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Team:ETH Zurich/modeling/parameters
From 2014.igem.org
(Difference between revisions)
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|d<sub>LuxAHL</sub>||0.004 min<sup>-1</sup>||Degradation rate of LuxAHL (30C6HSL)||Estimated | |d<sub>LuxAHL</sub>||0.004 min<sup>-1</sup>||Degradation rate of LuxAHL (30C6HSL)||Estimated | ||
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| - | |d<sub>LuxR</sub>||0.0231 min<sup>-1</sup>||Degradation rate of LuxR|| | + | |d<sub>LuxR</sub>||0.0231 min<sup>-1</sup>||Degradation rate of LuxR||Literature <sup>[[Team:ETH_Zurich/project/references|[20]]]</sup> |
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| - | |d<sub>RLux</sub>||0.0231 min<sup>-1</sup>||Degradation rate of RLux|| | + | |d<sub>RLux</sub>||0.0231 min<sup>-1</sup>||Degradation rate of RLux||Literature <sup>[[Team:ETH_Zurich/project/references|[20]]]</sup> |
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|d<sub>Bxb1</sub>||0.01 min<sup>-1</sup>||Degradation rate of Bxb1||Assumed | |d<sub>Bxb1</sub>||0.01 min<sup>-1</sup>||Degradation rate of Bxb1||Assumed | ||
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|α<sub>LasR</sub>||60 nMmin<sup>-1</sup>||Production rate of LasR||Estimated | |α<sub>LasR</sub>||60 nMmin<sup>-1</sup>||Production rate of LasR||Estimated | ||
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| - | |k<sub>RLas</sub>||0.1 nM<sup>-1</sup>min<sup>-1</sup>|| Rate of formation of RLas from LasAHL and LasR|| | + | |k<sub>RLas</sub>||0.1 nM<sup>-1</sup>min<sup>-1</sup>|| Rate of formation of RLas from LasAHL and LasR||Literature <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup> |
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| - | |k<sub>-RLas</sub>||10 min<sup>-1</sup>||Dissociation rate of RLas || | + | |k<sub>-RLas</sub>||10 min<sup>-1</sup>||Dissociation rate of RLas ||Literature <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup> |
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|K<sub>mLas</sub>||0.1145 nM||Lumped parameter for the Las system ||Fitted | |K<sub>mLas</sub>||0.1145 nM||Lumped parameter for the Las system ||Fitted | ||
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|d<sub>LasAHL</sub>||0.004 min<sup>-1</sup>||Degradation rate of LasAHL (30C12HSL)||Estimated | |d<sub>LasAHL</sub>||0.004 min<sup>-1</sup>||Degradation rate of LasAHL (30C12HSL)||Estimated | ||
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| - | |d<sub>LasR</sub>||0.0231 min<sup>-1</sup>||Degradation rate of LasR||(Assumed to be same | + | |d<sub>LasR</sub>||0.0231 min<sup>-1</sup>||Degradation rate of LasR||Literature <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup> (Assumed to be the same for Lux system) |
|- | |- | ||
| - | |d<sub>RLas</sub>||0.0231 min<sup>-1</sup>||Degradation rate of RLas||(Assumed to be same | + | |d<sub>RLas</sub>||0.0231 min<sup>-1</sup>||Degradation rate of RLas||Literature <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup> (Assumed to be the same for Lux system) |
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|d<sub>ϕc31</sub>||0.01 min<sup>-1</sup>||Degradation rate of ϕC31||Assumed | |d<sub>ϕc31</sub>||0.01 min<sup>-1</sup>||Degradation rate of ϕC31||Assumed | ||
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| - | |L<sub>PLux</sub>||0.02461 nM<sup>-1</sup>min<sup>-1</sup>||Leakiness after using riboswitch for PLas||Fitted | + | |L<sub>PLux</sub>||0.02461 nM<sup>-1</sup>min<sup>-1</sup>||Leakiness after using riboswitch for PLas||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
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| - | |k<sub>DBxb1</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of Bxb1||Fitted | + | |k<sub>DBxb1</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of Bxb1||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
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| - | |k<sub>-DBxb1</sub>||10<sup>- | + | |k<sub>-DBxb1</sub>||10<sup>-6</sup> min<sup>-1</sup>||Dissociation rate of DBxb1||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
