Team:ETH Zurich/modeling/parameters

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|k<sub>-RLux</sub>||10 min<sup>-1</sup>||Dissociation rate of RLux ||Literature <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup>
|k<sub>-RLux</sub>||10 min<sup>-1</sup>||Dissociation rate of RLux ||Literature <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup>
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|K<sub>mLux</sub>||0.0124 nM||Lumped parameter for the Lux system|| [https://2014.igem.org/Team:ETH_Zurich/modeling/qs Fitted to experimental data]
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|K<sub>mLux</sub>||10 nM||Lumped parameter for the Lux system|| [https://2014.igem.org/Team:ETH_Zurich/modeling/qs#Parameters Fitted to experimental data]
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|d<sub>LuxAHL</sub>||0.004 min<sup>-1</sup>||Degradation rate of LuxAHL (30C6HSL)||Estimated from experimental data
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|d<sub>LuxAHL</sub>||0.004 min<sup>-1</sup>||External degradation rate of LuxAHL (30C6HSL)||[https://2014.igem.org/Team:ETH_Zurich/modeling/qs#Degradation Fitted to experimental data]
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|d<sub>LuxR</sub>||0.0231 min<sup>-1</sup>||Degradation rate of LuxR||Literature <sup>[[Team:ETH_Zurich/project/references|[21]]]</sup>
|d<sub>LuxR</sub>||0.0231 min<sup>-1</sup>||Degradation rate of LuxR||Literature <sup>[[Team:ETH_Zurich/project/references|[21]]]</sup>
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|α<sub>LasR</sub>||0.005 μMmin<sup>-1</sup>||Production rate of LasR||Literature <sup>[[Team:ETH_Zurich/project/references|[20]]]</sup>(Assumed to be the same as Lux system)
|α<sub>LasR</sub>||0.005 μMmin<sup>-1</sup>||Production rate of LasR||Literature <sup>[[Team:ETH_Zurich/project/references|[20]]]</sup>(Assumed to be the same as Lux system)
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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||Literature <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup>(Assumed to be the same as Lux system)
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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||Literature <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup> (Assumed to be the same as Lux system)
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|k<sub>-RLas</sub>||10 min<sup>-1</sup>||Dissociation rate of RLas ||Literature  <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup>(Assumed to be the same as Lux system)
|k<sub>-RLas</sub>||10 min<sup>-1</sup>||Dissociation rate of RLas ||Literature  <sup>[[Team:ETH_Zurich/project/references|[19]]]</sup>(Assumed to be the same as Lux system)
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|K<sub>mLas</sub>||0.3818 nM||Lumped parameter for the Las system ||[https://2014.igem.org/Team:ETH_Zurich/modeling/qs Fitted to experimental data]
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|K<sub>mLas</sub>||0.45 nM||Lumped parameter for the Las system ||[https://2014.igem.org/Team:ETH_Zurich/modeling/qs Fitted to experimental data]
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|d<sub>LasAHL</sub>||0.004 min<sup>-1</sup>||Degradation rate of LasAHL (30C12HSL)||Fitted to experimental data
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|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||Literature <sup>[[Team:ETH_Zurich/project/references|[21]]]</sup> (Assumed to be the same as Lux system)
|d<sub>LasR</sub>||0.0231 min<sup>-1</sup>||Degradation rate of LasR||Literature <sup>[[Team:ETH_Zurich/project/references|[21]]]</sup> (Assumed to be the same as Lux system)
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|d<sub>mRNAGFP</sub>||0.2773 min<sup>-1</sup>||Degradation rate of mRNA<sub>GFP</sub>||Literature <sup>[[Team:ETH_Zurich/project/references|[22]]]</sup>
|d<sub>mRNAGFP</sub>||0.2773 min<sup>-1</sup>||Degradation rate of mRNA<sub>GFP</sub>||Literature <sup>[[Team:ETH_Zurich/project/references|[22]]]</sup>
