Revision as of 06:48, 11 September 2015

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

Parameters

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
\(K_\mathrm{a,LuxRAHL}\)	0.45 nM	Activation coefficient of LuxRAHL	ETHZ 2014
\(K_\mathrm{LuxRAHL,ribo}\)	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
\(k_\mathrm{cat}\)	1.63 10³min^-1	Turnover number of AiiA	Wang, 2004
\(C_\mathrm{AiiA}\)	varied	Concentration of AiiA
\(K_\mathrm{M,AiiA}\)	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

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
\(N_{b}\)	12798	Number of E. coli in the bulk	Considering the maximal OD is 2

Name	Description	Minimum Value	Maximum Value	References/Estimation
\(\text{B}\)	\(\frac{Lac_\mathrm{ini}^2}{K_\mathrm{d,DLL}}\)	0.000001	4
\(\text{Lac}_{\text{ini}}\)	Initial concentration of lactate in the medium	0.1 μM	2 μM	Low concentration of lactate in the medium
\(K_\mathrm{d,DLL}\)	Dissociation constant between the dimer of Lldr and Lactate	10 μM²	10000 μM²
\(\alpha\)	Multiplication factor between the initial concentration of Lactate and Production of normal cells	1	150	estimated
\(F_\mathrm{C}\)	Fold change between Lactate production by cancer and normal cells	2	4	estimated
\(a_1\)	\(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\)	0.05	1000
\( a_\mathrm{LacI}\)	Maximal production rate of LacI	0.05 μM.min^-1	1 μM.min^-1	Basu, 2005
\( d_\mathrm{LacI}\)	Degradation rate of LacI	0.01 min^-1	0.1 min^-1	Basu, 2005
\( K_\mathrm{R,LacI}\)	Repression coefficient of LacI	0.1 μM	10 μM	Basu, 2005
\( \gamma_1\)	\( \frac{L_\mathrm{2tot}}{K_\mathrm{R,L}}\)	5	10000	estimated
\( L_\mathrm{2tot}\)	Total concentration of LldR dimer	0.5 μM	10 μM	estimated from paxdb
\( K_\mathrm{R,L}\)	Repression coefficient of LldR	0.001 μM	0.1 μM	estimated
\( \gamma_2\)	\(\frac{IPTG_{tot}}{K_{IL}}\)	0	500	estimated
\( \frac{a_1}{\gamma_2+1}\)		0.001	1000	estimated
\( n_1\)	Hill coefficient of LldR	0.5	2.5	estimated
\( n_2\)	Hill coefficient of LacI	1.5	2.5	estimated

Name	Description	Minimum Value	Maximum Value	References/Estimation
\(D_\text{AHL,agar}\)	Diffusion coefficient of AHL in agar	\(3.0\times 10^{-10} m^2/s\)	\(4.41\times 10^{-10} m^2/s\)	Trovato, 2014 Fatin-Rouge, 2004

@@ Line 32: / Line 32: @@
 <table>
 <tr> <th>Name </th> <th>Value</th><th>Description </th><th>References/Estimation </th> </tr>
-<tr> <th>\(N_{d}\) </th> <th>150</th><th>Number of <i> E. coli </i> in the doughnut </th><th>Maximal number of <i>E. coli </i> that would fit on the surface </th> </tr>
+<tr> <td>\(N_{d}\) </td> <td>150</td><td>Number of <i> E. coli </i> in the doughnut </td><td>Maximal number of <i>E. coli </i> that would fit on the surface </td> </tr>
-<tr> <th>\(N_{b}\) </th> <th>12798</th><th>Number of <i> E. coli </i> in the bulk </th><th>Considering the maximal OD is 2</th> </tr>
+<tr> <td>\(N_{b}\) </td> <td>12798</td><td>Number of <i> E. coli </i> in the bulk </td><td>Considering the maximal OD is 2</td> </tr>
 </table>
 <h2>Lactate module</h2>