Team:ETH Zurich/Modeling/Parameters

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|style="font-size:2em; height: 30px" class="modeling"|Parameters
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|style="font-family: helvetica, arial, sans-serif;font-size:1.5em;"|
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= Modeling - Parameters =
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{|class="linkMap modelingTitle" align="right"
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'''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.'''
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
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{{:Team:ETH Zurich/Templates/SectionStart}}
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 +
= Single-Cell Model =
 +
a. - assumption
 +
{|style="margin: 1em auto 1em auto; width: 80%;" class="wikitable sortable"
 +
!Parameter
 +
!Description
 +
!Value
 +
!Reference
|-
|-
-
|style="border-left: none;"|[[#Single-Cell Model|Single-Cell Model]]
+
|α<sub>TetR</sub>
-
|[[#Microfluidics Model|Microfluidics Model]]
+
|TetR max. production rate
-
|[[#Combined Model|Combined Model]]
+
|3.93 μM/min, updated to 1 μM/min
-
|}
+
|[[Team:ETH_Zurich/Modeling/References#Ref5|[5]]]
|-
|-
-
|colspan="2"|'''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 here.'''
+
|α<sub>C</sub>
 +
|CI max. production rate
 +
|1 μM/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|α<sub>L1</sub>
 +
|LacI max. production rate
 +
|1 μM/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|α<sub>L2</sub>
 +
|LacI<sub>M1</sub> max. production rate
 +
|1 μM/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|α<sub>G</sub>
 +
|GFP max. production rate
 +
|2 μM/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|α<sub>LuxI</sub>
 +
|LuxI max. production rate
 +
|1 μM/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|k<sub>s1</sub>
 +
|AHL<sub>i</sub> production rate
 +
|0.01 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
 +
|-
 +
|ρ<sub>R</sub>
 +
|LuxR-AHL dimerization rate
 +
|0.5 1/(μM<sup>3</sup>*min)
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|α<sub>RFP</sub>
 +
|RFP max. production rate
 +
|1 μM/min
 +
|a.
 +
|-
 +
|β<sub>AcA</sub>
 +
|Acetaldehyde repression coefficient
 +
|7.124 μM
 +
|[[Team:ETH_Zurich/Modeling/References#Ref5|[5]]]
 +
|-
 +
|β<sub>T</sub>
 +
|TetR repression coefficient
 +
|0.01 μM, updated to 0.1 μM/min
 +
|a.
 +
|-
 +
|β<sub>C</sub>
 +
|CI repression coefficient
 +
|0.008 μM
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|β<sub>L</sub>
 +
|LacI repression coefficient
 +
|0.8 μM
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|θ<sub>R</sub>
 +
|LuxR-AHL repression coefficient
 +
|0.01 μM
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|γ<sub>TetR</sub>
 +
|TetR degradation rate
 +
|0.0692 1/min
 +
|a.
 +
|-
 +
|γ<sub>C</sub>
 +
|CI degradation rate
 +
|0.0692 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|γ<sub>L</sub>
 +
|LacI degradation rate
 +
|0.0231 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|γ<sub>G</sub>
 +
|GFP degradation rate
 +
|0.0692 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|γ<sub>LuxI</sub>
 +
|LuxI degradation rate
 +
|0.0167 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref3|[3]]]
 +
|-
 +
|k<sub>s0</sub>
 +
|AHL<sub>i</sub> degradation rate
 +
|1 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
 +
|-
 +
|k<sub>se</sub>
 +
|AHL<sub>e</sub> degradation rate
 +
|1 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref2|[2]]]
 +
|-
 +
|γ<sub>R</sub>
 +
|LuxR-AHL degradation rate
 +
|0.0231 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref1|[1]]]
 +
|-
 +
|γ<sub>RFP</sub>
 +
|RFP degradation rate
 +
|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]]]
 +
|-
 +
|n<sub>7</sub>
 +
|XylR cooperativity coefficient
 +
|5
 +
|[[Team:ETH_Zurich/Modeling/References#Ref5|[6]]]
 +
|-
 +
|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 max. production rate
 +
|95.5 μM/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref7|[6]]]
 +
|-
 +
|γ<sub>XylRi</sub>
 +
|XylRi degradation rate
 +
|0.03553 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref7|[6]]]
 +
|-
 +
|γ<sub>XylRa</sub>
 +
|XylRa degradation rate
 +
|0.04527 1/min
 +
|[[Team:ETH_Zurich/Modeling/References#Ref7|[6]]]
 +
|-
 +
|K<sub>XylR</sub>
 +
|XylR activation coefficient
 +
|1.419*10-3 μM
 +
|[[Team:ETH_Zurich/Modeling/References#Ref6|[6]]]
 +
|-
 +
|r<sub>XylR</sub>
 +
|XylRi oligomerization constant
 +
|0.04315e-3 1/(μM*min)
 +
|[[Team:ETH_Zurich/Modeling/References#Ref6|[6]]]
 +
|-
 +
|r<sub>RXylR</sub>
 +
|XylRa dissociation constant
 +
|0.1301e-3 1/(μM*min)
 +
|[[Team:ETH_Zurich/Modeling/References#Ref6|[6]]]
|}
|}
-
<table border="2" align="center">
+
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
-
<tr align="center">
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= Diffusion Model =
-
<td> <b>Parameter</b> </td><td> <b>Description</b> </td><td> <b>Value</b></td><td> <b>Reference</b></td></tr>
+
{|style="margin: 1em auto 1em auto; width: 80%;" class="wikitable sortable"
-
 
