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

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<tr><td>\(a_\mathrm{LuxI,ribo}\)</td><td>0.1 &mu;M.min<SUP>-1</SUP></td><td>Maximal production rate of LuxI</td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr>
 
<tr><td>\(a_\mathrm{LuxI,ribo}\)</td><td>0.1 &mu;M.min<SUP>-1</SUP></td><td>Maximal production rate of LuxI</td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr>
 
<tr><td>\(k_\mathrm{leaky}\)</td><td>0.0375 &mu;M<SUP>-1</SUP></td><td>Coefficient for leakiness dependency on LuxR concentration of P<SUB>LuxR</SUB> promoter </td><td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter"> ETHZ 2013 </a></td></tr>
 
<tr><td>\(k_\mathrm{leaky}\)</td><td>0.0375 &mu;M<SUP>-1</SUP></td><td>Coefficient for leakiness dependency on LuxR concentration of P<SUB>LuxR</SUB> promoter </td><td><a href="https://2013.igem.org/Team:ETH_Zurich/Parameter"> ETHZ 2013 </a></td></tr>
<tr><td>\(K_\mathrm{a,LuxRAHL}\)</td><td>9.89 nM</td><td>Activation coefficient of LuxRAHL </td><td>Estimated from our own data</td></tr>
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<tr><td>\(K_\mathrm{a,LuxRAHL}\)</td><td>9.89 nM</td><td>Activation coefficient of LuxRAHL </td><td>Estimated from our < a href="https://2015.igem.org/Team:ETH_Zurich/Modeling/AHL_Module#_Dose_response_curves_and_apparent_K_M__values">own data</a></td></tr>
 
<tr><td>\(K_\mathrm{LuxRAHL,ribo}\)</td><td>285 nM</td><td>Activation coefficient of LuxRAHL in case of a riboregulated LuxR responsive promoter </td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr>
 
<tr><td>\(K_\mathrm{LuxRAHL,ribo}\)</td><td>285 nM</td><td>Activation coefficient of LuxRAHL in case of a riboregulated LuxR responsive promoter </td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr>
 
<tr><td>\(L_\mathrm{lux,ribo}\)</td><td>0.01463  nM.min<SUP>-1</SUP></td><td>Leakiness after using riboswitch for P<SUB>lux</SUB> </td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr>
 
<tr><td>\(L_\mathrm{lux,ribo}\)</td><td>0.01463  nM.min<SUP>-1</SUP></td><td>Leakiness after using riboswitch for P<SUB>lux</SUB> </td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr>

Revision as of 21:49, 15 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
\(K_\mathrm{a,LuxRAHL}\)9.89 nMActivation coefficient of LuxRAHL Estimated from our < a href="https://2015.igem.org/Team:ETH_Zurich/Modeling/AHL_Module#_Dose_response_curves_and_apparent_K_M__values">own data
\(K_\mathrm{LuxRAHL,ribo}\)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