Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"

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<h2>Lactate module</h2>
 
<h2>Lactate module</h2>
 
<h3>Single cell model</h3>
 
<h3>Single cell model</h3>
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<h4>Assumptions</h4>
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<table>
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<tr> <th>Name </th> <th>Description </th><th>Minimum Value</th><th>Maximum Value</th><th>References/Estimation </th> </tr>
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<tr> <td>\(\text{B}\)</td> <td> \(\frac{Lac_\mathrm{ini}^2}{K_\mathrm{d,DLL}}\) </td><td> 0.000001</td> <td> 4</td>  <td></td> </tr>
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<tr> <td>\(\text{Lac}_{\text{ini}}\)</td> <td> Initial concentration of lactate in the medium </td><td> 0.1 &mu;M</td> <td> 2 &mu;M</td>  <td>Low concentration of lactate in the medium</td> </tr>
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<tr> <td>\(K_\mathrm{d,DLL}\)</td> <td> Dissociation constant between the dimer of Lldr and Lactate</td><td>10 &mu;M<SUP>2</SUP> </td> <td>10000 &mu;M<SUP>2</SUP></td> <td> </td> </tr>
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<tr> <td>\(\alpha\)</td> <td> Multiplication factor between the initial concentration of Lactate and Production of normal cells</td><td>1 </td> <td>150</td> <td>estimated </td> </tr>
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<tr> <td>\(F_\mathrm{C}\)</td> <td> Fold change between Lactate production by cancer and normal cells</td><td>2 </td> <td>4</td> <td>estimated </td> </tr>
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<tr> <td>\(a_1\)</td> <td> \(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\)</td><td>0.05 </td> <td>1000</td> <td></td> </tr>
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<tr> <td>\( a_\mathrm{LacI}\)</td> <td> Maximal production rate of LacI</td><td>0.05 &mu;M.min<SUP>-1</SUP> </td> <td>1 &mu;M.min<SUP>-1</SUP> </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr>
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<tr> <td>\( d_\mathrm{LacI}\)</td> <td> Degradation rate of LacI</td><td>0.01 min<SUP>-1</SUP> </td> <td>0.1 min<SUP>-1</SUP> </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr>
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<tr> <td>\(  K_\mathrm{R,LacI}\)</td> <td>Repression coefficient of LacI</td><td>0.1 &mu;M </td> <td>10 &mu;M </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr>
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<tr> <td>\( \gamma_1\)</td> <td> \( \frac{L_\mathrm{2tot}}{K_\mathrm{R,L}}\)</td><td>5 </td> <td>10000</td> <td>estimated </td> </tr>
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<tr> <td>\(  L_\mathrm{2tot}\)</td> <td> Total concentration of LldR dimer  </td><td>0.5 &mu;M</td> <td>10 &mu;M</td> <td>estimated from paxdb</td> </tr>
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<tr> <td>\(  K_\mathrm{R,L}\)</td> <td> Repression coefficient of LldR</td><td>0.001 &mu;M</td> <td>0.1 &mu;M</td> <td>estimated</td> </tr>
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<tr> <td>\(  \gamma_2\)</td> <td> \(\frac{IPTG_{tot}}{K_{IL}}\)</td><td>0</td> <td>500</td> <td>estimated</td> </tr>
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<tr> <td>\(  \frac{a_1}{\gamma_2+1}\)</td> <td></td><td>0.001</td> <td>1000</td> <td>estimated</td> </tr>
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<tr> <td>\(  n_1\)</td> <td>Hill coefficient of LldR</td><td>0.5</td> <td>2.5</td> <td>estimated</td> </tr>
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<tr> <td>\(  n_2\)</td> <td>Hill coefficient of LacI</td><td>1.5</td> <td>2.5</td> <td>estimated</td> </tr>
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</table>
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<h2>Reaction-diffusion model</h2>
 
<h2>Reaction-diffusion model</h2>
 
<table>
 
<table>

Revision as of 11:59, 14 September 2015

"What I cannot create I do not understand."
- Richard Feynmann

Parameters

AHL module

Single cell model

Name ValueDescription References/Estimation
\(K_{d,\text{LuxRAHL}}\)100 nMDissociation constant between luxR and AHLWeber, 2013
\(\text{LuxR}_\text{tot}\)0.0025 μMTotal concentration of LuxR estimated
\(a_\mathrm{LuxI}\)1 μM.min-1Maximal production rate of LuxIBasu, 2005
\(a_\mathrm{LuxI,ribo}\)0.1 μM.min-1Maximal production rate of LuxIETHZ 2014
\(k_\mathrm{leaky}\)0.0375 μM-1Coefficient for leakiness dependency on LuxR concentration of PLuxR promoter ETHZ 2013
\(K_\mathrm{a,LuxRAHL}\)0.45 nMActivation coefficient of LuxRAHL ETHZ 2014
\(K_\mathrm{LuxRAHL,ribo}\)285 nMActivation coefficient of LuxRAHL in case of a riboregulated LuxR responsive promoter ETHZ 2014
\(L_\mathrm{lux,ribo}\)0.01463 nM.min-1Leakiness after using riboswitch for Plux ETHZ 2014
\(n_\mathrm{lux}\)1.7Hill coefficient for LuxRAHL activation ETHZ 2014
\(d_\mathrm{LuxI}\)0.0167 min-1Degradation rate of LuxI MIT 2010
\(a_\mathrm{AHL}\)0.04 μM.min-1Production rate of AHL Weber, 2013
\(d_\mathrm{AHL}\)0.01 min-1Degradation rate of AHLBasu, 2005
\(v_\mathrm{AiiA}\)\(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \)Maximal conversion rate of AiiA
\(k_\mathrm{cat}\)1.63 103min-1Turnover number of AiiA Wang, 2004
\(C_\mathrm{AiiA}\)variedConcentration of AiiA
\(K_\mathrm{M,AiiA}\)2.95 103 μM Half-maximal rate substrate concentration of AiiA Wang, 2004
\(a_\mathrm{GFP}\)2 μM.min-1Maximal production rate of GFP Basu, 2005
\(d_\mathrm{GFP}\)0.01 min-1Degradation rate of GFP estimated from doubling time of E. coli

Compartment model

Name ValueDescription References/Estimation
\(N_{d}\) 150Number of E. coli in the doughnut Maximal number of E. coli that would fit on the surface
\(N_{b,max}\) 12798Maximum number of E. coli in the bulk Considering the maximal OD is 2
\(V_{cell,d}\) 6 μm3Volume around an E. coli in the doughnut estimated
\(V_{cell,b,worst}\) 78 μm3Volume around an E. coli in the bulkWorst case, estimated from \(N_{b,max}\)
\(V_{cell,b,norm}\) 1000 μm3Volume around an E. coli in the bulkNormal case

Lactate module

Single cell model

Reaction-diffusion model

Name Description Minimum ValueMaximum ValueReferences/Estimation
\(D_\text{AHL,agar}\)Diffusion coefficient of AHL in agar\(3.0\times 10^{-10} m^2/s\)\(4.41\times 10^{-10} m^2/s\)Trovato, 2014
Fatin-Rouge, 2004