Diauxic Growth Model

Model version: 13

UPDATE submodel

Submodel for dynamically updating the metabolite count. This updates the ode model based on the FBA fluxes.

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_update

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-11-11 22:19
Modified: 2017-11-11 22:19

id diauxic_update meta_diauxic_update
namediauxic (UPDATE)
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
Access SBML model  L3V1 comp-V1

SBO:0000293
BQB_IS_VERSION_OF
GO:0006007
Ports [9] name referenced element port ref id ref unit ref metaid ref sbo cvterm
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
pEX_Ac_port port pEX_Ac Parameter: pEX_Ac pEX_Ac
pEX_X_port port pEX_X Parameter: pEX_X pEX_X
pEX_Glcxt_port port pEX_Glcxt Parameter: pEX_Glcxt pEX_Glcxt
pEX_O2_port port pEX_O2 Parameter: pEX_O2 pEX_O2

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 [4] name constant value unit derived unit sbo cvterm
pEX_Ac 1.0 mmol_per_h 10 3 mole 3600 s
pEX_X 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

Reactions [4] name equation modifiers kinetic law derived units sbo cvterm
update_Ac
Ac ⇆ X pEX_Ac X 1 0.001 mole litre 3600 s
update_X
X ⇆ X pEX_X X 1 0.001 mole litre 3600 s
update_Glcxt
Glcxt ⇆ X pEX_Glcxt X 1 0.001 mole litre 3600 s
update_O2
O2 ⇆ X pEX_O2 X 1 0.001 mole litre 3600 s