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: 2017-03-03 16:05
Modified: 2017-03-03 16:05

SBML model


iddiauxic_top
nameTop level model
versionL3V1
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
UnitDefinitions [60] name units sbo cvterm
h 3600 s
g g
m m
m2 m 2
l litre
per_h 1 3600 s
mmol_per_l 10 3 mole litre
g_per_l g litre
mmol 10 3 mole
per_g 1 g
g_per_mmol g 10 3 mole
mmol_per_h 10 3 mole 3600 s
mmol_per_hg 10 3 mole g 3600 s
mmol_per_lh 10 3 mole litre 3600 s
g_per_lh g litre 3600 s
bounds__h 3600 s
bounds__g g
bounds__m m
bounds__m2 m 2
bounds__l litre
bounds__per_h 1 3600 s
bounds__mmol_per_l 10 3 mole litre
bounds__g_per_l g litre
bounds__mmol 10 3 mole
bounds__per_g 1 g
bounds__g_per_mmol g 10 3 mole
bounds__mmol_per_h 10 3 mole 3600 s
bounds__mmol_per_hg 10 3 mole g 3600 s
bounds__mmol_per_lh 10 3 mole litre 3600 s
bounds__g_per_lh g litre 3600 s
fba__h 3600 s
fba__g g
fba__m m
fba__m2 m 2
fba__l litre
fba__per_h 1 3600 s
fba__mmol_per_l 10 3 mole litre
fba__g_per_l g litre
fba__mmol 10 3 mole
fba__per_g 1 g
fba__g_per_mmol g 10 3 mole
fba__mmol_per_h 10 3 mole 3600 s
fba__mmol_per_hg 10 3 mole g 3600 s
fba__mmol_per_lh 10 3 mole litre 3600 s
fba__g_per_lh g litre 3600 s
update__h 3600 s
update__g g
update__m m
update__m2 m 2
update__l litre
update__per_h 1 3600 s
update__mmol_per_l 10 3 mole litre
update__g_per_l g litre
update__mmol 10 3 mole
update__per_g 1 g
update__g_per_mmol g 10 3 mole
update__mmol_per_h 10 3 mole 3600 s
update__mmol_per_hg 10 3 mole g 3600 s
update__mmol_per_lh 10 3 mole litre 3600 s
update__g_per_lh g litre 3600 s

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 [21] name value unit derived unit constant sbo cvterm
dt fba timestep 0.1 h 3600 s
ub_vGlcxt ub vGlcxt 10.0 mmol_per_hg 10 3 mole g 3600 s
vGlcxt vGlcxt (FBA flux) 1.0 mmol_per_hg 10 3 mole g 3600 s
vAc vAc (FBA flux) 1.0 mmol_per_hg 10 3 mole g 3600 s
vO2 vO2 (FBA flux) 1.0 mmol_per_hg 10 3 mole g 3600 s
vX vX (FBA flux) 1.0 mmol_per_hg 10 3 mole g 3600 s
bounds__dt fba timestep 0.1 bounds__h 3600 s
bounds__Vmax_vGlcxt Vmax_vGlcxt 15.0 bounds__mmol_per_hg 10 3 mole g 3600 s
bounds__Km_vGlcxt Km_vGlcxt 0.015 bounds__mmol_per_l 10 3 mole litre
fba__lb_irrev lower bound 0.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__lb lower bound -1000.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__ub upper bound 1000.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__lb_vAc lb vAc 0.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__ub_vAc ub vAc 1000.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__lb_vGlcxt lb vGlcxt 0.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__lb_vO2 lb vAc -1000.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__ub_vO2 ub vO2 15.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__lb_vX lb vX 0.0 fba__mmol_per_hg 10 3 mole g 3600 s
fba__ub_vX ub vX 1000.0 fba__mmol_per_hg 10 3 mole g 3600 s
update__Y biomass [g_per_l] 1.0 update__g_per_l g litre
update__Km_vFBA Km_vFBA 0.02 update__mmol_per_l 10 3 mole litre

Rules [6]   assignment derived units sbo cvterm
vGlcxt = dummy_vGlcxt 10 3 mole 3600 s
vAc = dummy_vAc 10 3 mole 3600 s
vO2 = dummy_vO2 10 3 mole 3600 s
vX = dummy_vX 10 3 mole 3600 s
ub_vGlcxt = bounds__Vmax_vGlcxt Glcxt bounds__Km_vGlcxt Glcxt 0.001 mole g 3600 s
update__Y = 1 X g litre

Reactions [12] name equation modifiers formula derived units sbo cvterm
dummy_vO2 O2 import (vO2) ➞ O2
dummy_vGlcxt Glcxt import (vGlcxt) ➞ Glcxt
dummy_vAc Ac import (vAc) ⇆ Ac
dummy_vX biomass generation (vX) X ➞
fba__v1 v1 39.43 Ac + 35.0 O2 ➞ X
fba__v2 v2 9.46 Glcxt + 12.92 O2 ➞ X
fba__v3 v3 9.84 Glcxt + 12.73 O2 ➞ X + 1.24 Ac
fba__v4 v4 19.23 Glcxt ➞ X + 12.12 Ac
update__update_Glcxt Glcxt ➞ vGlcxt update__Y bioreactor Glcxt update__Km_vFBA Glcxt 0.001 mole 3600 s
update__update_Ac Ac ➞ vAc update__Y bioreactor Ac update__Km_vFBA Ac 0.001 mole 3600 s
update__update_O2 O2 ➞ vO2 update__Y bioreactor O2 update__Km_vFBA O2 0.001 mole 3600 s
update__update_X ➞ X vX update__Y bioreactor 10 3 mole 3600 s