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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>||Fitted | + | |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>||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
|- | |- | ||
| - | |k<sub>-SABxb1</sub>||10<sup>- | + | |k<sub>-SABxb1</sub>||10<sup>-6</sup> min<sup>-1</sup>||Dissociation rate of SA<sub>Bxb1</sub>||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
|- | |- | ||
|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>ϕc31</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of ϕc31||Fitted | + | |k<sub>ϕc31</sub>||1 nM<sup>-1</sup>min<sup>-1</sup>||Dimerization rate of ϕc31||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
|- | |- | ||
| - | |k<sub>-Dϕc31</sub>||10<sup>- | + | |k<sub>-Dϕc31</sub>||10<sup>-6</sup> min<sup>-1</sup>||Rate of dissociation of Dϕc31||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
|- | |- | ||
| - | |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 | + | |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 Integrase module] |
|- | |- | ||
| - | |k<sub>-SAϕc31</sub>||10<sup>- | + | |k<sub>-SAϕc31</sub>||10<sup>-6</sup> min<sup>-1</sup>||Rate of dissociation of SA<sub>ϕc31</sub>||Fitted [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase module] |
|- | |- | ||
|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 11:34, 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 | 60 nMmin-1 | Production rate of LuxR | Estimated |
| 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 | 0.0124nM | Lumped parameter for the Lux system | Fitted |
| dLuxAHL | 0.004 min-1 | Degradation rate of LuxAHL (30C6HSL) | Estimated |
| dLuxR | 0.0231 min-1 | Degradation rate of LuxR | Literature [20] |
| dRLux | 0.0231 min-1 | Degradation rate of RLux | Literature [20] |
| dBxb1 | 0.01 min-1 | Degradation rate of Bxb1 | Assumed |
| LPLux | 0.01463 nM-1min-1 | Leakiness after using riboswitch for PLux | Fitted |
| αLasR | 60 nMmin-1 | Production rate of LasR | Estimated |
| kRLas | 0.1 nM-1min-1 | Rate of formation of RLas from LasAHL and LasR | Literature [19] |
| k-RLas | 10 min-1 | Dissociation rate of RLas | Literature [19] |
| KmLas | 0.1145 nM | Lumped parameter for the Las system | Fitted |
| 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 for Lux system) |
| dRLas | 0.0231 min-1 | Degradation rate of RLas | Literature [19] (Assumed to be the same for Lux system) |
| dϕc31 | 0.01 min-1 | Degradation rate of ϕC31 | Assumed |
| LPLux | 0.02461 nM-1min-1 | Leakiness after using riboswitch for PLas | Fitted Integrase module |
| kDBxb1 | 1 nM-1min-1 | Dimerization rate of Bxb1 | Fitted Integrase module |
| k-DBxb1 | 10-6 min-1 | Dissociation rate of DBxb1 | Fitted Integrase module |
| kSABxb1 | 1 nM-1min-1 | Rate of formation of SABxb1 from DBxb1 and SIBxb1 | Fitted Integrase module |
| k-SABxb1 | 10-6 min-1 | Dissociation rate of SABxb1 | Fitted Integrase module |
| dDBxb1 | 0.02 min-1 | Degradation rate of DBxb1 | Assumed |
| kϕc31 | 1 nM-1min-1 | Dimerization rate of ϕc31 | Fitted Integrase module |
| k-Dϕc31 | 10-6 min-1 | Rate of dissociation of Dϕc31 | Fitted Integrase module |
| kSAϕc31 | 1 nM-1min-1 | Rate of formation of SAϕc31 from Dϕc31 and SIϕc31 | Fitted Integrase module |
| k-SAϕc31 | 10-6 min-1 | Rate of dissociation of SAϕc31 | Fitted Integrase module |
| dDϕc31 | 0.02 min-1 | Degradation rate of Dϕc31 | Assumed |
| kToffBxb1 | 100 nM-2min-1 | Rate of flipping of Ton,i to ToffBxb1 | Assumed |
| k-ToffBxb1 | 100 nM-2min-1 | Rate of flipping of ToffBxb1 to Ton,f | Assumed |
| kToffϕc31 | 100 nM-2min-1 | Rate of flipping of Ton,i to Toffϕc31 | Assumed |
| k-Toffϕc31 | 100 nM-2min-1 | Rate of flipping of Toffϕc31 to Ton,f | Assumed |
| kGFP | 10 min-1 | Production rate of GFP | Assumed |
| kLuxI | 10 min-1 | Production rate of LuxI | Assumed |
| kLasI | 10 min-1 | Production rate of LasI | Assumed |
| dGFP | 0.0049 min-1 | Degradation rate of GFP | Estimated |
| dLuxI | 0.0167 min-1 | Degradation rate of LuxI | Weber |
| dLasI | 0.0167 min-1 | Degradation rate of LasI | Weber |
| kLuxAHL | 0.04 min-1 | Production rate of LuxAHL (30C6HSL) from the LuxI | Weber |
| kLasAHL | 0.04 min-1 | Production rate of LasAHL (30C12HSL) from the LasI | Weber |
