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Team:ETH Zurich/modeling/parameters
From 2014.igem.org
(Difference between revisions)
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|k<sub>DBxb1</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of Bxb1||[https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] | |k<sub>DBxb1</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of Bxb1||[https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] | ||
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| - | |k<sub>-DBxb1</sub>||10<sup>-6</sup> min<sup>-1</sup>||Dissociation rate of DBxb1|| | + | |k<sub>-DBxb1</sub>||10<sup>-6</sup> min<sup>-1</sup>||Dissociation rate of DBxb1|| [https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] |
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| - | |k<sub>SABxb1</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Rate of formation of SA<sub>Bxb1</sub> from DBxb1 and SI<sub>Bxb1</sub>|| | + | |k<sub>SABxb1</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Rate of formation of SA<sub>Bxb1</sub> from DBxb1 and SI<sub>Bxb1</sub>|| [https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] |
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| - | |k<sub>-SABxb1</sub>||10<sup>-6</sup> min<sup>-1</sup>||Dissociation rate of SA<sub>Bxb1</sub>|| | + | |k<sub>-SABxb1</sub>||10<sup>-6</sup> min<sup>-1</sup>||Dissociation rate of SA<sub>Bxb1</sub>|| [https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] |
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|d<sub>DBxb1</sub>||0.02 min<sup>-1</sup>||Degradation rate of DBxb1||Assumed | |d<sub>DBxb1</sub>||0.02 min<sup>-1</sup>||Degradation rate of DBxb1||Assumed | ||
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| - | |k<sub>Dϕc31</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of ϕc31|| | + | |k<sub>Dϕc31</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of ϕc31|| [https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] |
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| - | |k<sub>-Dϕc31</sub>||10<sup>-6</sup> min<sup>-1</sup>||Rate of dissociation of Dϕc31|| | + | |k<sub>-Dϕc31</sub>||10<sup>-6</sup> min<sup>-1</sup>||Rate of dissociation of Dϕc31|| [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
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|k<sub>SAϕc31</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Rate of formation of SA<sub>ϕc31</sub> from Dϕc31 and SI<sub>ϕc31</sub>||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] | |k<sub>SAϕc31</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Rate of formation of SA<sub>ϕc31</sub> from Dϕc31 and SI<sub>ϕc31</sub>||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] | ||
|- | |- | ||
| - | |k<sub>-SAϕc31</sub>||10<sup>-6</sup> min<sup>-1</sup>||Rate of dissociation of SA<sub>ϕc31</sub>|| | + | |k<sub>-SAϕc31</sub>||10<sup>-6</sup> min<sup>-1</sup>||Rate of dissociation of SA<sub>ϕc31</sub>|| [https://2014.igem.org/Team:ETH_Zurich/modeling/int Fitted] |
|- | |- | ||
|d<sub>Dϕc31</sub>||0.02 min<sup>-1</sup>||Degradation rate of Dϕc31||Assumed | |d<sub>Dϕc31</sub>||0.02 min<sup>-1</sup>||Degradation rate of Dϕc31||Assumed | ||
Revision as of 15:05, 14 October 2014
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] |
| KmLas | 0.1145 nM | Lumped parameter for the Las system | Fitted: QS module |
| dLasAHL | 0.004 min-1 | Degradation rate of LasAHL (30C12HSL) | Estimated |
| dLasR | 0.0231 min-1 | Degradation rate of LasR | Literature [19] (Assumed to be the same as Lux system) |
| dRLas | 0.0231 min-1 | Degradation rate of RLas | Literature [19] (Assumed to be the same as
Lux system) |
| dmRNAϕc31 | 0.2773 min-1 | Degradation rate of mRNAϕc31 | Bionumbers |
| dϕc31 | 0.01 min-1 | Degradation rate of ϕC31 | Assumed |
| LPLas | 0.02461 nMmin-1 | Leakiness after using riboswitch for Plas | Fitted: QS module |
| KmRNAϕc31 | 5 nMmin-1 | Rate of transcription of ϕc31 | Estimated |
| kϕc31 | 0.1 min-1 | Rate of formation of ϕc31 | Estimated |
| 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 | Integrase module |
| kSAϕc31 | 1 nM-1min-1 | Rate of formation of SAϕc31 from Dϕc31 and SIϕc31 | Fitted Fitted |
| k-SAϕc31 | 10-6 min-1 | Rate of dissociation of SAϕc31 | Fitted |
| dDϕc31 | 0.02 min-1 | Degradation rate of Dϕc31 | Assumed |
| kToffBxb1 | 1 nM-2min-1 | Rate of flipping of Ton,i to ToffBxb1 | Assumed |
| k-ToffBxb1 | 1 nM-2min-1 | Rate of flipping of ToffBxb1 to Ton,f | Assumed |
| kToffϕc31 | 1 nM-2min-1 | Rate of flipping of Ton,i to Toffϕc31 | Assumed |
| k-Toffϕc31 | 1 nM-2min-1 | Rate of flipping of Toffϕc31 to Ton,f | Assumed |
| kmRNAGFP | 5 min-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 | bionumbers |
| dGFP | 0.0049 min-1 | Degradation rate of GFP | Estimated |
| kmRNALasI | 5 min-1 | Production rate of mRNALasI | Estimated |
| kLasI | 1 min-1 | Rate of formation of LasI | Estimated |
| dmRNALasI | 0.2773 min-1 | Degradation rate of mRNALasI | Literature bionumbers |
| 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 |
| θ | 0.01 μM | Km value for the production of mRNAGFP and mRNALasI | Literature [20] |
