Diauxic Growth Model
Model version: 13
BOUNDS submodel
Submodel for dynamically calculating the flux bounds.
The dynamically changing flux bounds are the input to the
FBA model.
Description
Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli
The key variables in the mathematical model of the metabolic
network are the glucose concentration (Glcxt), the acetate concentration (Ac),
the biomass concentration (X), and the oxygen concentration (O2) in the gas phase.
Terms of use
Copyright © 2017 Matthias Koenig
Redistribution and use of any part of this model, with or without modification, are permitted provided that
the following conditions are met:
Redistributions of this SBML file must retain the above copyright notice, this list of conditions
and the following disclaimer.
Redistributions in a different form must reproduce the above copyright notice, this list of
conditions and the following disclaimer in the documentation and/or other materials provided
with the distribution.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Model : diauxic_bounds
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2017-11-11 22:19
Modified: 2017-11-11 22:19
id diauxic_bounds meta_diauxic_bounds
name diauxic (BOUNDS)
time h
substance mmol
extent mmol
volume l
area m2
length m
L3V1 comp-V1
type
Ports [14]
name
referenced element
port ref
id ref
unit ref
metaid ref
sbo
cvterm
Port
dt_port
port dt
Parameter: dt
dt
Port
bioreactor_port
port bioreactor
Compartment: bioreactor
bioreactor
Port
Ac_port
port Ac
Species: Ac
Ac
Port
X_port
port X
Species: X
X
Port
Glcxt_port
port Glcxt
Species: Glcxt
Glcxt
Port
O2_port
port O2
Species: O2
O2
Port
lb_EX_Ac_port
port lb_EX_Ac
Parameter: lb_EX_Ac
lb_EX_Ac
Port
ub_EX_Ac_port
port ub_EX_Ac
Parameter: ub_EX_Ac
ub_EX_Ac
Port
lb_EX_X_port
port lb_EX_X
Parameter: lb_EX_X
lb_EX_X
Port
ub_EX_X_port
port ub_EX_X
Parameter: ub_EX_X
ub_EX_X
Port
lb_EX_Glcxt_port
port lb_EX_Glcxt
Parameter: lb_EX_Glcxt
lb_EX_Glcxt
Port
ub_EX_Glcxt_port
port ub_EX_Glcxt
Parameter: ub_EX_Glcxt
ub_EX_Glcxt
Port
lb_EX_O2_port
port lb_EX_O2
Parameter: lb_EX_O2
lb_EX_O2
Port
ub_EX_O2_port
port ub_EX_O2
Parameter: ub_EX_O2
ub_EX_O2
type
FunctionDefinitions [2]
name
math
sbo
cvterm
FunctionDefinition
max
min
x
y
x
x
y
y
FunctionDefinition
min
max
x
y
x
x
y
y
type
UnitDefinitions [14]
name
units
sbo
cvterm
UnitDefinition
h meta_h
hour
3600
s
UnitDefinition
g
gram
g
UnitDefinition
m meta_m
meter
m
UnitDefinition
m2 meta_m2
cubic meter
m
2
UnitDefinition
l
liter
litre
UnitDefinition
mmol
10
3
mole
UnitDefinition
per_h
1
3600
s
UnitDefinition
mmol_per_h
10
3
mole
3600
s
UnitDefinition
mmol_per_hg
10
3
mole
g
3600
s
UnitDefinition
mmol_per_l
10
3
mole
litre
UnitDefinition
mmol_per_lg
10
3
mole
g
litre
UnitDefinition
l_per_mmol
litre
10
3
mole
UnitDefinition
g_per_l
g
litre
UnitDefinition
g_per_mmol
g
10
3
mole
type
Compartments [1]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
bioreactor
bioreactor
1.0
T
3
l
litre
type
Species [4]
name
compartment
boundary condition
constant
initial amount
initial concentration
conversion factor
units
substance units
derived units
sbo
cvterm
Species
Ac meta_Ac
acetate
bioreactor
F
F
1.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
X meta_X
biomass
bioreactor
F
F
1.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
Glcxt meta_Glcxt
glucose
bioreactor
F
F
1.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
O2 meta_O2
oxygen
bioreactor
F
F
1.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
type
Parameters [18]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
dt
T
0.1
h
3600
s
Parameter
lb_EX_Ac
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
ub_EX_Ac
F
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_EX_X
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
ub_EX_X
F
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_EX_Glcxt
F
-10.0
mmol_per_h
10
3
mole
3600
s
Parameter
ub_EX_Glcxt
F
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_EX_O2
F
-15.0
mmol_per_h
10
3
mole
3600
s
Parameter
ub_EX_O2
F
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_fba_EX_Ac
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_fba_EX_X
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_fba_EX_Glcxt
F
-10.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_fba_EX_O2
F
-15.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_kin_EX_Glcxt
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_kin_EX_O2
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
Vmax_EX_O2
T
15.0
mmol_per_h
10
3
mole
3600
s
Parameter
Vmax_EX_Glcxt
T
10.0
mmol_per_h
10
3
mole
3600
s
Parameter
Km_EX_Glcxt
Km_vGlcxt
T
0.015
mmol_per_l
10
3
mole
litre
type
Rules [6]
assignment
name
derived units
sbo
cvterm
Rule
lb_kin_EX_Glcxt
=
Vmax_EX_Glcxt
Glcxt
Km_EX_Glcxt
Glcxt
0.001
mole
litre
3600
s
Rule
lb_kin_EX_O2
=
Vmax_EX_O2
10
3
mole
3600
s
Rule
lb_EX_Ac
=
max
lb_fba_EX_Ac
Ac
X
1
bioreactor
dt
10
3
mole
3600
s
Rule
lb_EX_X
=
max
lb_fba_EX_X
X
X
1
bioreactor
dt
10
3
mole
3600
s
Rule
lb_EX_Glcxt
=
max
lb_kin_EX_Glcxt
Glcxt
X
1
bioreactor
dt
10
3
mole
3600
s
Rule
lb_EX_O2
=
max
lb_kin_EX_O2
O2
X
1
bioreactor
dt
10
3
mole
3600
s