Latest revision as of 03:41, 19 September 2015

"What I cannot create I do not understand."
- Richard Feynmann

Parameters

AHL module

Single cell model

Name	Value	Description	References/Estimation
\(K_{d,\text{LuxRAHL}}\)	100 nM	Dissociation constant between luxR and AHL	Weber, 2013
\(\text{LuxR}_\text{tot}\)	0.0025 μM	Total concentration of LuxR	estimated
\(a_\mathrm{LuxI}\)	1 μM.min^-1	Maximal production rate of LuxI	Basu, 2005
\(a_\mathrm{LuxI,ribo}\)	0.1 μM.min^-1	Maximal production rate of LuxI	ETHZ 2014
\(k_\mathrm{leaky}\)	0.0375 μM^-1	Coefficient for leakiness dependency on LuxR concentration of P_LuxR promoter	ETHZ 2013
\(K_\mathrm{a,LuxRAHL}\)	9.89 nM	Activation coefficient of LuxRAHL	Estimated from our own data
\(K_\mathrm{LuxRAHL,ribo}\)	285 nM	Activation coefficient of LuxRAHL in case of a riboregulated LuxR responsive promoter	ETHZ 2014
\(L_\mathrm{lux,ribo}\)	0.01463 nM.min^-1	Leakiness after using riboswitch for P_lux	ETHZ 2014
\(n_\mathrm{lux}\)	1.7	Hill coefficient for LuxRAHL activation	ETHZ 2014
\(d_\mathrm{LuxI}\)	0.0167 min^-1	Degradation rate of LuxI	MIT 2010
\(a_\mathrm{AHL}\)	0.04 μM.min^-1	Production rate of AHL	Weber, 2013
\(d_\mathrm{AHL}\)	0.01 min^-1	Degradation rate of AHL	Basu, 2005
\(v_\mathrm{AiiA}\)	\(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \)	Maximal conversion rate of AiiA	calculated
\(k_\mathrm{cat}\)	1.63×10³min^-1	Turnover number of AiiA	Wang, 2004
\(C_\mathrm{AiiA}\)	varied	Concentration of AiiA	estimated
\(K_\mathrm{M,AiiA}\)	2.95×10³ μM	Half-maximal rate substrate concentration of AiiA	Wang, 2004
\(a_\mathrm{GFP}\)	2 μM.min^-1	Maximal production rate of GFP	Basu, 2005
\(d_\mathrm{GFP}\)	0.01 min^-1	Degradation rate of GFP	estimated from doubling time of E. coli

Compartment model

Name	Value	Description	References/Estimation
\(N_{d}\)	150	Number of E. coli in the doughnut	Maximal number of E. coli that would fit on the surface
\(N_{b,max}\)	12798	Maximum number of E. coli in the bulk	Considering the maximal OD is 2
\(V_{cell,d}\)	6 μm³	Volume around an E. coli in the doughnut	estimated
\(V_{cell,b,worst}\)	78 μm³	Volume around an E. coli in the bulk	Worst case, estimated from \(N_{b,max}\)
\(V_{cell,b,norm}\)	1000 μm³	Volume around an E. coli in the bulk	Normal case

Lactate module

Name	Description	Value	References/Estimation
\(K_{\mathrm{A,Lact}}\)	Lumped parameter for the lactate sensor	175 μM	Based on the characterization of the promoters.
\( a_\mathrm{LacI}\)	Maximal production rate of LacI	1 μM.min^-1	Basu, 2005
\( d_\mathrm{LacI}\)	Degradation rate of LacI	0.0231 min^-1	Basu, 2005
\( K_\mathrm{R,LacI}\)	Repression coefficient of LacI	0.8 μM	Basu, 2005
\( n_1\)	Hill coefficient of LldR	1.7	estimated
\( n_2\)	Hill coefficient of LacI	1.7	estimated

Reaction-diffusion model

Name	Description	Value	References/Estimation
\(D_{aq,AHL}\)	Diffusion coefficient of AHL through water	4.9×10^-6cm²/s	ETHZ 2014
\(D_{m,AHL}\)	Diffusion coefficient of AHL through a cell membrane	4.629×10^-16 m²/s	Kaplan, et al., 1985
\(R_\text{Jurkat}\)	Radius of a Jurkat cell	5.75 μm	BioNumbers
\(R_\textit{E. coli}\)	Short-side radius of an E. coli cell	0.5 μm	BioNumbers
\(k_\text{int;Lact}\)	Lactate import rate by LldP	0.008666/s	Dong, et al., 1993
\(t_\text{dub}\)	E. coli doubling time	30 min	BioNumbers

