Diauxic Growth Model
Model version: 10
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
CreatorMatthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.comCreated: 2017-04-03 16:49
Modified: 2017-04-03 16:49
|
id | diauxic_top_flat |
name | diauxic (TOP)_flat |
version | L3V1 |
time | h |
substance | mmol |
extent | mmol |
volume | l |
area | m2 |
length | m |
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type |
FunctionDefinitions [2] |
name |
math |
sbo |
cvterm |
FunctionDefinition |
bounds__max |
min |
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FunctionDefinition |
bounds__min |
max |
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type |
UnitDefinitions [12] |
name |
units |
sbo |
cvterm |
UnitDefinition |
h |
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UnitDefinition |
g |
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UnitDefinition |
m |
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UnitDefinition |
m2 |
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UnitDefinition |
l |
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UnitDefinition |
mmol |
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UnitDefinition |
per_h |
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UnitDefinition |
mmol_per_h |
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UnitDefinition |
mmol_per_l |
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UnitDefinition |
l_per_mmol |
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UnitDefinition |
g_per_l |
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UnitDefinition |
g_per_mmol |
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type |
Compartments [2] |
name |
size |
constant |
spatial dimensions |
unit |
derived unit |
sbo |
cvterm |
Compartment |
bioreactor |
bioreactor |
1.0
|
T |
3 |
l |
|
|
|
Compartment |
fba__bioreactor |
bioreactor |
1.0
|
T |
3 |
l |
|
|
|
type |
Species [9] |
name |
compartment |
boundary condition |
constant |
initial amount |
initial concentration |
substance units |
derived units |
sbo |
cvterm |
Species |
Glcxt |
glucose
|
bioreactor |
F |
F |
|
10.8
|
mmol |
|
|
|
Species |
Ac |
acetate
|
bioreactor |
F |
F |
|
0.4
|
mmol |
|
|
|
Species |
O2 |
oxygen
|
bioreactor |
F |
F |
|
0.21
|
mmol |
|
|
|
Species |
X |
biomass
|
bioreactor |
F |
F |
|
0.001
|
mmol |
|
|
|
Species |
dummy_S |
dummy_S
|
bioreactor |
F |
F |
|
0.0
|
mmol |
|
|
|
Species |
fba__Glcxt |
glucose
|
fba__bioreactor |
F |
F |
|
10.8
|
mmol |
|
|
|
Species |
fba__Ac |
acetate
|
fba__bioreactor |
F |
F |
|
0.4
|
mmol |
|
|
|
Species |
fba__O2 |
oxygen
|
fba__bioreactor |
F |
F |
|
0.21
|
mmol |
|
|
|
Species |
fba__X |
biomass
|
fba__bioreactor |
F |
F |
|
0.001
|
mmol |
|
|
|
type |
Parameters [27] |
name |
value |
unit |
derived unit |
constant |
sbo |
cvterm |
Parameter |
dt |
|
0.1
|
h |
|
T |
|
|
Parameter |
lb_EX_Glcxt |
|
-10.0
|
mmol_per_h |
|
F |
|
|
Parameter |
ub_EX_Glcxt |
|
1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
lb_EX_Ac |
|
-1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
ub_EX_Ac |
|
1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
lb_EX_O2 |
|
-15.0
|
mmol_per_h |
|
F |
|
|
Parameter |
ub_EX_O2 |
|
1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
lb_EX_X |
|
-1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
ub_EX_X |
|
