Diauxic Growth Model

Model version: 8

BOUNDS submodel

Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA 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_bounds

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-22 11:07
Modified: 2017-03-22 11:07

SBML model


iddiauxic_bounds
namediauxic (BOUNDS)
versionL3V1
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
FunctionDefinitions [2] name math sbo cvterm
max minimum of arguments x y x x y y
min maximum of arguments x y x x y y

UnitDefinitions [12] 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_l 10 3 mole 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 [4] 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

Parameters [17] name value unit derived unit constant sbo cvterm
dt fba timestep 0.01 h 3600 s
zero zero bound 0.0 mmol_per_h 10 3 mole 3600 s
lb_default default lower bound -1000.0 mmol_per_h 10 3 mole 3600 s
ub_default default upper bound 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_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
lb_kin_EX_Glcxt -1000.0 mmol_per_h 10 3 mole 3600 s
lb_kin_EX_O2 -1000.0 mmol_per_h 10 3 mole 3600 s
Vmax_EX_O2 15.0 mmol_per_h 10 3 mole 3600 s
Vmax_EX_Glcxt 10.0 mmol_per_h 10 3 mole 3600 s
Km_EX_Glcxt Km_vGlcxt 0.015 mmol_per_l 10 3 mole litre

Rules [6]   assignment derived units sbo cvterm
lb_kin_EX_Glcxt = Vmax_EX_Glcxt Glcxt Km_EX_Glcxt Glcxt 0.001 mole 3600 s
lb_kin_EX_O2 = Vmax_EX_O2 10 3 mole 3600 s
lb_EX_Ac = max lb_default Ac bioreactor dt 10 3 mole 3600 s
lb_EX_Glcxt = max lb_kin_EX_Glcxt Glcxt bioreactor dt 10 3 mole 3600 s
lb_EX_O2 = max lb_kin_EX_O2 O2 bioreactor dt 10 3 mole 3600 s
lb_EX_X = max lb_default X bioreactor dt 10 3 mole 3600 s