Latest revision as of 20:51, 26 October 2012

Cell Population Response Model

Parameters


Contents

Single-Cell/ System analysis Model

Parameter Description  Value  Reference
\(\alpha_{TetR} \) TetR max. production rate \(0.8~\mu \text{M}\cdot\text{min}^{-1} \) [5]
\(\alpha_{FadR} \) FadR max. production rate \(100~\mu\text{M}\cdot\text{min}^{-1} \) a.
\(\alpha_{GLP-1} \) GLP-1 max. production rate \(1.23~\mu\text{M}\cdot\text{min}^{-1} \) a.
\(\alpha_{LacI} \) LacI max. production rate \(0.8~\mu\text{M}\cdot\text{min}^{-1} \) [1]
\(k_{s1} \) AHL i production rate \(0.01~\text{min}^{-1} \) [2]
\(\rho_R \) LuxR-AHL dimerization rate \(0.5~\mu\text{M}^{-3}\cdot \text{min}^{-1} \) [1]
\(\beta_{TetR} \) TetR repression coefficient \(0.13~\mu\text{M} \) a.
\(\beta_{FA} \) FA repression coefficient \(10~\mu\text{M} \) [1]
\(\beta_{FadR} \) FadR repression coefficient \(0.13~\mu\text{M} \) [1]
\(\beta_{LacI} \) LacI repression coefficient \(0.8~\mu\text{M} \) [1]
\(\beta_R \) LuxR-AHL repression coefficient \(0.01~\mu\text{M} \) [1]
\(\gamma_{TetR} \) TetR degradation rate \(0.0692~\text{min}^{-1} \) a.
\(\gamma_{LacI} \) LacI degradation rate \(0.0231~\text{min}^{-1} \) [1]
\(\gamma_{GLP-1} \) GLP-1 degradation rate \(0.0731~\text{min}^{-1} \) [1]
\(\gamma_{LuxI} \) LuxI degradation rate \(0.0167~\text{min}^{-1} \) [3]
\(k_{s0} \) AHLi degradation rate \(1~\text{min}^{-1} \) [2]
\(k_{se} \) AHLe degradation rate \(1~\text{min}^{-1} \) [2]
\(\gamma_R \) LuxR-AHL degradation rate \(0.0231~\text{min}^{-1} \) [1]
\(\gamma_{RFP} \) RFP degradation rate \(0.0041~\text{min}^{-1} \) [4]
\(n_1\) FadR cooperativity coefficient \(3\) a.
\(n_2\) FA cooperativity coefficient \(2\) a.
\(n_3\) LuxR-AHL cooperativity coefficient \(3\) [1]
\(n_5\) TetR cooperativity coefficient \(2\) [2]
\(n_6\) LacI cooperativity coefficient \(4\) [1]
\(\eta\) AHL Diffusion rate across the cell membrane \(2\) [2]
\(\eta\)ext Average diffusion rate for all cells \(1\) [2]

Fatty Acid Reaction Absorption Model

Parameter Description Value Reference
\([E]_t \) Total active enzyme \(50~\text{U}\text{mL}^{-1} \) [8][10][11]
\(K_m \) Reaction rate constant \(47.9\) [6][7]
\(D_{FA} \) FA Diffusion Constant \( 6.46 \times 10^{-10}~\text{m}^2\text{s}^{-1} \) [9]
\(d\) Thickness of the unstirred water layer \( 190~\mu\text{m} \) [9]
\( K_{cat}\) Catalytic Rate constant \(1.3\times10^{-5}\text{min}^{-1}\) [6][7]

Cell-Cell Communication Model

Parameter Description Value Reference
\( cd \) Relative E. coli Cell Density \( 0.1 \)
\( D_{FA} \) FA Diffusion Constant \( 6.46 \times 10^{-10}\text{m}^2\text{s}^{-1} \) [9]
\(D_{AHL} \) AHL Diffusion Constant \( 4.9\times10^{-6}~\text{cm}^2\text{s}^{-1} \) [9]
\( \gamma_{AHL,ext} \) AHL cell-external degradation \( 8.0225\times10^{6}~\text{s}^{-1} \) Derived from 1 day half-life at pH 7 [7]

Reference

[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
[10] J Keller, P Layer, Human pancreatic exocrine response to nutrients in health and disease, Gut, 2005
[11] M Lingumsky, E Granot, D Branski, H Stankiewicz, R Goldstein, Isolated lipase and colipase deficiency in two brothers, Gut, 1990