Team:ETH Zurich/modeling/parameters
From 2014.igem.org
Parameters and Tools
Parameters
No model is complete without parameters. Our exhaustive list of parameters are summarised in the table below.
Parameter | Value | Description | Reference |
---|---|---|---|
αLuxR | 0.005 μMmin-1 | Production rate of LuxR | Literature [20] |
kRLux | 0.1 nM-1min-1 | Rate of formation of RLux from LuxAHL and LuxR | Literature [19] |
k-RLux | 10 min-1 | Dissociation rate of RLux | Literature [19] |
KmLux | 0.0124 nM | Lumped parameter for the Lux system | Fitted to experimental data |
dLuxAHL | 0.004 min-1 | Degradation rate of LuxAHL (30C6HSL) | Estimated from experimental data |
dLuxR | 0.0231 min-1 | Degradation rate of LuxR | Literature [21] |
dRLux | 0.0231 min-1 | Degradation rate of RLux | Literature [20] |
dmRNABxb1 | 0.2773 min-1 | Degradation rate of mRNABxb1 | Literature [22] |
dBxb1 | 0.01 min-1 | Degradation rate of Bxb1 | Assumed |
LPLux | 0.01463 nMmin-1 | Leakiness after using riboswitch for Plux | Fitted to experimental data |
KmRNABxb1 | 5 nMmin-1 | Rate of transcription of Bxb1 | Estimated |
kBxb1 | 0.1 min-1 | Rate of formation of Bxb1 | Assumed |
αLasR | 0.005 μMmin-1 | Production rate of LasR | Literature [20](Assumed to be the same as Lux system) |
kRLas | 0.1 nM-1min-1 | Rate of formation of RLas from LasAHL and LasR | Literature [19](Assumed to be the same as Lux system) |
k-RLas | 10 min-1 | Dissociation rate of RLas | Literature [19](Assumed to be the same as Lux system) |
KmLas | 0.3818 nM | Lumped parameter for the Las system | Fitted to experimental data |
dLasAHL | 0.004 min-1 | Degradation rate of LasAHL (30C12HSL) | Fitted to experimental data |
dLasR | 0.0231 min-1 | Degradation rate of LasR | Literature [21] (Assumed to be the same as Lux system) |
dRLas | 0.0231 min-1 | Degradation rate of RLas | Literature [20] (Assumed to be the same as
Lux system) |
dmRNAϕc31 | 0.2773 min-1 | Degradation rate of mRNAϕc31 | Literature [22] |
dϕc31 | 0.01 min-1 | Degradation rate of ϕC31 | Assumed |
LPLas | 0.02461 nMmin-1 | Leakiness after using riboswitch for Plas | Fitted to experimental data |
KmRNAϕc31 | 5 nMmin-1 | Rate of transcription of ϕc31 | Estimated |
kϕc31 | 0.1 min-1 | Rate of formation of ϕc31 | Assumed |
kDBxb1 | 1 nM-1min-1 | Dimerization rate of Bxb1 | Fitted |
k-DBxb1 | 10-6 min-1 | Dissociation rate of DBxb1 | Fitted |
kSABxb1 | 1 nM-1min-1 | Rate of formation of SABxb1 from DBxb1 and SIBxb1 | Fitted |
k-SABxb1 | 10-6 min-1 | Dissociation rate of SABxb1 | Fitted |
dDBxb1 | 0.02 min-1 | Degradation rate of DBxb1 | Assumed |
kDϕc31 | 1 nM-1min-1 | Dimerization rate of ϕc31 | Fitted |
k-Dϕc31 | 10-6 min-1 | Rate of dissociation of Dϕc31 | Fitted |
kSAϕc31 | 1 nM-1min-1 | Rate of formation of SAϕc31 from Dϕc31 and SIϕc31 | Fitted |
k-SAϕc31 | 10-6 min-1 | Rate of dissociation of SAϕc31 | Fitted |
dDϕc31 | 0.02 min-1 | Degradation rate of Dϕc31 | Assumed |
kToffBxb1 | 0.1 nM-2min-1 | Rate of flipping of Ton,i to ToffBxb1 | Assumed |
k-ToffBxb1 | 0.1 nM-2min-1 | Rate of flipping of ToffBxb1 to Ton,f | Assumed |
kToffϕc31 | 0.1 nM-2min-1 | Rate of flipping of Ton,i to Toffϕc31 | Assumed |
k-Toffϕc31 | 0.1 nM-2min-1 | Rate of flipping of Toffϕc31 to Ton,f | Assumed |
kmRNAGFP | 5 nMmin-1 | Production rate of mRNAGFP | Estimated |
kGFP | 1 min-1 | Rate of formation of folded GFP | Estimated |
dmRNAGFP | 0.2773 min-1 | Degradation rate of mRNAGFP | Literature [22] |
dGFP | 0.0049 min-1 | Degradation rate of GFP | Fitted to experimental data |
kmRNALasI | 5 nMmin-1 | Production rate of mRNALasI | Estimated |
kLasI | 20 min-1 | Rate of formation of LasI | Estimated |
dmRNALasI | 0.2773 min-1 | Degradation rate of mRNALasI | Literature [22] |
dLasI | 0.0167 min-1 | Degradation rate of LasI | Literature [21] |
kLasAHL | 0.04 min-1 | Production rate of LasAHL (30C12HSL) from the LasI | Literature [19] |
θ | 0.01 μM | Km value for the production of mRNAGFP and mRNALasI | Literature [20] (approximation) |
DAHLext | 4.9 10-6 cm2/s | Diffusion coefficient of extracellular AHL in liquid | Literature [27] |
Dm | 100 min-1 | Diffusion rate of AHL through the membrane | Estimated from literature [27] |
r | 100 min-1 | Growth rate of E. coli in our alginate beads | Estimated from literature [27] |
α | 100 min-1 | Ratio of E. coli volume to the volume of one bead | VE. coli from literature [27] |
Tools
We used the following tools for modelling and simulation:
- MATLAB version 8.3.0.532 (R2014a). Natick, Massachusetts: The MathWorks Inc., 2014. for deterministic model, curve fitting and parameter estimation.
- COMSOL Multiphysics software Version 4.4.0.248, COMSOL Ltd, 2014, for diffusion model and simulation.
- MEIGO Toolbox for parameter estimation.[26]