Team:ETH Zurich/Modeling/Parameters

"What I cannot create I do not understand."
- Richard Feynmann


AHL module

Single cell model

Name ValueDescription References/Estimation
\(K_{d,\text{LuxRAHL}}\)100 nMDissociation constant between luxR and AHLWeber, 2013
\(\text{LuxR}_\text{tot}\)0.0025 μMTotal concentration of LuxR estimated
\(a_\mathrm{LuxI}\)1 μM.min-1Maximal production rate of LuxIBasu, 2005
\(a_\mathrm{LuxI,ribo}\)0.1 μM.min-1Maximal production rate of LuxIETHZ 2014
\(k_\mathrm{leaky}\)0.0375 μM-1Coefficient for leakiness dependency on LuxR concentration of PLuxR promoter ETHZ 2013
\(K_\mathrm{a,LuxRAHL}\)9.89 nMActivation coefficient of LuxRAHL Estimated from our own data
\(K_\mathrm{LuxRAHL,ribo}\)285 nMActivation coefficient of LuxRAHL in case of a riboregulated LuxR responsive promoter ETHZ 2014
\(L_\mathrm{lux,ribo}\)0.01463 nM.min-1Leakiness after using riboswitch for Plux ETHZ 2014
\(n_\mathrm{lux}\)1.7Hill coefficient for LuxRAHL activation ETHZ 2014
\(d_\mathrm{LuxI}\)0.0167 min-1Degradation rate of LuxI MIT 2010
\(a_\mathrm{AHL}\)0.04 μM.min-1Production rate of AHL Weber, 2013
\(d_\mathrm{AHL}\)0.01 min-1Degradation rate of AHLBasu, 2005
\(v_\mathrm{AiiA}\)\(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \)Maximal conversion rate of AiiA calculated
\(k_\mathrm{cat}\)1.63×103min-1Turnover number of AiiA Wang, 2004
\(C_\mathrm{AiiA}\)variedConcentration of AiiA estimated
\(K_\mathrm{M,AiiA}\)2.95×103 μM Half-maximal rate substrate concentration of AiiA Wang, 2004
\(a_\mathrm{GFP}\)2 μM.min-1Maximal production rate of GFP Basu, 2005
\(d_\mathrm{GFP}\)0.01 min-1Degradation rate of GFP estimated from doubling time of E. coli

Compartment model

Name ValueDescription References/Estimation
\(N_{d}\) 150Number of E. coli in the doughnut Maximal number of E. coli that would fit on the surface
\(N_{b,max}\) 12798Maximum number of E. coli in the bulk Considering the maximal OD is 2
\(V_{cell,d}\) 6 μm3Volume around an E. coli in the doughnut estimated
\(V_{cell,b,worst}\) 78 μm3Volume around an E. coli in the bulkWorst case, estimated from \(N_{b,max}\)
\(V_{cell,b,norm}\) 1000 μm3Volume around an E. coli in the bulkNormal case

Lactate module

Name Description ValueReferences/Estimation
\(K_{\mathrm{A,Lact}}\) Lumped parameter for the lactate sensor 175 μMBased 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 LacI0.8 μM Basu, 2005
\( n_1\) Hill coefficient of LldR1.7 estimated
\( n_2\) Hill coefficient of LacI1.7 estimated

Reaction-diffusion model

Name Description ValueReferences/Estimation
\(D_{aq,AHL}\)Diffusion coefficient of AHL through water4.9×10-6cm2/sETHZ 2014
\(D_{m,AHL}\)Diffusion coefficient of AHL through a cell membrane4.629×10-16 m2/sKaplan, et al., 1985
\(R_\text{Jurkat}\)Radius of a Jurkat cell5.75 μmBioNumbers
\(R_\textit{E. coli}\)Short-side radius of an E. coli cell0.5 μmBioNumbers
\(k_\text{int;Lact}\)Lactate import rate by LldP0.008666/sDong, et al., 1993
\(t_\text{dub}\)E. coli doubling time30 minBioNumbers