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

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<tr> <th>Name </th> <th>Value</th><th>Description </th><th>References/Estimation </th> </tr>
 
<tr> <th>Name </th> <th>Value</th><th>Description </th><th>References/Estimation </th> </tr>
 
<tr> <td>\(N_{d}\) </td> <td>150</td><td>Number of <i> E. coli </i> in the doughnut </td><td>Maximal number of <i>E. coli </i> that would fit on the surface </td> </tr>
 
<tr> <td>\(N_{d}\) </td> <td>150</td><td>Number of <i> E. coli </i> in the doughnut </td><td>Maximal number of <i>E. coli </i> that would fit on the surface </td> </tr>
<tr> <td>\(N_{b}\) </td> <td>12798</td><td>Number of <i> E. coli </i> in the bulk </td><td>Considering the maximal OD is 2</td> </tr>
+
<tr> <td>\(N_{b,max}\) </td> <td>12798</td><td>Maximum number of <i> E. coli </i> in the bulk </td><td>Considering the maximal OD is 2</td> </tr>
 +
<tr> <td>\(V_{cell,d}\) </td> <td>6 &mu;m^3</td><td>Volume around an <i> E. coli </i> in the doughnut </td><td>estimated</td> </tr>
 +
<tr> <td>\(V_{cell,b,worst}\) </td> <td>78 &mu;m^3</td><td>Volume around an <i> E. coli </i> in the bulk</td><td>Worst case, estimated from \(N_{b,max}\) </td> </tr>
 +
<tr> <td>\(V_{cell,b,norm}\) </td> <td>1000 &mu;m^3</td><td>Volume around an <i> E. coli </i> in the bulk</td><td>Normal case</td> </tr>
 
</table>
 
</table>
 
<h2>Lactate module</h2>
 
<h2>Lactate module</h2>

Revision as of 16:41, 11 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 μm^3Volume around an E. coli in the doughnut estimated
\(V_{cell,b,worst}\) 78 μm^3Volume around an E. coli in the bulkWorst case, estimated from \(N_{b,max}\)
\(V_{cell,b,norm}\) 1000 μm^3Volume around an E. coli in the bulkNormal case

Lactate module

Single cell model

Assumptions

Name Description Minimum ValueMaximum ValueReferences/Estimation
\(\text{B}\) \(\frac{Lac_\mathrm{ini}^2}{K_\mathrm{d,DLL}}\) 0.000001 4
\(\text{Lac}_{\text{ini}}\) Initial concentration of lactate in the medium 0.1 μM 2 μM Low concentration of lactate in the medium
\(K_\mathrm{d,DLL}\) Dissociation constant between the dimer of Lldr and Lactate10 μM2 10000 μM2
\(\alpha\) Multiplication factor between the initial concentration of Lactate and Production of normal cells1 150 estimated
\(F_\mathrm{C}\) Fold change between Lactate production by cancer and normal cells2 4 estimated
\(a_1\) \(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\)0.05 1000
\( a_\mathrm{LacI}\) Maximal production rate of LacI0.05 μM.min-1 1 μM.min-1 Basu, 2005
\( d_\mathrm{LacI}\) Degradation rate of LacI0.01 min-1 0.1 min-1 Basu, 2005
\( K_\mathrm{R,LacI}\) Repression coefficient of LacI0.1 μM 10 μM Basu, 2005
\( \gamma_1\) \( \frac{L_\mathrm{2tot}}{K_\mathrm{R,L}}\)5 10000 estimated
\( L_\mathrm{2tot}\) Total concentration of LldR dimer 0.5 μM 10 μM estimated from paxdb
\( K_\mathrm{R,L}\) Repression coefficient of LldR0.001 μM 0.1 μM estimated
\( \gamma_2\) \(\frac{IPTG_{tot}}{K_{IL}}\)0 500 estimated
\( \frac{a_1}{\gamma_2+1}\) 0.001 1000 estimated
\( n_1\) Hill coefficient of LldR0.5 2.5 estimated
\( n_2\) Hill coefficient of LacI1.5 2.5 estimated

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