Team:ETH Zurich/Modeling/Parameters

From 2011.igem.org

(Difference between revisions)
(Single-Cell Model)
Line 21: Line 21:
<tr align="center">
<tr align="center">
-
<td> α<sub>TetR</sub> </td><td>TetR production rate</td><td>3.93 μM/min</td><td>[5]</td></tr>
+
<td> α<sub>TetR</sub> </td><td>TetR production rate</td><td>3.93 μM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref5|[5]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> α<sub>C</sub> </td><td>CI production rate</td><td>1 μM/min</td><td>[[#Ref1|[1]]]</td></tr>
+
<td> α<sub>C</sub> </td><td>CI production rate</td><td>1 μM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> α<sub>L1</sub> </td><td>LacI production rate</td><td>1 μM/min</td><td>[1]</td></tr>
+
<td> α<sub>L1</sub> </td><td>LacI production rate</td><td>1 μM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> α<sub>L2</sub> </td><td>LacI<sub>M1</sub>  production rate</td><td>1 μM/min</td><td>[1]</td></tr>
+
<td> α<sub>L2</sub> </td><td>LacI<sub>M1</sub>  production rate</td><td>1 μM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> α<sub>G</sub> </td><td>GFP production rate</td><td>2 μM/min</td><td>[1]</td></tr>
+
<td> α<sub>G</sub> </td><td>GFP production rate</td><td>2 μM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[7]</td></tr>
+
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[7]</td></tr>
+
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[7]</td></tr>
+
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> k<sub>s1</sub> </td><td>AHL<sub>i</sub> production rate</td><td>0.01 1/min</td><td>[2]</td></tr>
+
<td> k<sub>s1</sub> </td><td>AHL<sub>i</sub> production rate</td><td>0.01 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> ρ<sub>R</sub> </td><td>LuxR-AHL dimerization rate</td><td>0.5 1/μM<sup>3</sup>min</td><td>[1]</td></tr>
+
<td> ρ<sub>R</sub> </td><td>LuxR-AHL dimerization rate</td><td>0.5 1/μM<sup>3</sup>min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
Line 54: Line 54:
<tr align="center">
<tr align="center">
-
<td> β<sub>AcA</sub> </td><td>Acetaldehyde repression coefficient</td><td>7.124 μM</td><td>[5]</td></tr>
+
<td> β<sub>AcA</sub> </td><td>Acetaldehyde repression coefficient</td><td>7.124 μM</td><td>[[Team:ETH_Zurich/Modeling/References#Ref5|[5]]]</td></tr>
<tr align="center">
<tr align="center">
Line 60: Line 60:
<tr align="center">
<tr align="center">
-
<td> β<sub>C</sub> </td><td>CI repression coefficient</td><td>0.008 μM</td><td>[1]</td></tr>
+
<td> β<sub>C</sub> </td><td>CI repression coefficient</td><td>0.008 μM</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> β<sub>L</sub> </td><td>LacI repression coefficient</td><td>0.8 μM</td><td>[1]</td></tr>
+
<td> β<sub>L</sub> </td><td>LacI repression coefficient</td><td>0.8 μM</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> θ<sub>R</sub> </td><td>LuxR-AHL repression coefficient</td><td>0.01 μM</td><td>[1]</td></tr>
+
<td> θ<sub>R</sub> </td><td>LuxR-AHL repression coefficient</td><td>0.01 μM</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
Line 72: Line 72:
<tr align="center">
<tr align="center">
-
<td> γ<sub>C</sub> </td><td>CI degradation rate</td><td>0.0692 1/min</td><td>[1]</td></tr>
+
<td> γ<sub>C</sub> </td><td>CI degradation rate</td><td>0.0692 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> γ<sub>L</sub> </td><td>LacI degradation rate</td><td>0.0231 1/min</td><td>[1]</td></tr>
+
<td> γ<sub>L</sub> </td><td>LacI degradation rate</td><td>0.0231 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> γ<sub>G</sub> </td><td>GFP degradation rate</td><td>0.0692 1/min</td><td>[1]</td></tr>
+
<td> γ<sub>G</sub> </td><td>GFP degradation rate</td><td>0.0692 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> γ<sub>LuxI</sub> </td><td>LuxI degradation rate</td><td>0.0167 1/min</td><td>[3]</td></tr>
+
<td> γ<sub>LuxI</sub> </td><td>LuxI degradation rate</td><td>0.0167 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref3|[3]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> k<sub>s0</sub> </td><td>AHL<sub>i</sub> degradation rate</td><td>1 1/min</td><td>[2]</td></tr>
+
<td> k<sub>s0</sub> </td><td>AHL<sub>i</sub> degradation rate</td><td>1 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> k<sub>se</sub> </td><td>AHL<sub>e</sub> degradation rate</td><td>1 1/min</td><td>[2]</td></tr>
+
<td> k<sub>se</sub> </td><td>AHL<sub>e</sub> degradation rate</td><td>1 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> γ<sub>R</sub> </td><td>LuxR-AHL degradation rate</td><td>0.0231 1/min</td><td>[1]</td></tr>
+
<td> γ<sub>R</sub> </td><td>LuxR-AHL degradation rate</td><td>0.0231 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> γ<sub>RFP</sub> </td><td>RFP degradation rate</td><td>0.0041 1/min</td><td>[4]</td></tr>
+
<td> γ<sub>RFP</sub> </td><td>RFP degradation rate</td><td>0.0041 1/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref4|[4]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> n<sub>1</sub> </td><td>LacI cooperativity coefficient</td><td>2</td><td>[1]</td></tr>
+
<td> n<sub>1</sub> </td><td>LacI cooperativity coefficient</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> n<sub>2</sub> </td><td>CI cooperativity coefficient</td><td>2</td><td>[1]</td></tr>
+
<td> n<sub>2</sub> </td><td>CI cooperativity coefficient</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> n<sub>3</sub> </td><td>TetR cooperativity coefficient</td><td>2</td><td>[2]</td></tr>
+
<td> n<sub>3</sub> </td><td>TetR cooperativity coefficient</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> n<sub>4</sub> </td><td>LuxR-AHL cooperativity coefficient</td><td>1</td><td>[1]</td></tr>
+
<td> n<sub>4</sub> </td><td>LuxR-AHL cooperativity coefficient</td><td>1</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> n<sub>5</sub> </td><td>AlcR-AcA cooperativity coefficient</td><td>1.352</td><td>[5]</td></tr>
+
<td> n<sub>5</sub> </td><td>AlcR-AcA cooperativity coefficient</td><td>1.352</td><td>[[Team:ETH_Zurich/Modeling/References#Ref5|[5]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> η</td><td>Diffusion rate across the cell membrane</td><td>2</td><td>[2]</td></tr>
+
<td> η</td><td>Diffusion rate across the cell membrane</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> η<sub>ext</sub> </td><td>Average diffusion rate for all cells</td><td>1</td><td>[2]</td></tr>
+
<td> η<sub>ext</sub> </td><td>Average diffusion rate for all cells</td><td>1</td><td>[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]</td></tr>
<tr align="center">
<tr align="center">
Line 120: Line 120:
<tr align="center">
<tr align="center">
-
<td> a<sub>XylR</sub></td><td>XylR production rate</td><td>95.5 uM/min</td><td>[7]</td></tr>
+
<td> a<sub>XylR</sub></td><td>XylR production rate</td><td>95.5 uM/min</td><td>[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> n6</td><td>Xylene cooperativity coefficient</td><td>2</td><td>[7]</td></tr>
+
<td> n6</td><td>Xylene cooperativity coefficient</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]</td></tr>
<tr align="center">
<tr align="center">
Line 135: Line 135:
<tr align="center">
<tr align="center">
-
<td> K<sub>Xyl</sub></td><td>Xylene activation coefficient</td><td>40 uM</td><td>[7]</td></tr>
+
<td> K<sub>Xyl</sub></td><td>Xylene activation coefficient</td><td>40 uM</td><td>[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td> K<sub>XylR</sub></td><td>XylR activation coefficient</td><td>1.419*10-3 uM</td><td>[6]</td></tr>
+
<td> K<sub>XylR</sub></td><td>XylR activation coefficient</td><td>1.419*10-3 uM</td><td>[[Team:ETH_Zurich/Modeling/References#Ref6|[6]]]</td></tr>
<tr align="center">
<tr align="center">
-
<td>n7</td><td>XylR cooperativity coefficient</td><td>5</td><td>[6]</td></tr>
+
<td>n7</td><td>XylR cooperativity coefficient</td><td>5</td><td>[[Team:ETH_Zurich/Modeling/References#Ref6|[6]]]</td></tr>
</table>
</table>