+
!Parameter
-
<tr align="center">
+
!Description
-
<td> α<sub>TetR</sub> </td><td>TetR production rate</td><td>3.93 μM/min</td><td>[5]</td></tr>
+
!Value
 +
!Reference
 +
|-
 +
|z<sub>end</sub>
 +
|Microfluidics channel length
 +
|5 cm
 +
|[[Team:ETH_Zurich/Modeling/Microfluidics#Cell Density|Choice in diffusion model]]
 +
|-
 +
|R<sub>Channel</sub>
 +
|Microfluidics channel radius
 +
|1 mm
 +
|[[Team:ETH_Zurich/Modeling/Microfluidics#Cell Density|Choice in diffusion model]]
 +
|-
 +
|V<sub>eColi</sub>
 +
|''E. coli'' average volume
 +
|2 μm<sup>3</sup>
 +
|[[Team:ETH_Zurich/Modeling/References#Ref13|[13]]] [[Team:ETH_Zurich/Modeling/References#Ref14|[14]]]
 +
|-
 +
|cd<sub>OD600, undiluted</sub>
 +
|''E. coli'' Cell Density at OD<sub>600</sub> = 1
 +
|1e9 1/ml
 +
|[[Team:ETH_Zurich/Modeling/References#Ref13|[13]]] [[Team:ETH_Zurich/Modeling/References#Ref16|[16]]]
 +
|-
 +
|c<sub>Dilution</sub>
 +
|Dilution of cell culture in microfludics channel
 +
|1/8
 +
|[[Team:ETH_Zurich/Modeling/Microfluidics#Cell Density|Choice in diffusion model]]
 +
|-
 +
|style="white-space: nowrap;"|cdRel<sub>OD600, undiluted</sub>
 +
|Relative ''E. coli'' Cell Density at OD<sub>600</sub> = 1, undiluted
 +
|0.001
 +
|[[Team:ETH_Zurich/Modeling/Microfluidics#Cell Density|Derived from V<sub>eColi</sub>, cd<sub>OD600, undiluted</sub>]]
 +
|-
 +
|cdRel<sub>OD600, diluted</sub>
 +
|Relative ''E. coli'' Cell Density at OD<sub>600</sub> = 1, diluted
 +
|0.000125
 +
|[[Team:ETH_Zurich/Modeling/Microfluidics#Cell Density|Derived from cdRel<sub>OD600, undiluted</sub>, c<sub>Dilution</sub>]]
 +
|-
 +
|C<sub>Agarose</sub>
 +
|Scaling coefficient for diffusion of small molecules in agarose instead of water
 +
|0.9
 +
|a.
 +
|-
 +
|D<sub>AcAl</sub>
 +
|Acetaldehyde Diffusion Constant
 +
|1.23e-5 cm<sup>2</sup>/s
 +
|[[Team:ETH_Zurich/Modeling/References#Ref8|[8]]]
 +
|-
 +
|m<sub>AcAl</sub>
 +
|Acetaldehyde Molecular Weight
 +
|44.05316 u
 +
|[[Team:ETH_Zurich/Modeling/References#Ref8|[8]]]
 +
|-
 +
|K<sub>cat,AcAl</sub>
 +
|Specific enzyme activity of acetaldehyde dehydrogenase in ''E. coli''
 +
|14.1 μmol/(min*mg)
