Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"
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<tr><td>\(k_\mathrm{leaky}\)</td><td>0.0005 μM<SUP>-1</SUP></td><td>Leakiness of P<SUB>LuxR</SUB> promoter </td><td>estimated</td></tr> | <tr><td>\(k_\mathrm{leaky}\)</td><td>0.0005 μM<SUP>-1</SUP></td><td>Leakiness of P<SUB>LuxR</SUB> promoter </td><td>estimated</td></tr> | ||
<tr><td>\(K_\mathrm{a,LuxRAHL}\)</td><td>0.45 nM</td><td>Activation coefficient of LuxRAHL </td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr> | <tr><td>\(K_\mathrm{a,LuxRAHL}\)</td><td>0.45 nM</td><td>Activation coefficient of LuxRAHL </td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr> | ||
| − | <tr><td>\(K_\mathrm{ | + | <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{ | + | <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>\(n_\mathrm{lux}\)</td><td>1.7</td><td>Hill coefficient for LuxRAHL activation </td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr> | <tr><td>\(n_\mathrm{lux}\)</td><td>1.7</td><td>Hill coefficient for LuxRAHL activation </td><td><a href="https://2014.igem.org/Team:ETH_Zurich">ETHZ 2014</a></td></tr> | ||
<tr><td>\(d_\mathrm{LuxI}\)</td><td>0.0167 min<SUP>-1</SUP></td><td>Degradation rate of LuxI </td><td><a href="https://2010.igem.org/Team:MIT_tmodel">MIT 2010</a></td></tr> | <tr><td>\(d_\mathrm{LuxI}\)</td><td>0.0167 min<SUP>-1</SUP></td><td>Degradation rate of LuxI </td><td><a href="https://2010.igem.org/Team:MIT_tmodel">MIT 2010</a></td></tr> | ||
Revision as of 13:25, 8 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 |
| \(k_\mathrm{leaky}\) | 0.0005 μM-1 | Leakiness of PLuxR promoter | estimated |
| \(K_\mathrm{a,LuxRAHL}\) | 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 |
| \(C_\mathrm{AiiA}\) | 0.05 μM | Concentration of AiiA | |
| \(K_\mathrm{M,AiiA}\) | 2.95 103 μM | 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 |
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 |