Diauxic Growth Model
Model version: 12
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.
Terms of use
Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:
- Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
- 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.
Model : diauxic_top_flat
CreatorMatthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-06-07 19:49
Modified: 2017-06-07 19:49
![]() |
|
type | FunctionDefinitions [2] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | bounds__max | min | |||
FunctionDefinition | bounds__min | max |
type | UnitDefinitions [14] | name | units | sbo | cvterm |
---|---|---|---|---|---|
UnitDefinition | h | hour | BQB_IS
UO:0000032 |
||
UnitDefinition | g | gram | |||
UnitDefinition | m | meter | BQB_IS
UO:0000008 |
||
UnitDefinition | m2 | cubic meter | BQB_IS
UO:0000080 |
||
UnitDefinition | l | liter | |||
UnitDefinition | mmol | ||||
UnitDefinition | per_h | ||||
UnitDefinition | mmol_per_h | ||||
UnitDefinition | mmol_per_hg | ||||
UnitDefinition | mmol_per_l | ||||
UnitDefinition | mmol_per_lg | ||||
UnitDefinition | l_per_mmol | ||||
UnitDefinition | g_per_l | ||||
UnitDefinition | g_per_mmol |
type | Compartments [2] | name | size | constant | spatial dimensions | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Compartment | bioreactor | bioreactor | 1.0 | T | 3 | l | |||
Compartment | fba__bioreactor | bioreactor | 1.0 | T | 3 | l |
type | Species [9] | name | compartment | boundary condition | constant | initial amount | initial concentration | substance units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|---|---|
Species | Ac | acetate |
bioreactor | F | F | 0.4 | mmol | ||||
Species | X | biomass |
bioreactor | F | F | 0.001 | mmol | BQB_IS
OMIT:0018723 |
|||
Species | O2 | oxygen |
bioreactor | F | F | 0.21 | mmol | ||||
Species | Glcxt | glucose |
bioreactor | F | F | 10.8 | mmol | ||||
Species | dummy_S | dummy_S |
bioreactor | F | F | 0.0 | mmol | ||||
Species | fba__Glcxt | glucose C6H12O6 |
fba__bioreactor | F | F | 0.0 | mmol | ||||
Species | fba__Ac | acetate C2H4O2 |
fba__bioreactor | F | F | 0.0 | mmol | ||||
Species | fba__O2 | oxygen O2 |
fba__bioreactor | F | F | 0.0 | mmol | ||||
Species | fba__X | biomass |
fba__bioreactor | F | F | 0.0 | mmol | BQB_IS
OMIT:0018723 |
type | Parameters [26] | name | value | unit | derived unit | constant | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | dt | 0.1 | h | T | ||||
Parameter | lb_EX_Ac | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_Ac | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_X | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_X | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_O2 | -15.0 | mmol_per_h | F | ||||
Parameter | ub_EX_O2 | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_Glcxt | -10.0 | mmol_per_h | F | ||||
Parameter | ub_EX_Glcxt | 1000.0 | mmol_per_h | F | ||||
Parameter | pEX_Ac | 1.0 | mmol_per_h | F | ||||
Parameter | pEX_X | 1.0 | mmol_per_h | F | ||||
Parameter | pEX_O2 | 1.0 | mmol_per_h | F | ||||
Parameter | pEX_Glcxt | 1.0 | mmol_per_h | F | ||||
Parameter | O2_ref | O2 reference | 0.21 | mmol_per_l | T | |||
Parameter | kLa | O2 mass transfer | 7.5 | per_h | T | |||
Parameter | fba__zero | zero bound | 0.0 | mmol_per_h | T | |||
Parameter | fba__ub_default | default upper bound | 1000.0 | mmol_per_h | T | |||
Parameter | bounds__lb_fba_EX_Ac | -1000.0 | mmol_per_h | F | ||||
Parameter | bounds__lb_fba_EX_X | -1000.0 | mmol_per_h | F | ||||
Parameter | bounds__lb_fba_EX_O2 | -15.0 | mmol_per_h | F | ||||
Parameter | bounds__lb_fba_EX_Glcxt | -10.0 | mmol_per_h | F | ||||
Parameter | bounds__lb_kin_EX_Glcxt | -1000.0 | mmol_per_h | F | ||||
Parameter | bounds__lb_kin_EX_O2 | -1000.0 | mmol_per_h | F | ||||
Parameter | bounds__Vmax_EX_O2 | 15.0 | mmol_per_h | T | ||||
Parameter | bounds__Vmax_EX_Glcxt | 10.0 | mmol_per_h | T | ||||
Parameter | bounds__Km_EX_Glcxt | Km_vGlcxt | 0.015 | mmol_per_l | T |
type | Rules [10] | assignment | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|
Rule | pEX_Ac | = | ||||
Rule | pEX_X | = | ||||
Rule | pEX_O2 | = | ||||
Rule | pEX_Glcxt | = | ||||
Rule | bounds__lb_kin_EX_Glcxt | = | ||||
Rule | bounds__lb_kin_EX_O2 | = | ||||
Rule | lb_EX_Ac | = | ||||
Rule | lb_EX_X | = | ||||
Rule | lb_EX_Glcxt | = | ||||
Rule | lb_EX_O2 | = |
type | Reactions [13] | name | equation | modifiers | formula | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|
Reaction | vO2_transfer | oxygen transfer | ⇆ | ⇆ O2 | |||||
Reaction | fba__v1 | v1 (39.43 Ac + 35 O2 -> X) | ➞ | 39.43 fba__Ac + 35.0 fba__O2 ➞ fba__X | |||||
Reaction | fba__v2 | v2 (9.46 Glcxt + 12.92 O2 -> X) | ➞ | 9.46 fba__Glcxt + 12.92 fba__O2 ➞ fba__X | |||||
Reaction | fba__v3 | v3 (9.84 Glcxt + 12.73 O2 -> 1.24 Ac + X) | ➞ | 9.84 fba__Glcxt + 12.73 fba__O2 ➞ 1.24 fba__Ac + fba__X | |||||
Reaction | fba__v4 | v4 (19.23 Glcxt -> 12.12 Ac + X) | ➞ | 19.23 fba__Glcxt ➞ 12.12 fba__Ac + fba__X | |||||
Reaction | EX_Ac | ⇆ | fba__Ac ⇆ | ||||||
Reaction | EX_Glcxt | ⇆ | fba__Glcxt ⇆ | ||||||
Reaction | EX_O2 | ⇆ | fba__O2 ⇆ | ||||||
Reaction | EX_X | ⇆ | fba__X ⇆ | ||||||
Reaction | update__update_Ac | ⇆ | Ac ⇆ |
X |
|||||
Reaction | update__update_X | ⇆ | X ⇆ |
X |
|||||
Reaction | update__update_O2 | ⇆ | O2 ⇆ |
X |
|||||
Reaction | update__update_Glcxt | ⇆ | Glcxt ⇆ |
X |