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|d<sub>GFP</sub>||0.0049 min<sup>-1</sup>||Degradation rate of GFP||Fitted to experimental data
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|d<sub>GFP</sub>||0.0049 min<sup>-1</sup>||Degradation rate of GFP||[https://2014.igem.org/Team:ETH_Zurich/modeling/qs#Retrieving_degradation_rates Fitted to experimental data]
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|k<sub>mRNALasI</sub>||5 nMmin<sup>-1</sup>||Production rate of mRNA<sub>LasI</sub>||Estimated
|k<sub>mRNALasI</sub>||5 nMmin<sup>-1</sup>||Production rate of mRNA<sub>LasI</sub>||Estimated
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|θ||0.01 μM||K<sub>m</sub> value for the production of mRNA<sub>GFP</sub> and mRNA<sub>LasI</sub>||Literature <sup>[[Team:ETH_Zurich/project/references|[20]]]</sup> (approximation)
|θ||0.01 μM||K<sub>m</sub> value for the production of mRNA<sub>GFP</sub> and mRNA<sub>LasI</sub>||Literature <sup>[[Team:ETH_Zurich/project/references|[20]]]</sup> (approximation)
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|D_{AHLext}|4.9 10<sub>{-6}</sub> cm<sub>2/s||Diffusion coefficient if extracellular AHL in liquid||Literature <sup>[[Team:ETH_Zurich/project/references#Diffusion|[27]]]</sup>  
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|D<sub>AHLext</sub>||4.9 10<sup>-6</sup> cm<sup>2</sup>/s||Diffusion coefficient of extracellular AHL in liquid||Literature <sup>[[Team:ETH_Zurich/project/references#Stewart|[27]]]</sup>
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|D<sub>m</sub>||100 min<sup>-1</sup>||Diffusion rate of AHL through the membrane||[https://2014.igem.org/Team:ETH_Zurich/modeling/diffmodel#Estimation Estimated] from literature <sup>[[Team:ETH_Zurich/project/references|[27]]]</sup>
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|r||0.006 min<sup>-1</sup>||Growth rate of ''E. coli'' in our alginate beads||
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|&alpha;||100 min<sup>-1</sup>||Ratio of '' E. coli'' volume to the volume of one bead|| V<sub>'' E. coli''</sub> from literature <sup>[[Team:ETH_Zurich/project/references#Kaplan|[28]]]</sup>, bead volume from [https://2014.igem.org/Team:ETH_Zurich/expresults#Diffusion experimental setup]
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|N<sub>0</sub>||10<sup>7</sup> cells||Initial number of cells per bead|| [https://2014.igem.org/Team:ETH_Zurich/expresults#Diffusion Experimental setup]
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|N<sub>m</sub>||8 10<sup>7</sup> cells||Maximum number of cells per bead|| [https://2014.igem.org/Team:ETH_Zurich/modeling/diffmodel#Estimation Estimated] from literature <sup>[[Team:ETH_Zurich/project/references#Lars | [29]]]</sup>
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|C<sub>beads</sub>||1||Correction factor (a priori) for diffusion of LuxAHL in alginate beads|| [https://2014.igem.org/Team:ETH_Zurich/modeling/diffmodel#Estimation Estimated] from literature <sup>[[Team:ETH_Zurich/project/references#Cronenberg | [30]]]</sup>
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We used the following tools for modelling and simulation:
We used the following tools for modelling and simulation:
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* MATLAB version 8.3.0.532 (R2014a). Natick, Massachusetts: The MathWorks Inc., 2014. for deterministic model, curve fitting and parameter estimation.  
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* 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.
* COMSOL Multiphysics software Version 4.4.0.248, COMSOL Ltd, 2014, for diffusion model and simulation.
* MEIGO Toolbox for parameter estimation.<sup>[[Team:ETH_Zurich/project/references|[26]]]</sup>
* MEIGO Toolbox for parameter estimation.<sup>[[Team:ETH_Zurich/project/references|[26]]]</sup>
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Latest revision as of 03:39, 18 October 2014

iGEM ETH Zurich 2014