Team:ETH Zurich/modeling/parameters

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==Parameters==
No model is complete without parameters. Our exhaustive list of parameters are summarised in the table below.  
No model is complete without parameters. Our exhaustive list of parameters are summarised in the table below.  
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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>||0.1145 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)||Estimated from 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||Estimated from 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<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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==Tools==
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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 (function: fittype ; robustness option: LAR) and parameter estimation.
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* COMSOL Multiphysics software Version 4.4.0.248, COMSOL Ltd, 2014, for diffusion model and simulation.
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* 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