Team:ETH Zurich/Modeling/Parameters

From 2011.igem.org

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|[[Team:ETH_Zurich/Modeling/Microfluidics#Cell Density|Derived from cdRel<sub>OD600, undiluted</sub>, c<sub>Dilution</sub>]]
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|C<sub>Agarose</sub>
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|Scaling coefficient for diffusion of small molecules in agarose instead of water
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|1.23e-5 cm<sup>2</sup>/s
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|a.
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|D<sub>AcAl</sub>
|D<sub>AcAl</sub>

Revision as of 00:45, 20 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

a. - assumption

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]
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 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]

Microfluidics Model

Parameter Description Value Reference
lChannel Microfluidics channel length 5 cm a.
rChannel Microfluidics channel radius 1 mm a.
VeColi E. coli average volume 2 μm3 TODO: Bionumbers, Paper
cdOD600, undiluted E. coli Cell Density at OD600 = 1 1e9 1/ml TODO: Bionumbers, Paper
cDilution Dilution of cell culture in microfludics channel 1/8 Choice in Microfluidics 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 1.23e-5 cm2/s a.
DAcAl Acetaldehyde Diffusion Constant 1.23e-5 cm2/s TODO: Ref
mAcAl Acetaldehyde Molecular Weight 44.05316 u TODO: Ref
DAHL AHL Diffusion Constant 4.9e-6 cm2/s TODO: Ref
mAHL AHL Molecular Weight 213.13 u TODO: Ref
Kcat,AcAl Specific enzyme activity of acetaldehyde dehydrogenase in e. Coli 14.1 μmol/(min*mg) TODO: Ref
[E]T Mean acetaldehyde dehydrogenase enzyme concentration in e. Coli 1.6659 kg/m3 Estimation from cell extract, Ref X
vmax,AcAl Maximum reaction rate for acetaldehyde dehydrogenase degrading acetaldehyde 0.02349 M/min Estimation from cell extract, Ref X
KM,AcAl Michaelis-Menten constant for acetaldehyde dehydrogenase degrading acetaldehyde 10 μM TODO: Brenda, Paper
mADH Molecular mass of acetaldehyde dehydrogenase 33442 u TODO: Uniprot
nADH Mean number of acetaldehyde dehydrogenase protein molecules per e. Coli cell 28512.2, rounded to 30000 Estimation from cell extract, Ref X
[ADH]Extract acetaldehyde dehydrogenase concentration in e. Coli cell extract 19 mg/ml TODO: Ref
dilExtract e. Coli cell extract dilution 1/12 TODO: Ref

Combined Model

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