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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 | 10 nM | Lumped parameter for the Lux system | Fitted to experimental data |
| dLuxAHL | 0.004 min-1 | External degradation rate of LuxAHL (30C6HSL) | Fitted to 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 | 0.45 nM | Lumped parameter for the Las system | Fitted to experimental data |
| dLasAHL | 0.004 min-1 | Degradation rate of LasAHL (30C12HSL) | Estimated |
| 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 | 0.006 min-1 | Growth rate of E. coli in our alginate beads | |
| α | 100 min-1 | Ratio of E. coli volume to the volume of one bead | V E. coli from literature [28], bead volume from experimental setup |
| N0 | 107 cells | Initial number of cells per bead | Experimental setup |
| Nm | 8 107 cells | Maximum number of cells per bead | Estimated from literature [29] |
| Cbeads | 1 | Correction factor (a priori) for diffusion of LuxAHL in alginate beads | Estimated from literature [30] |
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 (function: fittype ; robustness option: LAR) 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]
