Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"
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<tr> <th>Name </th> <th>Description </th><th>Value </th><th>References/Estimation </th> </tr> | <tr> <th>Name </th> <th>Description </th><th>Value </th><th>References/Estimation </th> </tr> | ||
<tr><td>\(K_{d,\text{LuxRAHL}}\)</td><td>100 nM</td><td>Dissociation constant between luxR and AHL</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Weber2013">Weber, 2013</a></td></tr> | <tr><td>\(K_{d,\text{LuxRAHL}}\)</td><td>100 nM</td><td>Dissociation constant between luxR and AHL</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Weber2013">Weber, 2013</a></td></tr> | ||
| − | <tr><td>\(\text{LuxR}_\text{tot}\)</td><td>0.0025 μM</td><td>Total concentration of LuxR </td><td> | + | <tr><td>\(\text{LuxR}_\text{tot}\)</td><td>0.0025 μM</td><td>Total concentration of LuxR </td><td>estimated</td></tr> |
<tr><td>\(a_\mathrm{LuxI}\)</td><td>1 μM.min<SUP>-1</SUP></td><td>Maximal production rate of LuxI</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td></tr> | <tr><td>\(a_\mathrm{LuxI}\)</td><td>1 μM.min<SUP>-1</SUP></td><td>Maximal production rate of LuxI</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></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> | + | <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>0.01 μM</td><td>Activation coefficient of LuxRAHL </td><td> | + | <tr><td>\(K_\mathrm{a,LuxRAHL}\)</td><td>0.01 μM</td><td>Activation coefficient of LuxRAHL </td><td>estimated</td></tr> |
| − | <tr><td>\(d_\mathrm{LuxI}\)</td><td>0.0167 min<SUP>-1</SUP></td><td>Degradation rate of LuxI </td><td> | + | <tr><td>\(d_\mathrm{LuxI}\)</td><td>0.0167 min<SUP>-1</SUP></td><td>Degradation rate of LuxI </td><td>estimated</td></tr> |
| − | <tr><td>\a_\mathrm{AHL}\)</td><td>0.04 μM.min<SUP>-1</SUP></td><td>Production rate of AHL </td><td> | + | <tr><td>\(a_\mathrm{AHL}\)</td><td>0.04 μM.min<SUP>-1</SUP></td><td>Production rate of AHL </td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Weber2013">Weber, 2013</a></td></tr> |
| + | <tr><td>\(d_\mathrm{AHL}\)</td><td>0.01 min<SUP>-1</SUP></td><td>Degradation rate of AHL</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td></tr> | ||
| + | <tr><td>\(v_\mathrm{AiiA}\)</td><td>\(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \)</td><td>Maximal conversion rate of AiiA </td><td></td></tr> | ||
| + | <tr><td>\(k_\mathrm{cat}\)</td><td>1.63 10<SUP>3>/SUP>min<SUP>-1</SUP></td><td>Maximal conversion rate of AiiA </td><td></td></tr> | ||
| + | <tr><td>\(C_\mathrm{AiiA}\)</td><td>0.05 μM</td><td>Concentration of AiiA </td><td></td></tr> | ||
</table> | </table> | ||
Revision as of 15:23, 20 August 2015
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Parameters
AHL module
Single cell model
| Name | Description | Value | 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 |
| \(K_\mathrm{a,LuxRAHL}\) | 0.01 μM | Activation coefficient of LuxRAHL | estimated |
| \(d_\mathrm{LuxI}\) | 0.0167 min-1 | Degradation rate of LuxI | estimated |
| \(a_\mathrm{AHL}\) | 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 | |
| \(k_\mathrm{cat}\) | 1.63 103>/SUP>min-1 | Maximal conversion rate of AiiA | |
| \(C_\mathrm{AiiA}\) | 0.05 μM | Concentration of AiiA |
Lactate module
Single cell model
Assumptions
| Name | Description | Value | References/Estimation |
|---|---|---|---|
| \(\text{Lac}_{\text{ini}}\) | Initial concentration of lactate in the medium | 1 μM | Low concentration of lactate in the medium |
| Kdllini | Initial concentration of lactate in the medium |