Team:ETH Zurich/Modeling/Parameters

From 2011.igem.org

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== Single-Cell Model ==
== Single-Cell Model ==
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<table style="margin: 1em auto 1em auto;" class="wikitable sortable">
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{|style="margin: 1em auto 1em auto; " class="wikitable sortable"
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<tr align="center">
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!Parameter
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<td> <b>Parameter</b> </td><td> <b>Description</b> </td><td> <b>Value</b></td><td> <b>Reference</b></td></tr>
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!Description
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!Value
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<tr align="center">
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!Reference
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<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>
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|-
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|α<sub>TetR</sub>
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<tr align="center">
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|TetR production rate
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<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>
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|3.93 μM/min
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+
|[[Team:ETH_Zurich/Modeling/References#Ref5|[5]]]
-
<tr align="center">
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|-
-
<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>
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|α<sub>C</sub>
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|CI production rate
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<tr align="center">
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|1 μM/min
-
<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>
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|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
 
+
|-
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<tr align="center">
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|α<sub>L1</sub>
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<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>
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|LacI production rate
-
 
+
|1 μM/min
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<tr align="center">
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|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
<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>
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|-
-
 
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|α<sub>L2</sub>
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<tr align="center">
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|LacI<sub>M1</sub> production rate
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<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>
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|1 μM/min
-
 
+
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
<tr align="center">
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|-
-
<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>
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|α<sub>G</sub>
-
 
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|GFP production rate
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<tr align="center">
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|2 μM/min
-
<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>
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|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
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+
|-
-
<tr align="center">
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|α<sub>LuxI</sub>
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<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>
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|LuxI production rate
-
 
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|1 μM/min
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<tr align="center">
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|[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]
-
<td> α<sub>RFP</sub> </td><td>RFP production rate</td><td>1 μM/min</td><td>a.</td></tr>
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|-
-
 
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|α<sub>LuxI</sub>
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<tr align="center">
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|LuxI production rate
-
<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>
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|1 μM/min
-
 
+
|[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]
-
<tr align="center">
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|-
-
<td> β<sub>T</sub> </td><td>TetR repression coefficient</td><td>0.01 μM</td><td>a.</td></tr>
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|α<sub>LuxI</sub>
-
 
+
|LuxI production rate
-
<tr align="center">
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|1 μM/min
-
<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>
+
|[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]
-
 
+
|-
-
<tr align="center">
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|k<sub>s1</sub>
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<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>
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|AHL<sub>i</sub> production rate
-
 
+
|0.01 1/min
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<tr align="center">
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|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
-
<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>
+
|-
-
 
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|ρ<sub>R</sub>
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<tr align="center">
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|LuxR-AHL dimerization rate
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<td> γ<sub>TetR</sub> </td><td>TetR degradation rate</td><td>0.0692 1/min</td><td>a.</td></tr>
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|0.5 1/μM<sup>3</sup>min
-
 
+
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
<tr align="center">
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|-
-
<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>
+
|α<sub>RFP</sub>
-
 
+
|RFP production rate
-
<tr align="center">
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|1 μM/min
-
<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>
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|a.
-
 
+
|-
-
<tr align="center">
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|β<sub>AcA</sub>
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<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>
+
|Acetaldehyde repression coefficient
-
 
+
|7.124 μM
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<tr align="center">
+
|[[Team:ETH_Zurich/Modeling/References#Ref5|[5]]]
-
<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>
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|-
-
 
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|β<sub>T</sub>
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<tr align="center">
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|TetR repression coefficient
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<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>
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|0.01 μM
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|a.
-
<tr align="center">
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|-
-
<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>
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|β<sub>C</sub>
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|CI repression coefficient
-
<tr align="center">
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|0.008 μM
-
<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>
+
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
 
+
|-
-
<tr align="center">
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|β<sub>L</sub>
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<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>
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|LacI repression coefficient
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|0.8 μM
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<tr align="center">
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|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
<td> n<sub>1</sub> </td><td>LacI cooperativity coefficient</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
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|-
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|θ<sub>R</sub>
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<tr align="center">
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|LuxR-AHL repression coefficient
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<td> n<sub>2</sub> </td><td>CI cooperativity coefficient</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]</td></tr>
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|0.01 μM
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+
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
<tr align="center">
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|-
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<td> n<sub>3</sub> </td><td>TetR cooperativity coefficient</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]</td></tr>
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|γ<sub>TetR</sub>
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|TetR degradation rate
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<tr align="center">
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|0.0692 1/min
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<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>
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|a.
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|-
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<tr align="center">
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|γ<sub>C</sub>
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<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>
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|CI degradation rate
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|0.0692 1/min
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<tr align="center">
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|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
<td> η</td><td>Diffusion rate across the cell membrane</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]</td></tr>
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|-
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|γ<sub>L</sub>
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<tr align="center">
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|LacI degradation rate
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<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>
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|0.0231 1/min
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+
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
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<tr align="center">
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|-
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<td> N</td><td>Number of cells</td><td>1</td><td>a.</td></tr>
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|γ<sub>G</sub>
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|GFP degradation rate
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<tr align="center">
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|0.0692 1/min
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<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>
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|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
 
