Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"
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Revision as of 02:43, 18 September 2015
- Project
- Modeling
- Lab
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Practices - Parts
- About Us
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
Single cell model
Reaction-diffusion model
| Name | Value | Description | References/Estimation |
|---|---|---|---|