Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"
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<tr><td>\(a_\mathrm{LuxI,ribo}\)</td><td>0.1 μM.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 μM.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 μM<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 μM<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> | + | <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
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Parameters
AHL module
Single cell model
| Name | Value | Description | References/Estimation |
|---|---|---|---|
| \(K_{d,\text{LuxRAHL}}\) | 100 nM | Dissociation constant between luxR and AHL | Weber, 2013 |
| \(\text{LuxR}_\text{tot}\) | 0.0025 μM | Total concentration of LuxR | estimated |
| \(a_\mathrm{LuxI}\) | 1 μM.min-1 | Maximal production rate of LuxI | Basu, 2005 |
| \(a_\mathrm{LuxI,ribo}\) | 0.1 μM.min-1 | Maximal production rate of LuxI | ETHZ 2014 |
| \(k_\mathrm{leaky}\) | 0.0375 μM-1 | Coefficient for leakiness dependency on LuxR concentration of PLuxR promoter | ETHZ 2013 |
| \(K_\mathrm{a,LuxRAHL}\) | 9.89 nM | Activation 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 nM | Activation coefficient of LuxRAHL in case of a riboregulated LuxR responsive promoter | ETHZ 2014 |
| \(L_\mathrm{lux,ribo}\) | 0.01463 nM.min-1 | Leakiness after using riboswitch for Plux | ETHZ 2014 |
| \(n_\mathrm{lux}\) | 1.7 | Hill coefficient for LuxRAHL activation | ETHZ 2014 |
| \(d_\mathrm{LuxI}\) | 0.0167 min-1 | Degradation rate of LuxI | MIT 2010 |
| \(a_\mathrm{AHL}\) | 0.04 μM.min-1 | Production rate of AHL | Weber, 2013 |
| \(d_\mathrm{AHL}\) | 0.01 min-1 | Degradation rate of AHL | Basu, 2005 |
| \(v_\mathrm{AiiA}\) | \(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \) | Maximal conversion rate of AiiA | |
| \(k_\mathrm{cat}\) | 1.63 103min-1 | Turnover number of AiiA | Wang, 2004 |
| \(C_\mathrm{AiiA}\) | varied | Concentration 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-1 | Maximal production rate of GFP | Basu, 2005 |
| \(d_\mathrm{GFP}\) | 0.01 min-1 | Degradation rate of GFP | estimated from doubling time of E. coli |
Compartment model
| Name | Value | Description | References/Estimation |
|---|---|---|---|
| \(N_{d}\) | 150 | Number of E. coli in the doughnut | Maximal number of E. coli that would fit on the surface |
| \(N_{b,max}\) | 12798 | Maximum number of E. coli in the bulk | Considering the maximal OD is 2 |
| \(V_{cell,d}\) | 6 μm3 | Volume around an E. coli in the doughnut | estimated |
| \(V_{cell,b,worst}\) | 78 μm3 | Volume around an E. coli in the bulk | Worst case, estimated from \(N_{b,max}\) |
| \(V_{cell,b,norm}\) | 1000 μm3 | Volume around an E. coli in the bulk | Normal case |
Lactate module
Single cell model
Reaction-diffusion model
| Name | Description | Minimum Value | Maximum Value | References/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 |