"
Team:ETH Zurich/modeling/parameters
From 2014.igem.org
(Difference between revisions)
| Line 26: | Line 26: | ||
|- | |- | ||
|L<sub>PLux</sub>||0.01463 nM<sup>-1</sup>min<sup>-1</sup>||Leakiness after using riboswitch for PLux||Fitted: [https://2014.igem.org/Team:ETH_Zurich/modeling/qs QS module] | |L<sub>PLux</sub>||0.01463 nM<sup>-1</sup>min<sup>-1</sup>||Leakiness after using riboswitch for PLux||Fitted: [https://2014.igem.org/Team:ETH_Zurich/modeling/qs QS module] | ||
| + | |- | ||
| + | |K<sub>mRNABxb1</sub>||5 nMmin<sup>-1</sup>||Rate of transcription of Bxb1||Estimated | ||
| + | |- | ||
| + | |k<sub>Bxb1</sub>||0.1 min<sup>-1</sup>||Rate of formation of Bxb1||Estimated | ||
|- | |- | ||
|α<sub>LasR</sub>||0.005 μMmin<sup>-1</sup>||Production rate of LasR||Literature <sup>[[Team:ETH_Zurich/project/references|[20]]]</sup> | |α<sub>LasR</sub>||0.005 μMmin<sup>-1</sup>||Production rate of LasR||Literature <sup>[[Team:ETH_Zurich/project/references|[20]]]</sup> | ||
| Line 44: | Line 48: | ||
|- | |- | ||
|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/qs QS module] | |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/qs QS module] | ||
| + | |- | ||
| + | |K<sub>mRNAϕc31</sub>||5 nMmin<sup>-1</sup>||Rate of transcription of ϕc31||Estimated | ||
| + | |- | ||
| + | |k<sub>ϕc31</sub>||0.1 min<sup>-1</sup>||Rate of formation of ϕc31||Estimated | ||
|- | |- | ||
|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] | |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] | ||
| Line 72: | Line 80: | ||
|- | |- | ||
|k<sub>-Toffϕc31</sub>||1 nM<sup>-2</sup>min<sup>-1</sup>||Rate of flipping of T<sub>offϕc31</sub> to T<sub>on,f</sub>||Assumed | |k<sub>-Toffϕc31</sub>||1 nM<sup>-2</sup>min<sup>-1</sup>||Rate of flipping of T<sub>offϕc31</sub> to T<sub>on,f</sub>||Assumed | ||
| + | |- | ||
| + | |k<sub>mRNAGFP</sub>||5 min<sup>-1</sup>||Production rate of mRNA<sub>GFP</sub>||Estimated | ||
|- | |- | ||
|k<sub>GFP</sub>||10 min<sup>-1</sup>||Production rate of GFP||Assumed | |k<sub>GFP</sub>||10 min<sup>-1</sup>||Production rate of GFP||Assumed | ||
Revision as of 12:33, 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 | 0.0124nM | Lumped parameter for the Lux system | Fitted: QS module |
| 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: QS module |
| KmRNABxb1 | 5 nMmin-1 | Rate of transcription of Bxb1 | Estimated |
| kBxb1 | 0.1 min-1 | Rate of formation of Bxb1 | Estimated |
| αLasR | 0.005 μMmin-1 | Production rate of LasR | Literature [20] |
| 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: 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 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: 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: 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 | 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 | 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 | Literature [21] |
| dLasI | 0.0167 min-1 | Degradation rate of LasI | Literature [21] |
| kLuxAHL | 0.04 min-1 | Production rate of LuxAHL (30C6HSL) from the LuxI | Literature |
| kLasAHL | 0.04 min-1 | Production rate of LasAHL (30C12HSL) from the LasI | Literature |
