BIOMD0000000292
type: SBMLModel
parameter: A0
area units: area
volume units: volume
parameter: N0
units def: substance
units def: length
parameter: k1
parameter: k3
species: http://identifiers.org/biomodels.db/BIOMD0000000292#X
species: NADP
created:
  W3 CDTF: Thu Jan 06 23:40:34 GMT 2011
is: MODEL1101060001
species: ATP
modified:
  W3 CDTF: Wed Jul 11 19:04:33 BST 2012
time units: time
parameter: k4
creator:
  ORG:
    orgname: University of Vienna
  n:
    given: Rainer
    family: Machne
units def: 254783
reaction: v2
curated: true
parameter: k2
species: NADPH
occurs in: http://identifiers.org/taxonomy/33090
units def: 254867
substance units: substance
length unit: length
is described by: http://identifiers.org/pubmed/7772723
rule: CDMT00027
is version of: GO:0019253
species: ADP
units def: time
units def: 254819
units def: volume
name: Rovers1995_Photsynthetic_Oscillations
reaction: v1
reaction: v4
reaction: v3
notes: This is the model described in the article: Photosynthetic oscillations and the interdependence of photophosphorylation and electron transport as studied by a mathematical model. Rovers W, Giersch C. Biosystems. 1995;35(1):63-73. PMID: 7772723 Abstract: A simple mathematical model of photosynthetic carbon metabolism as driven by ATP and NADPH has been formulated to analyse photosynthetic oscillations. Two essential assumptions of this model are: (i) reduction of 3-phosphoglycerate to triosephosphate in the Clavin cycle is limited by ATP, not by NADPH, and (ii) photophosphorylation is affected by the availability of both ADP and NADP, while electron transport is limited by NADP only. The model produces oscillations of observed damping and period in ATP and NADP concentrations which are about 180 degrees out of phase, while three alternative proposals regarding coupling of electron transport and photophosphorylation do not produce oscillatory model solutions. The phases of ATP and NADPH are in reasonable agreement with the available experimental data. The model (which assumes that redox control of photophosphorylation is part of the oscillatory mechanism) is compared with an alternative proposal (that oscillations are due to interdependence of turnover of adenylates and Calvin cycle intermediates). From the similarity of the mathematical structures of both models it is inviting to speculate that both models are partial aspects of the oscillatory mechanism. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. To cite BioModels Database, please use: Li C, Donizelli M,…
species: http://identifiers.org/biomodels.db/BIOMD0000000292#Y
units def: area
rule: CDMT00026
is version of: rn00710
compartment: http://identifiers.org/biomodels.db/BIOMD0000000292#c

A0
type: Parameter
is: CHEBI:15422
is: CHEBI:16761
has part: C00008
has part: C00002
is: SBO:0000472
constant: true
units: 254783
value: 2.5

254783
type: SBMLUnitsDef
unit: 254807
unit: 254795
name: mM

254807
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

254795
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

area
type: SBMLUnitsDef
unit: CDMT00023
name: area

CDMT00023
type: SBMLUnit
exponent: 2.0
scale: 0
multipler: 1.0
kind: METRE

volume
type: SBMLUnitsDef
unit: CDMT00022
name: volume

CDMT00022
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

N0
type: Parameter
has part: C00006
has part: C00005
has part: CHEBI:18009
has part: CHEBI:16474
is: SBO:0000472
constant: true
units: 254783
value: 1.2

substance
type: SBMLUnitsDef
unit: CDMT00021
name: mmole

CDMT00021
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

length
type: SBMLUnitsDef
unit: CDMT00024
name: length

CDMT00024
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: METRE

k1
type: Parameter
is: SBO:0000035
constant: true
units: 254867
value: 0.123

254867
type: SBMLUnitsDef
unit: 254879
name: per_s

254879
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

k3
type: Parameter
is: SBO:0000036
constant: true
units: 254819
value: 0.3

254819
type: SBMLUnitsDef
unit: 254855
unit: 254843
unit: 254831
name: per_mM_per_s

