Team:ETH Zurich/Modeling/Parameters

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Revision as of 18:13, 17 September 2011

Can you feel the smoke tonight?

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
α_TetR	TetR production rate	3.93 μM/min	[5]
α_C	CI production rate	1 μM/min	[1]
α_L1	LacI production rate	1 μM/min	[1]
α_L2	LacI_M1 production rate	1 μM/min	[1]
α_G	GFP production rate	2 μM/min	[1]
α_LuxI	LuxI production rate	1 μM/min	[7]
α_LuxI	LuxI production rate	1 μM/min	[7]
α_LuxI	LuxI production rate	1 μM/min	[7]
k_s1	AHL_i production rate	0.01 1/min	[2]
ρ_R	LuxR-AHL dimerization rate	0.5 1/μM³min	[1]
α_RFP	RFP production rate	1 μM/min	a.
β_AcA	Acetaldehyde repression coefficient	7.124 μM	[5]
β_T	TetR repression coefficient	0.01 μM	a.
β_C	CI repression coefficient	0.008 μM	[1]
β_L	LacI repression coefficient	0.8 μM	[1]
θ_R	LuxR-AHL repression coefficient	0.01 μM	[1]
γ_TetR	TetR degradation rate	0.0692 1/min	a.
γ_C	CI degradation rate	0.0692 1/min	[1]
γ_L	LacI degradation rate	0.0231 1/min	[1]
γ_G	GFP degradation rate	0.0692 1/min	[1]
γ_LuxI	LuxI degradation rate	0.0167 1/min	[3]
k_s0	AHL_i degradation rate	1 1/min	[2]
k_se	AHL_e degradation rate	1 1/min	[2]
γ_R	LuxR-AHL degradation rate	0.0231 1/min	[1]
γ_RFP	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]
η_ext	Average diffusion rate for all cells	1	[2]
N	Number of cells	1	a.
a_XylR	XylR production rate	95.5 uM/min	[6]
γ_XylRi	XylRi degradation rate	0.03553 1/min	[6]
γ_XylRa	XylRa degradation rate	0.04527 1/min	[6]
K_XylR	XylR activation coefficient	1.419*10-3 uM	[6]
r_XylR	XylRi oligomerization constant	0.04315e-3 1/(uM*min)	[6]
r_RXylR	XylRa dissociation constant	0.1301e-3 1/(uM*min)	[6]

Microfluidics Model

Parameter	Description	Value	Reference
l_Channel	Microfluidics channel length	5 cm	a.
r_Channel	Microfluidics channel radius	1 mm	a.
V_eColi	E. coli average volume	2 μm³	TODO: Bionumbers, Paper
cd_{OD600, undiluted}	E. coli Cell Density at OD₆₀₀ = 1	1e9 1/ml	TODO: Bionumbers, Paper
c_Dilution	Dilution of cell culture in microfludics channel	1/8	Choice in Microfluidics Model
cdRel_{OD600, undiluted}	Relative E. coli Cell Density at OD₆₀₀ = 1, undiluted	0.001	Derived from V_eColi, cd_{OD600, undiluted}
cdRel_{OD600, diluted}	Relative E. coli Cell Density at OD₆₀₀ = 1, diluted	0.000125	Derived from cdRel_{OD600, undiluted}, c_Dilution
D_AcAl	Acetaldehyde Diffusion Constant	1.23e-5 cm²/s	TODO: Ref
m_AcAl	Acetaldehyde Molecular Weight	44.05316 u	TODO: Ref
D_AHL	AHL Diffusion Constant	4.9e-6 cm²/s	TODO: Ref
m_AHL	AHL Molecular Weight	213.13 u	TODO: Ref
K_cat,AcAl	Specific enzyme activity of acetaldehyde dehydrogenase in e. Coli		TODO: Ref
[E]^T	Mean acetaldehyde dehydrogenase enzyme concentration in e. Coli		TODO: Estimation
v_max,AcAl	Maximum reaction rate for acetaldehyde dehydrogenase degrading acetaldehyde	0.02349 M/min	TODO: Estimation
K_M,AcAl	Michaelis-Menten constant for acetaldehyde dehydrogenase degrading acetaldehyde	10 μM	TODO: Brenda, Paper
m_ADH	Molecular mass of acetaldehyde dehydrogenase	33442 u	TODO: Uniprot
n_ADH	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		TODO: Ref
dil_Extract	e. Coli cell extract dilution		TODO: Ref

@@ Line 295: / Line 295: @@
 |v<sub>max,AcAl</sub>
 |Maximum reaction rate for acetaldehyde dehydrogenase degrading acetaldehyde
-|
+|0.02349 M/min
 |TODO: Estimation
 |-
 |K<sub>M,AcAl</sub>
 |Michaelis-Menten constant for acetaldehyde dehydrogenase degrading acetaldehyde
-|
+|10 μM
 |TODO: Brenda, Paper
 |-
 |m<sub>ADH</sub>
 |Molecular mass of acetaldehyde dehydrogenase
-|
+|33442 u
 |TODO: Uniprot
 |-