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 <tr><td>\(a_\mathrm{AHL}\)</td><td>0.04 &mu;M.min<SUP>-1</SUP></td><td>Production rate of AHL </td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Weber2013">Weber, 2013</a></td></tr>
 <tr><td>\(d_\mathrm{AHL}\)</td><td>0.01 min<SUP>-1</SUP></td><td>Degradation rate of AHL</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td></tr>
-<tr><td>\(v_\mathrm{AiiA}\)</td><td>\(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \)</td><td>Maximal conversion rate of AiiA </td><td></td></tr>
+<tr><td>\(v_\mathrm{AiiA}\)</td><td>\(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \)</td><td>Maximal conversion rate of AiiA </td><td>calculated</td></tr>
 <tr><td>\(k_\mathrm{cat}\)</td><td>1.63&times;10<SUP>3</SUP>min<SUP>-1</SUP></td><td>Turnover number of AiiA </td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Wang2004">Wang, 2004</a></td></tr>
-<tr><td>\(C_\mathrm{AiiA}\)</td><td>varied</td><td>Concentration of AiiA </td><td></td></tr>
+<tr><td>\(C_\mathrm{AiiA}\)</td><td>varied</td><td>Concentration of AiiA </td><td>estimated</td></tr>
 <tr><td>\(K_\mathrm{M,AiiA}\)</td><td>2.95&times;10<SUP>3</SUP> &mu;M</td><td> Half-maximal rate substrate concentration of AiiA </td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Wang2004">Wang, 2004</a></td></tr>
 <tr><td>\(a_\mathrm{GFP}\)</td><td>2 &mu;M.min<SUP>-1</SUP></td><td>Maximal production rate of GFP </td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td></tr>
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 <tr> <th>Name </th> <th>Description </th><th>Value</th><th>References/Estimation </th> </tr>
-<tr> <td>\(K_{\mathrm{A,Lact}}\)</td> <td> Lumped parameter for the lactate sensor </td><td>175 &mu;M</td><td>Based on the <a href="#Parameter_fitting">characterization</a> of the promoters. </td> </tr>
+<tr> <td>\(K_{\mathrm{A,Lact}}\)</td> <td> Lumped parameter for the lactate sensor </td><td>175 &mu;M</td><td>Based on the <a href="https://2015.igem.org/Team:ETH_Zurich/Modeling/Experiments_Model">characterization</a> of the promoters. </td> </tr>
 <tr> <td>\( a_\mathrm{LacI}\)</td> <td> Maximal production rate of LacI</td> <td>1 &mu;M.min<SUP>-1</SUP> </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr>
 <tr> <td>\( d_\mathrm{LacI}\)</td> <td> Degradation rate of LacI</td> <td>0.0231 min<SUP>-1</SUP> </td> <td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Basu2005">Basu, 2005</a></td> </tr>
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 <tr><td>\(D_{aq,AHL}\)</td><td>Diffusion coefficient of AHL through water</td><td>4.9&times;10<sup>-6</sup>cm<sup>2</sup>/s</td><td>ETHZ 2014</td></tr>
 <tr><td>\(D_{m,AHL}\)</td><td>Diffusion coefficient of AHL through a cell membrane</td><td>4.629&times;10<sup>-16</sup> m<sup>2</sup>/s</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Kaplan1985">Kaplan, <i>et al.</i>, 1985</a></td></tr>
-<tr><td>\(R_\text{Jurkat}\)</td><td>Radius of a Jurkat cell</td><td>5.75 &mu;m</td><td></td></tr>
+<tr><td>\(R_\text{Jurkat}\)</td><td>Radius of a Jurkat cell</td><td>5.75 &mu;m</td><td><a href="http://bionumbers.hms.harvard.edu/">BioNumbers</a></td></tr>
-<tr><td>\(R_\textit{E. coli}\)</td><td>Short-side radius of an <i>E. coli</i> cell</td><td>0.5 &mu;m</td><td></td></tr>
+<tr><td>\(R_\textit{E. coli}\)</td><td>Short-side radius of an <i>E. coli</i> cell</td><td>0.5 &mu;m</td><td><a href="http://bionumbers.hms.harvard.edu/">BioNumbers</a></td></tr>
-<tr><td>\(k_\text{int;Lact}\)</td><td>Lactate import rate by LldP</td><td>0.008666/s</td><td></td></tr>
+<tr><td>\(k_\text{int;Lact}\)</td><td>Lactate import rate by LldP</td><td>0.008666/s</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Dong1993">Dong, <i>et al.</i>, 1993</a></td></tr>
-<tr><td>\(t_\text{dub}</td><td><i>E. coli</i> doubling time</td><td>30 min</td><td></td></tr>
+<tr><td>\(t_\text{dub}\)</td><td><i>E. coli</i> doubling time</td><td>30 min</td><td><a href="http://bionumbers.hms.harvard.edu/">BioNumbers</a></td></tr>
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Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"

Latest revision as of 03:41, 19 September 2015

Parameters

AHL module

Single cell model

Compartment model

Lactate module

Reaction-diffusion model