254855
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

254843
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

254831
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

http://identifiers.org/biomodels.db/BIOMD0000000292#X
type: Species
has part: CHEBI:48153
has part: C05382
has part: CHEBI:17969
name: X
has part: CHEBI:16108
has part: CHEBI:17363
has part: C00447
is: SBO:0000247
has part: C00117
constant: false
has part: C00279
in compartment: http://identifiers.org/biomodels.db/BIOMD0000000292#c
has part: C00118
has part: CHEBI:29052
initial concentration: 2.0
boundary condition: false
initial amount: NaN
has only substance units: false
has part: CHEBI:15721
has part: C00111
has part: C00085
has part: CHEBI:17797
has part: C00354
has part: CHEBI:15946
has part: C00199
has part: CHEBI:16905

http://identifiers.org/biomodels.db/BIOMD0000000292#c
type: Compartment
is: GO:0009570
is: SBO:0000290
constant: true
units: volume
size: 1.0
spatial dimensions: 3.0

NADP
type: Species
constant: false
is: CHEBI:18009
boundary condition: true
initial amount: NaN
name: NADP_super_+
is: C00006
initial concentration: 0.5
in compartment: http://identifiers.org/biomodels.db/BIOMD0000000292#c
is: SBO:0000247
has only substance units: false

ATP
type: Species
is: CHEBI:15422
is: C00002
boundary condition: false
name: ATP
in compartment: http://identifiers.org/biomodels.db/BIOMD0000000292#c
is: SBO:0000247
has only substance units: false
initial amount: NaN
constant: false
initial concentration: 0.5

time
type: SBMLUnitsDef
unit: CDMT00025
name: time

CDMT00025
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND

k4
type: Parameter
is: SBO:0000035
constant: true
units: 254867
value: 0.614

v2
type: Reaction
reactant: CDMT00011
has version: http://identifiers.org/ec-code/2.7.2.3
has version: R01063
is: SBO:0000182
product: CDMT00012
reversible: false
fast: false
reactant: CDMT00009
has version: http://identifiers.org/ec-code/1.2.1.13
reactant: CDMT00010
name: v2
has version: http://identifiers.org/ec-code/1.2.1.59
product: CDMT00013
has version: R01512
kinetic law: CDMT00015
product: CDMT00014

CDMT00011
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: ATP

CDMT00012
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: http://identifiers.org/biomodels.db/BIOMD0000000292#X

CDMT00009
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: http://identifiers.org/biomodels.db/BIOMD0000000292#Y

http://identifiers.org/biomodels.db/BIOMD0000000292#Y
type: Species
has part: C01182
in compartment: http://identifiers.org/biomodels.db/BIOMD0000000292#c
boundary condition: true
initial amount: NaN
name: Y
constant: true
has only substance units: false
has part: CHEBI:17794
initial concentration: 1.0
has part: CHEBI:16710
has part: C00197
is: SBO:0000247

CDMT00010
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: NADPH

NADPH
type: Species
boundary condition: false
is: SBO:0000247
is: CHEBI:16474
in compartment: http://identifiers.org/biomodels.db/BIOMD0000000292#c
has only substance units: false
constant: false
name: NADPH
initial amount: NaN
is: C00005
initial concentration: 0.7

CDMT00013
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: ADP

ADP
type: Species
is: SBO:0000247
constant: false
has only substance units: false
initial concentration: 2.0
is: C00008
initial amount: NaN
is: CHEBI:16761
name: ADP
boundary condition: true
in compartment: http://identifiers.org/biomodels.db/BIOMD0000000292#c

CDMT00014
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: NADP

k2
type: Parameter
is: SBO:0000035
constant: true
units: 254867
value: 0.625

v1
type: Reaction
is version of: http://identifiers.org/ec-code/2.7.1.19
fast: false
is: SBO:0000216
reactant: CDMT00017
kinetic law: CDMT00020
product: CDMT00019
reactant: CDMT00016
is version of: R01523
product: CDMT00018
name: v1
reversible: false

CDMT00017
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: ATP

CDMT00019
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: ADP

CDMT00016
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: http://identifiers.org/biomodels.db/BIOMD0000000292#X

CDMT00018
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: http://identifiers.org/biomodels.db/BIOMD0000000292#Y

v4
type: Reaction
kinetic law: CDMT00004
product: CDMT00003
reactant: CDMT00002
is version of: GO:0009780
is: SBO:0000202
fast: false
reversible: false
name: v4

CDMT00003
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: NADPH

CDMT00002
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: NADP

v3
type: Reaction
product: CDMT00006
modifier: CDMT00007
name: v3
reversible: false
kinetic law: CDMT00008
fast: false
is: SBO:0000216
reactant: CDMT00005
is version of: GO:0009777

CDMT00006
type: SpeciesReference
is: SBO:0000011
stoichiometry: 2.0
species: ATP

CDMT00005
type: SpeciesReference
is: SBO:0000010
stoichiometry: 2.0
species: ADP