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.

This file has been produced by Matthias Koenig.

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:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. 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: 2018-10-23 17:57
Modified: 2018-10-23 17:57

id diauxic_top_flat meta_diauxic_top
namediauxic (TOP)_flat
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
Access SBML model  L3V1 fbc-V2

SBO:0000293
BQB_IS_VERSION_OF
GO:0006007
FunctionDefinitions [2] name math sbo cvterm
bounds__max min x y x x y y
bounds__min max x y x x y y

UnitDefinitions [14] name units sbo cvterm
h meta_h hour 3600 s
g gram g
m meta_m meter m
m2 meta_m2 cubic meter m 2
l liter litre
mmol 10 3 mole
per_h 1 3600 s
mmol_per_h 10 3 mole 3600 s
mmol_per_hg 10 3 mole g 3600 s
mmol_per_l 10 3 mole litre
mmol_per_lg 10 3 mole g litre
l_per_mmol litre 10 3 mole
g_per_l g litre
g_per_mmol g 10 3 mole

Compartments [2] name size constant spatial dimensions units derived units sbo cvterm
bioreactor bioreactor 1.0 3 l litre
fba__bioreactor bioreactor 1.0 3 l litre

Species [9] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
Ac meta_Ac acetate bioreactor 0.4 mmol mmol 10 3 mole litre
Glcxt meta_Glcxt glucose bioreactor 10.8 mmol mmol 10 3 mole litre
O2 meta_O2 oxygen bioreactor 0.21 mmol mmol 10 3 mole litre
X meta_X biomass bioreactor 0.001 mmol mmol 10 3 mole litre
dummy_S dummy_S bioreactor 0.0 mmol mmol 10 3 mole litre
fba__Glcxt fba__meta_Glcxt glucose
C6H12O6
fba__bioreactor 0.0 mmol mmol 10 3 mole litre
fba__Ac fba__meta_Ac acetate
C2H4O2
fba__bioreactor 0.0 mmol mmol 10 3 mole litre
fba__O2 fba__meta_O2 oxygen
O2
fba__bioreactor 0.0 mmol mmol 10 3 mole litre
fba__X fba__meta_X biomass fba__bioreactor 0.0 mmol mmol 10 3 mole litre

Parameters [26] name constant value unit derived unit sbo cvterm
dt 0.1 h 3600 s
lb_EX_Ac -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_Ac 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_Glcxt -10.0 mmol_per_h 10 3 mole 3600 s
ub_EX_Glcxt 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_O2 -15.0 mmol_per_h 10 3 mole 3600 s
ub_EX_O2 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_X -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_X 1000.0 mmol_per_h 10 3 mole 3600 s
pEX_Ac 1.0 mmol_per_h 10 3 mole 3600 s
pEX_Glcxt 1.0 mmol_per_h 10 3 mole 3600 s
pEX_O2 1.0 mmol_per_h 10 3 mole 3600 s
pEX_X 1.0 mmol_per_h 10 3 mole 3600 s
O2_ref O2 reference 0.21 mmol_per_l 10 3 mole litre
kLa O2 mass transfer 7.5 per_h 1 3600 s
fba__zero zero bound 0.0 mmol_per_h 10 3 mole 3600 s
fba__ub_default default upper bound 1000.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_fba_EX_Ac -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_fba_EX_Glcxt -10.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_fba_EX_O2 -15.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_fba_EX_X -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_kin_EX_Glcxt -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_kin_EX_O2 -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__Vmax_EX_O2 15.0 mmol_per_h 10 3 mole 3600 s
bounds__Vmax_EX_Glcxt 10.0 mmol_per_h 10 3 mole 3600 s
bounds__Km_EX_Glcxt Km_vGlcxt 0.015 mmol_per_l 10 3 mole litre

Rules [10]   assignment name derived units sbo cvterm
pEX_Ac = EX_Ac 10 3 mole 3600 s
pEX_Glcxt = EX_Glcxt 10 3 mole 3600 s
pEX_O2 = EX_O2 10 3 mole 3600 s
pEX_X = EX_X 10 3 mole 3600 s
bounds__lb_kin_EX_Glcxt = bounds__Vmax_EX_Glcxt Glcxt bounds__Km_EX_Glcxt Glcxt 0.001 mole 3600 s
bounds__lb_kin_EX_O2 = bounds__Vmax_EX_O2 10 3 mole 3600 s
lb_EX_Ac = bounds__max bounds__lb_fba_EX_Ac Ac X 1 bioreactor dt 10 3 mole 3600 s
lb_EX_X = bounds__max bounds__lb_fba_EX_X X X 1 bioreactor dt 10 3 mole 3600 s
lb_EX_Glcxt = bounds__max bounds__lb_kin_EX_Glcxt Glcxt X 1 bioreactor dt 10 3 mole 3600 s
lb_EX_O2 = bounds__max bounds__lb_kin_EX_O2 O2 X 1 bioreactor dt 10 3 mole 3600 s

Reactions [13] name equation modifiers kinetic law derived units sbo cvterm
vO2_transfer oxygen transfer
⇆ O2 kLa O2_ref O2 bioreactor 10 3 mole 3600 s
fba__v1 fba__meta_v1 v1 (39.43 Ac + 35 O2 -> X)
[0.0 1000.0]
39.43 fba__Ac + 35.0 fba__O2 ➞ fba__X
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
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 ➞ 1.24 fba__Ac + fba__X
fba__v4 fba__meta_v4 v4 (19.23 Glcxt -> 12.12 Ac + X)
[0.0 1000.0]
19.23 fba__Glcxt ➞ 12.12 fba__Ac + fba__X
EX_Ac
[-1000.0 1000.0]
fba__Ac ⇆
EX_Glcxt
[-10.0 1000.0]
fba__Glcxt ⇆
EX_O2
[-15.0 1000.0]
fba__O2 ⇆
EX_X
[-1000.0 1000.0]
fba__X ⇆
update__update_Ac
Ac ⇆ X pEX_Ac X 1 0.001 mole 3600 s
update__update_Glcxt
Glcxt ⇆ X pEX_Glcxt X 1 0.001 mole 3600 s
update__update_O2
O2 ⇆ X pEX_O2 X 1 0.001 mole 3600 s
update__update_X
X ⇆ X pEX_X X 1 0.001 mole 3600 s

Objectives [1] name type flux objectives sbo cvterm
fba__biomass_max maximize +1.0*fba__v1 +1.0*fba__v2 +1.0*fba__v3 +1.0*fba__v4