Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"
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</table> | </table> | ||
<h2>Lactate module</h2> | <h2>Lactate module</h2> | ||
| − | < | + | <table> |
| − | + | <tr> <th>Name </th> <th>Description </th><th>Value</th><th>References/Estimation </th> </tr> | |
| + | <tr> <td>\(K_{\mathrm{A,Lact}}\)</td> <td> Lumped parameter for the lactate sensor </td><td>175 μM</td><td>Based on the <a href="#Parameter_fitting">characterization</a> of the promoters. </td> </tr> | ||
| + | <tr> <td>\( a_\mathrm{LacI}\)</td> <td> Maximal production rate of LacI</td> <td>1 μM.min<SUP>-1</SUP> </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr> | ||
| + | <tr> <td>\( d_\mathrm{LacI}\)</td> <td> Degradation rate of LacI</td> <td>0.0231 min<SUP>-1</SUP> </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr> | ||
| + | <tr> <td>\( K_\mathrm{R,LacI}\)</td> <td>Repression coefficient of LacI</td><td>0.8 μM </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr> | ||
| + | <tr> <td>\( n_1\)</td> <td>Hill coefficient of LldR</td><td>1.7</td> <td>estimated</td> </tr> | ||
| + | <tr> <td>\( n_2\)</td> <td>Hill coefficient of LacI</td><td>1.7</td> <td>estimated</td> </tr> | ||
| + | </table> | ||
<h2>Reaction-diffusion model</h2> | <h2>Reaction-diffusion model</h2> | ||
<table> | <table> | ||
Revision as of 00:01, 19 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 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
| Name | Description | Value | References/Estimation |
|---|---|---|---|
| \(K_{\mathrm{A,Lact}}\) | Lumped parameter for the lactate sensor | 175 μM | Based on the characterization of the promoters. |
| \( a_\mathrm{LacI}\) | Maximal production rate of LacI | 1 μM.min-1 | Basu, 2005 |
| \( d_\mathrm{LacI}\) | Degradation rate of LacI | 0.0231 min-1 | Basu, 2005 |
| \( K_\mathrm{R,LacI}\) | Repression coefficient of LacI | 0.8 μM | Basu, 2005 |
| \( n_1\) | Hill coefficient of LldR | 1.7 | estimated |
| \( n_2\) | Hill coefficient of LacI | 1.7 | estimated |
Reaction-diffusion model
| Name | Value | Description | References/Estimation |
|---|---|---|---|
| \(D_{aq,AHL}\) | Diffusion coefficient of AHL through water | 4.9×10-6cm2/s | ETHZ 2014 |
| \(D_{m,AHL}\) | Diffusion coefficient of AHL through a cell membrane | ETHZ 2014 | |
| \(R_\text{Jurkat}\) | Radius of a Jurkat cell | 5.75 μm | |
| \(R_\textit{E. coli}\) | Short-side radius of an E. coli cell | 0.5 μm | |
| \(k_\text{int;Lact}\) | Lactate import rate by LldP | 0.008666/s | |
| \(t_\text{dub} | E. coli doubling time | 30 min |