Difference between revisions of "Team:ETH Zurich/Modeling/Parameters"

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<tr> <td>\(  n_1\)</td> <td>Hill coefficient of LldR</td><td>0.5</td> <td>2.5</td> <td>estimated</td> </tr>
 
<tr> <td>\(  n_1\)</td> <td>Hill coefficient of LldR</td><td>0.5</td> <td>2.5</td> <td>estimated</td> </tr>
 
<tr> <td>\(  n_2\)</td> <td>Hill coefficient of LacI</td><td>1.5</td> <td>2.5</td> <td>estimated</td> </tr>
 
<tr> <td>\(  n_2\)</td> <td>Hill coefficient of LacI</td><td>1.5</td> <td>2.5</td> <td>estimated</td> </tr>
 +
</table>
 +
<h2>Reaction-diffusion model</h2>
 +
<table>
 +
<tr> <th>Name </th> <th>Description </th><th>Minimum Value</th><th>Maximum Value</th><th>References/Estimation </th> </tr>
 +
<tr><td>\(D_\text{AHL,agar}\)</td><td>Diffusion coefficient of AHL in agar</td><td>\(3.0\times 10^{-10} m^2/s\)</td><td><a href="https://2015.igem.org/Team:ETH_Zurich/References#Trovato2014">Trovato, 2014</a></td>
 
</table>
 
</table>
  

Revision as of 16:06, 5 September 2015

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

Parameters

AHL module

Single cell model

Name ValueDescription References/Estimation
\(K_{d,\text{LuxRAHL}}\)100 nMDissociation constant between luxR and AHLWeber, 2013
\(\text{LuxR}_\text{tot}\)0.0025 μMTotal concentration of LuxR estimated
\(a_\mathrm{LuxI}\)1 μM.min-1Maximal production rate of LuxIBasu, 2005
\(k_\mathrm{leaky}\)0.0005 μM-1Leakiness of PLuxR promoter estimated
\(K_\mathrm{a,LuxRAHL}\)0.01 μMActivation coefficient of LuxRAHL estimated
\(d_\mathrm{LuxI}\)0.0167 min-1Degradation rate of LuxI estimated
\(a_\mathrm{AHL}\)0.04 μM.min-1Production rate of AHL Weber, 2013
\(d_\mathrm{AHL}\)0.01 min-1Degradation rate of AHLBasu, 2005
\(v_\mathrm{AiiA}\)\(k_\mathrm{cat} \cdot C_\mathrm{AiiA} \)Maximal conversion rate of AiiA
\(k_\mathrm{cat}\)1.63 103min-1Turnover number of AiiA Wang, 2004
\(C_\mathrm{AiiA}\)0.05 μMConcentration of AiiA
\(K_\mathrm{M,AiiA}\)2.95 103 μM of AiiA Wang, 2004
\(a_\mathrm{GFP}\)2 μM.min-1Maximal production rate of GFP Basu, 2005
\(d_\mathrm{GFP}\)0.01 min-1Degradation rate of GFP estimated

Lactate module

Single cell model

Assumptions

Name Description Minimum ValueMaximum ValueReferences/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 Lactate10 μM2 10000 μM2
\(\alpha\) Multiplication factor between the initial concentration of Lactate and Production of normal cells1 150 estimated
\(F_\mathrm{C}\) Fold change between Lactate production by cancer and normal cells2 4 estimated
\(a_1\) \(\frac{a_\mathrm{LacI}}{d_\mathrm{LacI}\cdot K_{RLacI}}\)0.05 1000
\( a_\mathrm{LacI}\) Maximal production rate of LacI0.05 μM.min-1 1 μM.min-1 Basu, 2005
\( d_\mathrm{LacI}\) Degradation rate of LacI0.01 min-1 0.1 min-1 Basu, 2005
\( K_\mathrm{R,LacI}\) Repression coefficient of LacI0.1 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 LldR0.001 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 LldR0.5 2.5 estimated
\( n_2\) Hill coefficient of LacI1.5 2.5 estimated

Reaction-diffusion model

Name Description Minimum ValueMaximum ValueReferences/Estimation
\(D_\text{AHL,agar}\)Diffusion coefficient of AHL in agar\(3.0\times 10^{-10} m^2/s\)Trovato, 2014