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> | + | <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 μm^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 μm^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 μm^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
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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 |
| \(K_\mathrm{a,LuxRAHL}\) | 0.45 nM | Activation coefficient of LuxRAHL | ETHZ 2014 |
| \(K_\mathrm{LuxRAHL,ribo}\) | 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 μm^3 | Volume around an E. coli in the doughnut | estimated |
| \(V_{cell,b,worst}\) | 78 μm^3 | Volume around an E. coli in the bulk | Worst case, estimated from \(N_{b,max}\) |
| \(V_{cell,b,norm}\) | 1000 μm^3 | Volume around an E. coli in the bulk | Normal case |
Lactate module
Single cell model
Assumptions
| Name | Description | Minimum Value | Maximum Value | References/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 Lactate | 10 μM2 | 10000 μM2 | |
| \(\alpha\) | Multiplication factor between the initial concentration of Lactate and Production of normal cells | 1 | 150 | estimated |
| \(F_\mathrm{C}\) | Fold change between Lactate production by cancer and normal cells | 2 | 4 | estimated |
| \(a_1\) | \(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\) | 0.05 | 1000 | |
| \( a_\mathrm{LacI}\) | Maximal production rate of LacI | 0.05 μM.min-1 | 1 μM.min-1 | Basu, 2005 |
| \( d_\mathrm{LacI}\) | Degradation rate of LacI | 0.01 min-1 | 0.1 min-1 | Basu, 2005 |
| \( K_\mathrm{R,LacI}\) | Repression coefficient of LacI | 0.1 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 LldR | 0.001 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 LldR | 0.5 | 2.5 | estimated |
| \( n_2\) | Hill coefficient of LacI | 1.5 | 2.5 | estimated |
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 |