Team:ETH Zurich/Modeling/Parameters
- Project
- Modeling
- Lab
- Human
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 |
\(k_\mathrm{leaky}\) | 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 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 | \(3.0\times 10^{-10} m^2/s\) | Trovato, 2014 |