Diauxic Growth Model

Model version: 11

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

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-04-26 19:27
Modified: 2017-04-26 19:27

SBML model


iddiauxic_top
namediauxic (TOP)
versionL3V1
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
UnitDefinitions [14] name units sbo cvterm
h 3600 s
g g
m m
m2 m 2
l 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 [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 [15] name value unit derived unit constant sbo cvterm
dt 0.1 h 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_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_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_Glcxt 1.0 mmol_per_h 10 3 mole 3600 s
pEX_Ac 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

Rules [4]   assignment derived units sbo cvterm
pEX_Glcxt = EX_Glcxt 10 3 mole 3600 s
pEX_Ac = EX_Ac 10 3 mole 3600 s
pEX_O2 = EX_O2 10 3 mole 3600 s
pEX_X = EX_X 10 3 mole 3600 s

Reactions [5] name equation modifiers formula derived units sbo cvterm
EX_Glcxt ➞ dummy_S 0 10 3 mole 3600 s
EX_Ac ➞ dummy_S 0 10 3 mole 3600 s
EX_O2 ➞ dummy_S 0 10 3 mole 3600 s
EX_X ➞ dummy_S 0 10 3 mole 3600 s
vO2_transfer oxygen transfer ⇆ O2 kLa O2_ref O2 bioreactor 10 3 mole 3600 s