Revision as of 12:24, 15 September 2011

Menu image preload Menu image preload Menu image preload Menu image preload Menu image preload Menu image preload


Parameters
Single-Cell Model Microfluidics Model Combined Model
Of course, our models do not work without parameters, and in our case, there are quite a lot of them. In order to keep track of all of their respective values and units, we gathered them in a series of tables on this page.

Single-Cell Model




Parameter Description Value Reference
αTetR TetR production rate3.93 μM/min[5]
αC CI production rate1 μM/min[1]
αL1 LacI production rate1 μM/min[1]
αL2 LacIM1 production rate1 μM/min[1]
αG GFP production rate2 μM/min[1]
αLuxI LuxI production rate1 μM/min[7]
αLuxI LuxI production rate1 μM/min[7]
αLuxI LuxI production rate1 μM/min[7]
ks1 AHLi production rate0.01 1/min[2]
ρR LuxR-AHL dimerization rate0.5 1/μM3min[1]
αRFP RFP production rate1 μM/mina.
βAcA Acetaldehyde repression coefficient7.124 μM[5]
βT TetR repression coefficient0.01 μMa.
βC CI repression coefficient0.008 μM[1]
βL LacI repression coefficient0.8 μM[1]
θR LuxR-AHL repression coefficient0.01 μM[1]
γTetR TetR degradation rate0.0692 1/mina.
γC CI degradation rate0.0692 1/min[1]
γL LacI degradation rate0.0231 1/min[1]
γG GFP degradation rate0.0692 1/min[1]
γLuxI LuxI degradation rate0.0167 1/min[3]
ks0 AHLi degradation rate1 1/min[2]
kse AHLe degradation rate1 1/min[2]
γR LuxR-AHL degradation rate0.0231 1/min[1]
γRFP RFP degradation rate0.0041 1/min[4]
n1 LacI cooperativity coefficient2[1]
n2 CI cooperativity coefficient2[1]
n3 TetR cooperativity coefficient2[2]
n4 LuxR-AHL cooperativity coefficient1[1]
n5 AlcR-AcA cooperativity coefficient1.352[5]
ηDiffusion rate across the cell membrane2[2]
ηext Average diffusion rate for all cells1[2]
NNumber of cells1a.
aXylRXylR production rate95.5 uM/min[7]
n6Xylene cooperativity coefficient2[7]
γXylRXylR degradation rate0.03553 1/mina.
KXylXylene activation coefficient40 uM[7]
KXylRXylR activation coefficient1.419*10-3 uM[6]
n7XylR cooperativity coefficient5[6]

a. - assumption