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_flat
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2017-11-11 22:19
Modified: 2017-11-11 22:19
id diauxic_top_flat meta_diauxic_top
name diauxic (TOP)_flat
time h
substance mmol
extent mmol
volume l
area m2
length m
L3V1 fbc-V2
type
FunctionDefinitions [2]
name
math
sbo
cvterm
FunctionDefinition
bounds__max
min
x
y
x
x
y
y
FunctionDefinition
bounds__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 [2]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
bioreactor
bioreactor
1.0
T
3
l
litre
Compartment
fba__bioreactor
bioreactor
1.0
T
3
l
litre
type
Species [9]
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
0.4
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
X meta_X
biomass
bioreactor
F
F
0.001
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
Glcxt meta_Glcxt
glucose
bioreactor
F
F
10.8
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
O2 meta_O2
oxygen
bioreactor
F
F
0.21
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
dummy_S
dummy_S
bioreactor
F
F
0.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
fba__Glcxt fba__meta_Glcxt
glucoseC6H12O6
fba__bioreactor
F
F
0.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
fba__Ac fba__meta_Ac
acetateC2H4O2
fba__bioreactor
F
F
0.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
fba__O2 fba__meta_O2
oxygenO2
fba__bioreactor
F
F
0.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
Species
fba__X fba__meta_X
biomass
fba__bioreactor
F
F
0.0
mmol_per_l
mmol_per_l
10
3
mole
litre
litre
type
Parameters [26]
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
pEX_Ac
F
1.0
mmol_per_h
10
3
mole
3600
s
Parameter
pEX_X
F
1.0
mmol_per_h
10
3
mole
3600
s
Parameter
pEX_Glcxt
F
1.0
mmol_per_h
10
3
mole
3600
s
Parameter
pEX_O2
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
Parameter
fba__zero
zero bound
T
0.0
mmol_per_h
10
3
mole
3600
s
Parameter
fba__ub_default
default upper bound
T
1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__lb_fba_EX_Ac
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__lb_fba_EX_X
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__lb_fba_EX_Glcxt
F
-10.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__lb_fba_EX_O2
F
-15.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__lb_kin_EX_Glcxt
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__lb_kin_EX_O2
F
-1000.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__Vmax_EX_O2
T
15.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__Vmax_EX_Glcxt
T
10.0
mmol_per_h
10
3
mole
3600
s
Parameter
bounds__Km_EX_Glcxt
Km_vGlcxt
T
0.015
mmol_per_l
10
3
mole
litre
type
Rules [10]
assignment
name
derived units
sbo
cvterm
Rule
pEX_Ac
=
EX_Ac
10
3
mole
3600
s
Rule
pEX_X
=
EX_X
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
bounds__lb_kin_EX_Glcxt
=
bounds__Vmax_EX_Glcxt
Glcxt
bounds__Km_EX_Glcxt
Glcxt
0.001
mole
litre
3600
s
Rule
bounds__lb_kin_EX_O2
=
bounds__Vmax_EX_O2
10
3
mole
3600
s
Rule
lb_EX_Ac
=
bounds__max
bounds__lb_fba_EX_Ac
Ac
X
1
bioreactor
dt
10
3
mole
3600
s
Rule
lb_EX_X
=
bounds__max
bounds__lb_fba_EX_X
X
X
1
bioreactor
dt
10
3
mole
3600
s
Rule
lb_EX_Glcxt
=
bounds__max
bounds__lb_kin_EX_Glcxt
Glcxt
X
1
bioreactor
dt
10
3
mole
3600
s
Rule
lb_EX_O2
=
bounds__max
bounds__lb_kin_EX_O2
O2
X
1
bioreactor
dt
10
3
mole
3600
s
type
Reactions [13]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
vO2_transfer
oxygen transfer
⇆
⇆ O2
kLa
O2_ref
O2
bioreactor
10
3
mole
3600
s
Reaction
fba__v1 fba__meta_v1
v1 (39.43 Ac + 35 O2 -> X)
[0.0 1000.0]
➞
35.0 fba__O2 + 39.43 fba__Ac ➞ fba__X
Reaction
fba__v2 fba__meta_v2
v2 (9.46 Glcxt + 12.92 O2 -> X)
[0.0 1000.0]
➞
9.46 fba__Glcxt + 12.92 fba__O2 ➞ fba__X
Reaction
fba__v3 fba__meta_v3
v3 (9.84 Glcxt + 12.73 O2 -> 1.24 Ac + X)
[0.0 1000.0]
➞
9.84 fba__Glcxt + 12.73 fba__O2 ➞ fba__X + 1.24 fba__Ac
Reaction
fba__v4 fba__meta_v4
v4 (19.23 Glcxt -> 12.12 Ac + X)
[0.0 1000.0]
➞
19.23 fba__Glcxt ➞ fba__X + 12.12 fba__Ac
Reaction
EX_Ac
[-1000.0 1000.0]
⇆
fba__Ac ⇆
Reaction
EX_Glcxt
[-10.0 1000.0]
⇆
fba__Glcxt ⇆
Reaction
EX_O2
[-15.0 1000.0]
⇆
fba__O2 ⇆
Reaction
EX_X
[-1000.0 1000.0]
⇆
fba__X ⇆
Reaction
update__update_Ac
⇆
Ac ⇆
X
pEX_Ac
X
1
0.001
mole
litre
3600
s
Reaction
update__update_X
⇆
X ⇆
X
pEX_X
X
1
0.001
mole
litre
3600
s
Reaction
update__update_Glcxt
⇆
Glcxt ⇆
X
pEX_Glcxt
X
1
0.001
mole
litre
3600
s
Reaction
update__update_O2
⇆
O2 ⇆
X
pEX_O2
X
1
0.001
mole
litre
3600
s
type
Objectives [1]
name
type
flux objectives
sbo
cvterm
Objective
fba__biomass_max
maximize
+1.0*fba__v1 +1.0*fba__v2 +1.0*fba__v4 +1.0*fba__v3