 +
|[[Team:ETH_Zurich/Modeling/References#Ref10|[10]]] [[Team:ETH_Zurich/Modeling/References#Ref11|[11]]]
 +
|-
 +
|[E]<sup>T</sup>
 +
|Mean acetaldehyde dehydrogenase enzyme concentration in ''E. coli''
 +
|1.6659 kg/m<sup>3</sup>
 +
|[[Team:ETH_Zurich/Modeling/Microfluidics#Estimation of vmax.2CAcAl|Estimation from cell extract]], [[Team:ETH_Zurich/Modeling/References#Ref11|[11]]]
 +
|-
 +
|v<sub>max,AcAl</sub>
 +
|Maximum reaction rate for acetaldehyde dehydrogenase degrading acetaldehyde
 +
|0.02349 M/min
 +
|[[Team:ETH_Zurich/Modeling/Microfluidics#Estimation of vmax.2CAcAl|Estimation from cell extract]], [[Team:ETH_Zurich/Modeling/References#Ref11|[11]]]
 +
|-
 +
|K<sub>M,AcAl</sub>
 +
|Michaelis-Menten constant for acetaldehyde dehydrogenase degrading acetaldehyde
 +
|10 μM
 +
|[[Team:ETH_Zurich/Modeling/References#Ref10|[10]]] [[Team:ETH_Zurich/Modeling/References#Ref11|[11]]]
 +
|-
 +
|m<sub>ADH</sub>
 +
|Molecular mass of acetaldehyde dehydrogenase
 +
|33442 u
 +
|[[Team:ETH_Zurich/Modeling/References#Ref12|[12]]]
 +
|-
 +
|n<sub>ADH</sub>
 +
|Mean number of acetaldehyde dehydrogenase protein molecules per ''E. coli'' cell
 +
|style="white-space: nowrap;"|28512.2, rounded to 30000
 +
|[[Team:ETH_Zurich/Modeling/Microfluidics#Estimation of vmax.2CAcAl|Estimation from cell extract]], [[Team:ETH_Zurich/Modeling/References#Ref11|[11]]]
 +
|-
 +
|[ADH]<sub>Extract</sub>
 +
|acetaldehyde dehydrogenase concentration in ''E. coli'' cell extract
 +
|19 mg/ml
 +
|[[Team:ETH_Zurich/Modeling/References#Ref11|[11]]]
 +
|-
 +
|dil<sub>Extract</sub>
 +
|''E. coli'' cell extract dilution
 +
|1/12
 +
|[[Team:ETH_Zurich/Modeling/References#Ref11|[11]]]
 +
|}
-
<tr align="center">
+
{{:Team:ETH Zurich/Templates/SectionEnd}}
-
<td> α<sub>C</sub> </td><td>CI production rate</td><td>1 μM/min</td><td>[[#Ref1|[1]]]</td></tr>
+
{{:Team:ETH Zurich/Templates/SectionStart}}
-
<tr align="center">
+
= Combined Model =
-
<td> α<sub>L1</sub> </td><td>LacI production rate</td><td>1 μM/min</td><td>[1]</td></tr>
+
{|style="margin: 1em auto 1em auto; width: 80%;" class="wikitable sortable"
-
 
+
!Parameter
-
<tr align="center">
+
!Description
-
<td> α<sub>L2</sub> </td><td>LacI<sub>M1</sub>  production rate</td><td>1 μM/min</td><td>[1]</td></tr>
+
!Value
-
 
+
!Reference
-
<tr align="center">
+
|-
-
<td> α<sub>G</sub> </td><td>GFP production rate</td><td>2 μM/min</td><td>[1]</td></tr>
+
|D<sub>AHL</sub>
-
 
+
|AHL Diffusion Constant
-
<tr align="center">
+
|4.9e-6 cm<sup>2</sup>/s
-
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[7]</td></tr>
+
|[[Team:ETH_Zurich/Modeling/References#Ref9|[9]]]
-
 
+
|-
-
<tr align="center">
+
|m<sub>AHL</sub>
-
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[7]</td></tr>
+
|AHL Molecular Weight
-
 
+
|297.38990 u
-
<tr align="center">
+
|[[Team:ETH_Zurich/Modeling/References#Ref15|[15]]]
-
<td> α<sub>LuxI</sub> </td><td>LuxI production rate</td><td>1 μM/min</td><td>[7]</td></tr>
+
|-
-
 
+
|γ<sub>AHL,ext</sub>
-
<tr align="center">
+
|AHL cell-external degradation
-
<td> k<sub>s1</sub> </td><td>AHL<sub>i</sub> production rate</td><td>0.01 1/min</td><td>[2]</td></tr>
+
|8.0225e-006/s
-
 
+
|Derived from 1 day half-life at pH 7 [[Team:ETH_Zurich/Modeling/References#Ref7|[7]]]
-
<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>
+
{{:Team:ETH Zurich/Templates/SectionEnd}}
-
 
+
{{:Team:ETH Zurich/Templates/HeaderNewEnd}}
-
<tr align="center">
+
-
<td> α<sub>RFP</sub> </td><td>RFP production rate</td><td>1 μM/min</td><td>a.</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> β<sub>AcA</sub> </td><td>Acetaldehyde repression coefficient</td><td>7.124 μM</td><td>[5]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> β<sub>T</sub> </td><td>TetR repression coefficient</td><td>0.01 μM</td><td>a.</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> β<sub>C</sub> </td><td>CI repression coefficient</td><td>0.008 μM</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> β<sub>L</sub> </td><td>LacI repression coefficient</td><td>0.8 μM</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> θ<sub>R</sub> </td><td>LuxR-AHL repression coefficient</td><td>0.01 μM</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> γ<sub>TetR</sub> </td><td>TetR degradation rate</td><td>0.0692 1/min</td><td>a.</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> γ<sub>C</sub> </td><td>CI degradation rate</td><td>0.0692 1/min</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> γ<sub>L</sub> </td><td>LacI degradation rate</td><td>0.0231 1/min</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> γ<sub>G</sub> </td><td>GFP degradation rate</td><td>0.0692 1/min</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> γ<sub>LuxI</sub> </td><td>LuxI degradation rate</td><td>0.0167 1/min</td><td>[3]</td></tr>
+
-
 
+
-
<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>
+
-
 
+
-
<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>
+
-
 
+
-
<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>
+
-
 
+
-
<tr align="center">
+
-
<td> γ<sub>RFP</sub> </td><td>RFP degradation rate</td><td>0.0041 1/min</td><td>[4]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> n<sub>1</sub> </td><td>LacI cooperativity coefficient</td><td>2</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> n<sub>2</sub> </td><td>CI cooperativity coefficient</td><td>2</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> n<sub>3</sub> </td><td>TetR cooperativity coefficient</td><td>2</td><td>[2]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> n<sub>4</sub> </td><td>LuxR-AHL cooperativity coefficient</td><td>1</td><td>[1]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> n<sub>5</sub> </td><td>AlcR-AcA cooperativity coefficient</td><td>1.352</td><td>[5]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> η</td><td>Diffusion rate across the cell membrane</td><td>2</td><td>[2]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> η<sub>ext</sub> </td><td>Average diffusion rate for all cells</td><td>1</td><td>[2]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> N</td><td>Number of cells</td><td>1</td><td>a.</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> a<sub>XylR</sub></td><td>XylR production rate</td><td>95.5 uM/min</td><td>[7]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<td> n6</td><td>Xylene cooperativity coefficient</td><td>2</td><td>[7]</td></tr>
+
-
 
+
-
<tr align="center">
+
-
<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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<tr align="center">
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<td> K<sub>Xyl</sub></td><td>Xylene activation coefficient</td><td>40 uM</td><td>[7]</td></tr>
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<td> K<sub>XylR</sub></td><td>XylR activation coefficient</td><td>1.419*10-3 uM</td><td>[6]</td></tr>
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<td>n7</td><td>XylR cooperativity coefficient</td><td>5</td><td>[6]</td></tr>
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</table>
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a. - assumption
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Latest revision as of 13:36, 28 October 2011

Can you feel the smoke tonight?
 

Contents

Modeling - 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

Parameter Description Value Reference
αTetR TetR max. production rate 3.93 μM/min, updated to 1 μM/min [5]
αC CI max. production rate 1 μM/min [1]
αL1 LacI max. production rate 1 μM/min [1]
αL2 LacIM1 max. production rate 1 μM/min [1]
αG GFP max. production rate 2 μM/min [1]
αLuxI LuxI max. production rate 1 μM/min [1]
ks1 AHLi production rate 0.01 1/min [2]
ρR LuxR-AHL dimerization rate 0.5 1/(μM3*min) [1]
αRFP RFP max. production rate 1 μM/min a.
βAcA Acetaldehyde repression coefficient 7.124 μM [5]
βT TetR repression coefficient 0.01 μM, updated to 0.1 μM/min 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]
n7 XylR cooperativity coefficient 5 [6]
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 max. production rate 95.5 μM/min [6]
γXylRi XylRi degradation rate 0.03553 1/min [6]
γXylRa XylRa degradation rate 0.04527 1/min [6]
KXylR XylR activation coefficient 1.419*10-3 μM [6]
rXylR XylRi oligomerization constant 0.04315e-3 1/(μM*min) [6]
rRXylR XylRa dissociation constant 0.1301e-3 1/(μM*min) [6]


Diffusion Model

Parameter Description Value Reference
zend Microfluidics channel length 5 cm Choice in diffusion model
RChannel Microfluidics channel radius 1 mm Choice in diffusion model
VeColi E. coli average volume 2 μm3 [13] [14]
cdOD600, undiluted E. coli Cell Density at OD600 = 1 1e9 1/ml [13] [16]
cDilution Dilution of cell culture in microfludics channel 1/8 Choice in diffusion model
cdRelOD600, undiluted Relative E. coli Cell Density at OD600 = 1, undiluted 0.001 Derived from VeColi, cdOD600, undiluted
cdRelOD600, diluted Relative E. coli Cell Density at OD600 = 1, diluted 0.000125 Derived from cdRelOD600, undiluted, cDilution
CAgarose Scaling coefficient for diffusion of small molecules in agarose instead of water 0.9 a.
DAcAl Acetaldehyde Diffusion Constant 1.23e-5 cm2/s [8]
mAcAl Acetaldehyde Molecular Weight 44.05316 u [8]
Kcat,AcAl Specific enzyme activity of acetaldehyde dehydrogenase in E. coli 14.1 μmol/(min*mg) [10] [11]
[E]T Mean acetaldehyde dehydrogenase enzyme concentration in E. coli 1.6659 kg/m3 Estimation from cell extract, [11]
vmax,AcAl Maximum reaction rate for acetaldehyde dehydrogenase degrading acetaldehyde 0.02349 M/min Estimation from cell extract, [11]
KM,AcAl Michaelis-Menten constant for acetaldehyde dehydrogenase degrading acetaldehyde 10 μM [10] [11]
mADH Molecular mass of acetaldehyde dehydrogenase 33442 u [12]
nADH Mean number of acetaldehyde dehydrogenase protein molecules per E. coli cell 28512.2, rounded to 30000 Estimation from cell extract, [11]
[ADH]Extract acetaldehyde dehydrogenase concentration in E. coli cell extract 19 mg/ml [11]
dilExtract E. coli cell extract dilution 1/12 [11]


Combined Model

Parameter Description Value Reference
DAHL AHL Diffusion Constant 4.9e-6 cm2/s [9]
mAHL AHL Molecular Weight 297.38990 u [15]
γAHL,ext AHL cell-external degradation 8.0225e-006/s Derived from 1 day half-life at pH 7 [7]


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