1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
EX_Glcxt |
|
1.0
|
mmol_per_h |
|
F |
|
|
Parameter |
EX_Ac |
|
1.0
|
mmol_per_h |
|
F |
|
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Parameter |
EX_O2 |
|
1.0
|
mmol_per_h |
|
F |
|
|
Parameter |
EX_X |
|
1.0
|
mmol_per_h |
|
F |
|
|
Parameter |
Y |
biomass [g_per_l] |
1.0
|
g_per_l |
|
T |
|
|
Parameter |
O2_ref |
O2 reference |
0.21
|
mmol_per_l |
|
T |
|
|
Parameter |
kLa |
O2 mass transfer |
7.5
|
per_h |
|
T |
|
|
Parameter |
fba__zero |
zero bound |
0.0
|
mmol_per_h |
|
T |
|
|
Parameter |
fba__ub_default |
default upper bound |
1000.0
|
mmol_per_h |
|
T |
|
|
Parameter |
bounds__lb_fba_EX_Glcxt |
|
-10.0
|
mmol_per_h |
|
F |
|
|
Parameter |
bounds__lb_fba_EX_Ac |
|
-1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
bounds__lb_fba_EX_O2 |
|
-15.0
|
mmol_per_h |
|
F |
|
|
Parameter |
bounds__lb_fba_EX_X |
|
-1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
bounds__lb_kin_EX_Glcxt |
|
-1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
bounds__lb_kin_EX_O2 |
|
-1000.0
|
mmol_per_h |
|
F |
|
|
Parameter |
bounds__Vmax_EX_O2 |
|
15.0
|
mmol_per_h |
|
T |
|
|
Parameter |
bounds__Vmax_EX_Glcxt |
|
10.0
|
mmol_per_h |
|
T |
|
|
Parameter |
bounds__Km_EX_Glcxt |
Km_vGlcxt |
0.015
|
mmol_per_l |
|
T |
|
|
type |
Rules [10] |
|
assignment |
derived units |
sbo |
cvterm |
Rule |
EX_Glcxt |
= |
|
|
|
|
Rule |
EX_Ac |
= |
|
|
|
|
Rule |
EX_O2 |
= |
|
|
|
|
Rule |
EX_X |
= |
|
|
|
|
Rule |
bounds__lb_kin_EX_Glcxt |
= |
|
|
|
|
Rule |
bounds__lb_kin_EX_O2 |
= |
|
|
|
|
Rule |
lb_EX_Ac |
= |
|
|
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|
Rule |
lb_EX_X |
= |
|
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|
Rule |
lb_EX_Glcxt |
= |
|
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Rule |
lb_EX_O2 |
= |
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type |
Reactions [13] |
name |
|
equation |
modifiers |
formula |
derived units |
sbo |
cvterm |
Reaction |
vO2_transfer |
oxygen transfer |
⇆ |
⇆ O2 |
|
|
|
|
|
Reaction |
fba__v1 |
v1 (39.43 Ac + 35 O2 -> X) |
➞ |
39.43 fba__Ac + 35.0 fba__O2 ➞ fba__X |
|
|
|
|
|
Reaction |
fba__v2 |
v2 (9.46 Glcxt + 12.92 O2 -> X) |
➞ |
9.46 fba__Glcxt + 12.92 fba__O2 ➞ fba__X |
|
|
|
|
|
Reaction |
fba__v3 |
v3 (9.84 Glcxt + 12.73 O2 -> 1.24 Ac + X) |
➞ |
9.84 fba__Glcxt + 12.73 fba__O2 ➞ fba__X + 1.24 fba__Ac |
|
|
|
|
|
Reaction |
fba__v4 |
v4 (19.23 Glcxt -> 12.12 Ac + X) |
➞ |
19.23 fba__Glcxt ➞ fba__X + 12.12 fba__Ac |
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|
Reaction |
dummy_EX_Ac |
|
⇆ |
fba__Ac ⇆ |
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|
Reaction |
dummy_EX_Glcxt |
|
⇆ |
fba__Glcxt ⇆ |
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Reaction |
dummy_EX_O2 |
|
⇆ |
fba__O2 ⇆ |
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|
Reaction |
dummy_EX_X |
|
⇆ |
fba__X ⇆ |
|
|
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|
Reaction |
update__update_Glcxt |
|
⇆ |
Glcxt ⇆ |
X
|
|
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|
Reaction |
update__update_Ac |
|
⇆ |
Ac ⇆ |
X
|
|
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|
Reaction |
update__update_O2 |
|
⇆ |
O2 ⇆ |
X
|
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Reaction |
update__update_X |
|
⇆ |
X ⇆ |
X
|
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|