Team:ETH Zurich/Modeling/Parameters

From 2011.igem.org

(Difference between revisions)
(→Microfluidics Model)
(→Microfluidics Model)
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|V<sub>eColi</sub>
|V<sub>eColi</sub>
|e. Coli average volume
|e. Coli average volume
-
|1 μm<sup>3</sup>
+
|5 μm<sup>3</sup>
-
|X
+
|TODO
 +
|-
 +
|cd<sub>OD600, undiluted</sub>
 +
|e. Coli Cell Density at OD<sub>600</sub> = 1
 +
|1e8 1/ml
 +
|TODO
 +
|-
 +
|c<sub>Dilution</sub>
 +
|Dilution of cell culture in microfludics channel
 +
|0.01
 +
|TODO: Choice in Microfluidics Model
 +
|-
 +
|cdRel<sub>OD600, undiluted</sub>
 +
|Relative e. Coli Cell Density at OD<sub>600</sub> = 1, undiluted
 +
|0.0125
 +
|TODO: Derivation in Microfluidics Model
 +
|-
 +
|cdRel<sub>OD600, diluted</sub>
 +
|Relative e. Coli Cell Density at OD<sub>600</sub> = 1, diluted
 +
|0.000125
 +
|TODO: Derivation in Microfluidics Model
|-
|-
|D<sub>AcAl</sub>
|D<sub>AcAl</sub>
|Acetaldehyde Diffusion Constant
|Acetaldehyde Diffusion Constant
|1.23e-5 cm<sup>2</sup>/s
|1.23e-5 cm<sup>2</sup>/s
-
|X
+
|TODO
|-
|-
|D<sub>AHL</sub>
|D<sub>AHL</sub>
|AHL Diffusion Constant
|AHL Diffusion Constant
|4.9e-6 cm<sup>2</sup>/s
|4.9e-6 cm<sup>2</sup>/s
-
|X
+
|TODO
|}
|}

Revision as of 14:42, 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

Parameter Description Value Reference
VeColi e. Coli average volume 5 μm3 TODO
cdOD600, undiluted e. Coli Cell Density at OD600 = 1 1e8 1/ml TODO
cDilution Dilution of cell culture in microfludics channel 0.01 TODO: Choice in Microfluidics Model
cdRelOD600, undiluted Relative e. Coli Cell Density at OD600 = 1, undiluted 0.0125 TODO: Derivation in Microfluidics Model
cdRelOD600, diluted Relative e. Coli Cell Density at OD600 = 1, diluted 0.000125 TODO: Derivation in Microfluidics Model
DAcAl Acetaldehyde Diffusion Constant 1.23e-5 cm2/s TODO
DAHL AHL Diffusion Constant 4.9e-6 cm2/s TODO

Combined Model

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