+
|-
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<tr align="center">
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|γ<sub>LuxI</sub>
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<td> n6</td><td>Xylene cooperativity coefficient</td><td>2</td><td>[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]</td></tr>
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|LuxI degradation rate
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|0.0167 1/min
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<tr align="center">
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|[[Team:ETH_Zurich/Modeling/References#Ref3|[3]]]
-
<td>γ<sub>XylR</sub></td><td>XylR degradation rate</td><td>0.03553 1/min</td><td>a.</td></tr>
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|-
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|k<sub>s0</sub>
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|AHL<sub>i</sub> degradation rate
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|1 1/min
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|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
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+
|-
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|k<sub>se</sub>
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|AHL<sub>e</sub> degradation rate
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<tr align="center">
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|1 1/min
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<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>
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|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
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|-
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<tr align="center">
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|γ<sub>R</sub>
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<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>
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|LuxR-AHL degradation rate
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|0.0231 1/min
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<tr align="center">
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|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
-
<td>n7</td><td>XylR cooperativity coefficient</td><td>5</td><td>[[Team:ETH_Zurich/Modeling/References#Ref6|[6]]]</td></tr>
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|-
-
 
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|γ<sub>RFP</sub>
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</table>
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|RFP degradation rate
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|0.0041 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref4|[4]]]
 +
|-
 +
|n<sub>1</sub>
 +
|LacI cooperativity coefficient
 +
|2
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|n<sub>2</sub>
 +
|CI cooperativity coefficient
 +
|2
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|n<sub>3</sub>
 +
|TetR cooperativity coefficient
 +
|2
 +
|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
 +
|-
 +
|n<sub>4</sub>
 +
|LuxR-AHL cooperativity coefficient
 +
|1
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|n<sub>5</sub>
 +
|AlcR-AcA cooperativity coefficient
 +
|1.352
 +
|[[Team:ETH_Zurich/Modeling/References#Ref5|[5]]]
 +
|-
 +
|η
 +
|Diffusion rate across the cell membrane
 +
|2
 +
|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
 +
|-
 +
|η<sub>ext</sub>
 +
|Average diffusion rate for all cells
 +
|1
 +
|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
 +
|-
 +
|N
 +
|Number of cells
 +
|1
 +
|a.
 +
|-
 +
|a<sub>XylR</sub>
 +
|XylR production rate
 +
|95.5 uM/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]
 +
|-
 +
|n6
 +
|Xylene cooperativity coefficient
 +
|2
 +
|[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]
 +
|-
 +
|γ<sub>XylR</sub>
 +
|XylR degradation rate
 +
|0.03553 1/min
 +
|a.
 +
|-
 +
|K<sub>Xyl</sub>
 +
|Xylene activation coefficient
 +
|40 uM
 +
|[[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]
 +
|-
 +
|K<sub>XylR</sub>
 +
|XylR activation coefficient
 +
|1.419*10-3 uM
 +
|[[Team:ETH_Zurich/Modeling/References#Ref6|[6]]]
 +
|-
 +
|n7
 +
|XylR cooperativity coefficient
 +
|5
 +
|[[Team:ETH_Zurich/Modeling/References#Ref6|[6]]]
 +
|}
a. - assumption
a. - assumption
|}
|}

Revision as of 13:21, 15 September 2011

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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 rate 3.93 μM/min [5]
αC CI production rate 1 μM/min [1]
αL1 LacI production rate 1 μM/min [1]
αL2 LacIM1 production rate 1 μM/min [1]
αG GFP production rate 2 μM/min [1]
αLuxI LuxI production rate 1 μM/min [7]
αLuxI LuxI production rate 1 μM/min [7]
αLuxI LuxI production rate 1 μM/min [7]
ks1 AHLi production rate 0.01 1/min [2]
ρR LuxR-AHL dimerization rate 0.5 1/μM3min [1]
αRFP RFP production rate 1 μM/min a.
βAcA Acetaldehyde repression coefficient 7.124 μM [5]
βT TetR repression coefficient 0.01 μM a.
βC CI repression coefficient 0.008 μM [1]
βL LacI repression coefficient 0.8 μM [1]
θR LuxR-AHL repression coefficient 0.01 μM [1]
γTetR TetR degradation rate 0.0692 1/min a.
γC CI degradation rate 0.0692 1/min [1]
γL LacI degradation rate 0.0231 1/min [1]
γG GFP degradation rate 0.0692 1/min [1]
γLuxI LuxI degradation rate 0.0167 1/min [3]
ks0 AHLi degradation rate 1 1/min [2]
kse AHLe degradation rate 1 1/min [2]
γR LuxR-AHL degradation rate 0.0231 1/min [1]
γRFP RFP degradation rate 0.0041 1/min [4]
n1 LacI cooperativity coefficient 2 [1]
n2 CI cooperativity coefficient 2 [1]
n3 TetR cooperativity coefficient 2 [2]
n4 LuxR-AHL cooperativity coefficient 1 [1]
n5 AlcR-AcA cooperativity coefficient 1.352 [5]
η Diffusion rate across the cell membrane 2 [2]
ηext Average diffusion rate for all cells 1 [2]
N Number of cells 1 a.
aXylR XylR production rate 95.5 uM/min [7]
n6 Xylene cooperativity coefficient 2 [7]
γXylR XylR degradation rate 0.03553 1/min a.
KXyl Xylene activation coefficient 40 uM [7]
KXylR XylR activation coefficient 1.419*10-3 uM [6]
n7 XylR cooperativity coefficient 5 [6]

a. - assumption

Microfluidics Model

Combined Model

Retrieved from "http://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters"