Diauxic Growth Model

Model version: 13

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: 2017-11-11 22:19
Modified: 2017-11-11 22:19

id diauxic_bounds meta_diauxic_bounds
namediauxic (BOUNDS)
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
Access SBML model  L3V1 comp-V1

SBO:0000293
BQB_IS_VERSION_OF
GO:0006007
Ports [14] name referenced element port ref id ref unit ref metaid ref sbo cvterm
dt_port port dt Parameter: dt dt
bioreactor_port port bioreactor Compartment: bioreactor bioreactor
Ac_port port Ac Species: Ac Ac
X_port port X Species: X X
Glcxt_port port Glcxt Species: Glcxt Glcxt
O2_port port O2 Species: O2 O2
lb_EX_Ac_port port lb_EX_Ac Parameter: lb_EX_Ac lb_EX_Ac
ub_EX_Ac_port port ub_EX_Ac Parameter: ub_EX_Ac ub_EX_Ac
lb_EX_X_port port lb_EX_X Parameter: lb_EX_X lb_EX_X
ub_EX_X_port port ub_EX_X Parameter: ub_EX_X ub_EX_X
lb_EX_Glcxt_port port lb_EX_Glcxt Parameter: lb_EX_Glcxt lb_EX_Glcxt
ub_EX_Glcxt_port port ub_EX_Glcxt Parameter: ub_EX_Glcxt ub_EX_Glcxt
lb_EX_O2_port port lb_EX_O2 Parameter: lb_EX_O2 lb_EX_O2
ub_EX_O2_port port ub_EX_O2 Parameter: ub_EX_O2 ub_EX_O2

FunctionDefinitions [2] name math sbo cvterm
max min x y x x y y
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 [1] name size constant spatial dimensions units derived units sbo cvterm
bioreactor bioreactor 1.0 3 l litre

Species [4] name compartment boundary condition constant initial amount initial concentration conversion factor units substance units derived units sbo cvterm
Ac meta_Ac acetate bioreactor 1.0 mmol_per_l mmol_per_l 10 3 mole litre litre
X meta_X biomass bioreactor 1.0 mmol_per_l mmol_per_l 10 3 mole litre litre
Glcxt meta_Glcxt glucose bioreactor 1.0 mmol_per_l mmol_per_l 10 3 mole litre litre
O2 meta_O2 oxygen bioreactor 1.0 mmol_per_l mmol_per_l 10 3 mole litre litre

Parameters [18] 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_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_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_fba_EX_Ac -1000.0 mmol_per_h 10 3 mole 3600 s
lb_fba_EX_X -1000.0 mmol_per_h 10 3 mole 3600 s
lb_fba_EX_Glcxt -10.0 mmol_per_h 10 3 mole 3600 s
lb_fba_EX_O2 -15.0 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 name derived units sbo cvterm
lb_kin_EX_Glcxt = Vmax_EX_Glcxt Glcxt Km_EX_Glcxt Glcxt 0.001 mole litre 3600 s
lb_kin_EX_O2 = Vmax_EX_O2 10 3 mole 3600 s
lb_EX_Ac = max lb_fba_EX_Ac Ac X 1 bioreactor dt 10 3 mole 3600 s
lb_EX_X = max lb_fba_EX_X X X 1 bioreactor dt 10 3 mole 3600 s
lb_EX_Glcxt = max lb_kin_EX_Glcxt Glcxt X 1 bioreactor dt 10 3 mole 3600 s
lb_EX_O2 = max lb_kin_EX_O2 O2 X 1 bioreactor dt 10 3 mole 3600 s