Diauxic Growth Model
Model version: 13
TOP model
Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top 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_top
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2018-10-23 17:57
Modified: 2018-10-23 17:57
id diauxic_top meta_diauxic_top
name diauxic (TOP)
time h
substance mmol
extent mmol
volume l
area m2
length m
L3V1 comp-V1
type
ModelDefinitions [3]
name
type
sbo
cvterm
ModelDefinition
diauxic_fba
diauxic_fba
ExternalModelDefinition (source=diauxic_fba.xml
)
ModelDefinition
diauxic_bounds
diauxic_bounds
ExternalModelDefinition (source=diauxic_bounds.xml
)
ModelDefinition
diauxic_update
diauxic_update
ExternalModelDefinition (source=diauxic_update.xml
)
type
Submodels [3]
name
model ref
deletions
time conversion
extent conversion
sbo
cvterm
Submodel
fba
diauxic_fba
Submodel
bounds
diauxic_bounds
Submodel
update
diauxic_update
type
UnitDefinitions [14]
name
units
sbo
cvterm
UnitDefinition
h meta_h
ReplacedElement bounds:unitRef=h
ReplacedElement fba:unitRef=h
ReplacedElement update:unitRef=h
hour
3600
s
UnitDefinition
g
ReplacedElement bounds:unitRef=g
ReplacedElement fba:unitRef=g
ReplacedElement update:unitRef=g
gram
g
UnitDefinition
m meta_m
ReplacedElement bounds:unitRef=m
ReplacedElement fba:unitRef=m
ReplacedElement update:unitRef=m
meter
m
UnitDefinition
m2 meta_m2
ReplacedElement bounds:unitRef=m2
ReplacedElement fba:unitRef=m2
ReplacedElement update:unitRef=m2
cubic meter
m
2
UnitDefinition
l
ReplacedElement bounds:unitRef=l
ReplacedElement fba:unitRef=l
ReplacedElement update:unitRef=l
liter
litre
UnitDefinition
mmol
ReplacedElement bounds:unitRef=mmol
ReplacedElement fba:unitRef=mmol
ReplacedElement update:unitRef=mmol
10
3
mole
UnitDefinition
per_h
ReplacedElement bounds:unitRef=per_h
ReplacedElement fba:unitRef=per_h
ReplacedElement update:unitRef=per_h
1
3600
s
UnitDefinition
mmol_per_h
ReplacedElement bounds:unitRef=mmol_per_h
ReplacedElement fba:unitRef=mmol_per_h
ReplacedElement update:unitRef=mmol_per_h
10
3
mole
3600
s
UnitDefinition
mmol_per_hg
ReplacedElement bounds:unitRef=mmol_per_hg
ReplacedElement fba:unitRef=mmol_per_hg
ReplacedElement update:unitRef=mmol_per_hg
10
3
mole
g
3600
s
UnitDefinition
mmol_per_l
ReplacedElement bounds:unitRef=mmol_per_l
ReplacedElement fba:unitRef=mmol_per_l
ReplacedElement update:unitRef=mmol_per_l
10
3
mole
litre
UnitDefinition
mmol_per_lg
ReplacedElement bounds:unitRef=mmol_per_lg
ReplacedElement fba:unitRef=mmol_per_lg
ReplacedElement update:unitRef=mmol_per_lg
10
3
mole
g
litre
UnitDefinition
l_per_mmol
ReplacedElement bounds:unitRef=l_per_mmol
ReplacedElement fba:unitRef=l_per_mmol
ReplacedElement update:unitRef=l_per_mmol
litre
10
3
mole
UnitDefinition
g_per_l
ReplacedElement bounds:unitRef=g_per_l
ReplacedElement fba:unitRef=g_per_l
ReplacedElement update:unitRef=g_per_l
g
litre
UnitDefinition
g_per_mmol
ReplacedElement bounds:unitRef=g_per_mmol
ReplacedElement fba:unitRef=g_per_mmol
ReplacedElement update:unitRef=g_per_mmol
g
10
3
mole
type
Compartments [1]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
bioreactor
ReplacedElement update:portRef=bioreactor_port
ReplacedElement bounds:portRef=bioreactor_port
bioreactor
1.0
T
3
l
litre
type
Species [5]
name
compartment
hasOnlySubstanceUnits
boundaryCondition
constant
initialAmount
initialConcentration
conversionFactor
units
substanceUnits
derivedUnits
sbo
cvterm
Species
Ac meta_Ac
ReplacedElement bounds:portRef=Ac_port
ReplacedElement update:portRef=Ac_port
acetate
bioreactor
F
F
F
0.4
mmol
mmol
10
3
mole
litre
Species
Glcxt meta_Glcxt
ReplacedElement bounds:portRef=Glcxt_port
ReplacedElement update:portRef=Glcxt_port
glucose
bioreactor
F
F
F
10.8
mmol
mmol
10
3
mole
litre
Species
O2 meta_O2
ReplacedElement bounds:portRef=O2_port
ReplacedElement update:portRef=O2_port
oxygen
bioreactor
F
F
F
0.21
mmol
mmol
10
3
mole
litre
Species
X meta_X
ReplacedElement bounds:portRef=X_port
ReplacedElement update:portRef=X_port
biomass
bioreactor
F
F
F
0.001
mmol
mmol
10
3
mole
litre
Species
dummy_S
dummy_S
bioreactor
F
F
F
0.0
mmol
mmol
10
3
mole
litre
type
Parameters [15]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
dt
ReplacedElement bounds:portRef=dt_port
T
0.1
h
3600
s
Parameter
lb_EX_Ac
ReplacedElement bounds:portRef=lb_EX_Ac_port
ReplacedElement fba:portRef=lb_EX_Ac_port
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
ub_EX_Ac
ReplacedElement bounds:portRef=ub_EX_Ac_port
ReplacedElement fba:portRef=ub_EX_Ac_port
F
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_EX_Glcxt
ReplacedElement bounds:portRef=lb_EX_Glcxt_port
ReplacedElement fba:portRef=lb_EX_Glcxt_port
F
-10.0
mmol_per_h
10
3
mole
3600
s
Parameter
ub_EX_Glcxt
ReplacedElement bounds:portRef=ub_EX_Glcxt_port
ReplacedElement fba:portRef=ub_EX_Glcxt_port
F
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_EX_O2
ReplacedElement bounds:portRef=lb_EX_O2_port
ReplacedElement fba:portRef=lb_EX_O2_port
F
-15.0
mmol_per_h
10
3
mole
3600
s
Parameter
ub_EX_O2
ReplacedElement bounds:portRef=ub_EX_O2_port
ReplacedElement fba:portRef=ub_EX_O2_port
F
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
lb_EX_X
ReplacedElement bounds:portRef=lb_EX_X_port
ReplacedElement fba:portRef=lb_EX_X_port
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
ub_EX_X
ReplacedElement bounds:portRef=ub_EX_X_port
ReplacedElement fba:portRef=ub_EX_X_port
F
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
pEX_Ac
ReplacedElement update:portRef=pEX_Ac_port
F
1.0
mmol_per_h
10
3
mole
3600
s
Parameter
pEX_Glcxt
ReplacedElement update:portRef=pEX_Glcxt_port
F
1.0
mmol_per_h
10
3
mole
3600
s
Parameter
pEX_O2
ReplacedElement update:portRef=pEX_O2_port
F
1.0
mmol_per_h
10
3
mole
3600
s
Parameter
pEX_X
ReplacedElement update:portRef=pEX_X_port
F
1.0
mmol_per_h
10
3
mole
3600
s
Parameter
O2_ref
O2 reference
T
0.21
mmol_per_l
10
3
mole
litre
Parameter
kLa
O2 mass transfer
T
7.5
per_h
1
3600
s
type
Rules [4]
assignment
name
derived units
sbo
cvterm
Rule
pEX_Ac
=
EX_Ac
10
3
mole
3600
s
Rule
pEX_Glcxt
=
EX_Glcxt
10
3
mole
3600
s
Rule
pEX_O2
=
EX_O2
10
3
mole
3600
s
Rule
pEX_X
=
EX_X
10
3
mole
3600
s
type
Reactions [5]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
EX_Ac
ReplacedBy fba:portRef=EX_Ac_port
➞
➞ dummy_S
0
10
3
mole
3600
s
Reaction
EX_Glcxt
ReplacedBy fba:portRef=EX_Glcxt_port
➞
➞ dummy_S
0
10
3
mole
3600
s
Reaction
EX_O2
ReplacedBy fba:portRef=EX_O2_port
➞
➞ dummy_S
0
10
3
mole
3600
s
Reaction
EX_X
ReplacedBy fba:portRef=EX_X_port
➞
➞ dummy_S
0
10
3
mole
3600
s
Reaction
vO2_transfer
oxygen transfer
⇆
⇆ O2
kLa
O2_ref
O2
bioreactor
10
3
mole
3600
s