Diauxic Growth 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

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-07 22:35
Modified: 2017-03-07 22:35

SBML model


iddiauxic_top
nameTop level model
versionL3V1
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
FunctionDefinitions [2] name math sbo cvterm
bounds__max minimum of arguments x y x x y y
bounds__min maximum of arguments x y x x y y

UnitDefinitions [10] name units sbo cvterm
h 3600 s
g g
m m
m2 m 2
l litre
mmol 10 3 mole
mmol_per_h 10 3 mole 3600 s
mmol_per_l 10 3 mole litre
g_per_l g litre
g_per_mmol g 10 3 mole

Compartments [1] name size constant spatial dimensions unit derived unit sbo cvterm
bioreactor bioreactor 1.0 3 l litre

Species [5] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
Glcxt glucose
bioreactor 10.8 mmol 10 3 mole litre
Ac acetate
bioreactor 0.4 mmol 10 3 mole litre
O2 oxygen
bioreactor 0.21 mmol 10 3 mole litre
X biomass
bioreactor 0.001 mmol 10 3 mole litre
dummy_S dummy_S
bioreactor 0.0 mmol 10 3 mole litre

Parameters [25] name value unit derived unit constant sbo cvterm
dt fba timestep 0.1 h 3600 s
Y biomass [g_per_l] 1.0 g_per_l g litre
EX_Glcxt 1.0 mmol_per_h 10 3 mole 3600 s
EX_Ac 1.0 mmol_per_h 10 3 mole 3600 s
EX_O2 1.0 mmol_per_h 10 3 mole 3600 s
EX_X 1.0 mmol_per_h 10 3 mole 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 -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_Glcxt 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_O2 -1000.0 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
bounds__Vmax_vGlcxt Vmax_vGlcxt 10.0 mmol_per_h 10 3 mole 3600 s
bounds__Km_vGlcxt Km_vGlcxt 0.015 mmol_per_l 10 3 mole litre
bounds__ub_vGlcxt 10.0 mmol_per_h 10 3 mole 3600 s
bounds__zero zero bound 0.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_default default lower bound -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__ub_default default upper bound 1000.0 mmol_per_h 10 3 mole 3600 s
fba__zero zero bound 0.0 mmol_per_h 10 3 mole 3600 s
fba__lb_default default lower bound -1000.0 mmol_per_h 10 3 mole 3600 s
fba__ub_default default upper bound 1000.0 mmol_per_h 10 3 mole 3600 s
fba__ub_vGlcxt 10.0 mmol_per_h 10 3 mole 3600 s
fba__ub_vO2 15.0 mmol_per_h 10 3 mole 3600 s

Rules [14]   assignment derived units sbo cvterm
EX_Glcxt = dummy_EX_Glcxt 10 3 mole 3600 s
EX_Ac = dummy_EX_Ac 10 3 mole 3600 s
EX_O2 = dummy_EX_O2 10 3 mole 3600 s
EX_X = dummy_EX_X 10 3 mole 3600 s
Y = 1 X g litre
bounds__ub_vGlcxt = bounds__Vmax_vGlcxt Glcxt bounds__Km_vGlcxt Glcxt 0.001 mole 3600 s
lb_EX_Ac = bounds__max bounds__lb_default Ac bioreactor dt 10 3 mole 3600 s
lb_EX_Glcxt = bounds__max bounds__lb_default Glcxt bioreactor dt 10 3 mole 3600 s
lb_EX_O2 = bounds__max bounds__lb_default O2 bioreactor dt 10 3 mole 3600 s
lb_EX_X = bounds__max bounds__lb_default X bioreactor dt 10 3 mole 3600 s
ub_EX_Ac = bounds__min bounds__ub_default Ac bioreactor dt 10 3 mole 3600 s
ub_EX_Glcxt = bounds__min bounds__ub_default Glcxt bioreactor dt 10 3 mole 3600 s
ub_EX_O2 = bounds__min bounds__ub_default O2 bioreactor dt 10 3 mole 3600 s
ub_EX_X = bounds__min bounds__ub_default X bioreactor dt 10 3 mole 3600 s

Reactions [14] name equation modifiers formula derived units sbo cvterm
dummy_EX_O2 O2 exchange O2 ➞
dummy_EX_Glcxt Glcxt exchange Glcxt ➞
dummy_EX_Ac Ac exchange Ac ⇆
dummy_EX_X biomass exchange X ➞
fba__vO2 O2 import (vO2) ➞ O2
fba__vGlcxt Glcxt import (vGlcxt) ➞ Glcxt
fba__v1 v1 (39.43 Ac + 35 O2 -> X) 39.43 Ac + 35.0 O2 ➞ X
fba__v2 v2 (9.46 Glcxt + 12.92 O2 -> X) 9.46 Glcxt + 12.92 O2 ➞ X
fba__v3 v3 (9.84 Glcxt + 12.73 O2 -> 1.24 Ac + X) 9.84 Glcxt + 12.73 O2 ➞ X + 1.24 Ac
fba__v4 v4 (19.23 Glcxt -> 12.12 Ac + X) 19.23 Glcxt ➞ X + 12.12 Ac
update__update_Glcxt Glcxt ⇆ EX_Glcxt 10 3 mole 3600 s
update__update_Ac Ac ⇆ EX_Ac 10 3 mole 3600 s
update__update_O2 O2 ⇆ EX_O2 10 3 mole 3600 s
update__update_X X ⇆ EX_X 10 3 mole 3600 s