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
Parameters |
| |||
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
a. - assumption |