592535
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

182678
value: 1.4
name: Km
type: LocalParameter

182680
value: 19.0
name: v
type: LocalParameter

182691
value: 2.0
name: Km
type: LocalParameter

182670
value: 3.0
name: v
type: LocalParameter

182698
value: 1.0
name: Km
type: LocalParameter

182688
value: 67000.0
name: E
type: LocalParameter

592691
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

COPASI18
is: SBO:0000291
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: 182351
name: junk
type: Species

COPASI9
initial amount: NaN
is version of: C00562
in compartment: 182351
is version of: A8J2S3
has only substance units: false
boundary condition: false
type: Species
constant: false
name: C1_phos
is: SBO:0000252
initial concentration: 1.0

COPASI37
kinetic law: 592799
product: 592787
reactant: 592775
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: C1_transl
type: Reaction

COPASI23
constant: true
value: 8.31447
name: R
type: Parameter

592571
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

592979
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

182669
value: 2.0
name: h
type: LocalParameter

592895
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

592485
unit: 592497
name: time
type: SBMLUnitsDef

182679
value: 5.0
name: v
type: LocalParameter

592667
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI8
initial amount: NaN
name: C1_mRNA
constant: true
initial concentration: 1.0
has only substance units: false
boundary condition: true
type: Species
is: SBO:0000278
encodes: A8J2S3
in compartment: 182351

COPASI19
is: SBO:0000147
constant: true
value: 291.0
name: T
type: Parameter

BIOMD0000000411
species: COPASI10
modified:
  W3 CDTF: Mon May 14 14:51:57 BST 2012
reaction: COPASI33
units def: 592510
parameter: COPASI24
function def: COPASI52
name: arhenius neg feedb tempvar
rule: 182700
reaction: COPASI42
notes: This model is from the article: Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii Ines Heiland, Christian Bodenstein, Thomas Hinze, Olga Weisheit, Oliver Ebenhoeh, Maria Mittag and Stefan Schuster Journal of Biological Physics 4 March 2012; pp 1-16; doi: 10.1007/s10867-012-9264-x , Abstract: Endogenous circadian rhythms allow living organisms to anticipate daily variations in their natural environment. Temperature regulation and entrainment mechanisms of circadian clocks are still poorly understood. To better understand the molecular basis of these processes, we built a mathematical model based on experimental data examining temperature regulation of the circadian RNA-binding protein CHLAMY1 from the unicellular green alga Chlamydomonas reinhardtii , simulating the effect of temperature on the rates by applying the Arrhenius equation. Using numerical simulations, we demonstrate that our model is temperature-compensated and can be entrained to temperature cycles of various length and amplitude. The range of periods that allow entrainment of the model depends on the shape of the temperature cycles and is larger for sinusoidal compared to rectangular temperature curves. We show that the response to temperature of protein (de)phosphorylation rates play a key role in facilitating temperature entrainment of the oscillator in Chlamydomonas reinhardtii . We systematically investigated the response of our model to single temperature pulses to explain experimentally observed phase response curves. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team. For more information see the terms of use . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C …
parameter: COPASI27
species: COPASI7
length unit: length
created:
  W3 CDTF: Mon Apr 02 16:49:46 BST 2012
parameter: COPASI30
reaction: COPASI37
species: COPASI5
parameter: COPASI20
rule: 182704
parameter: COPASI19
volume units: volume
is described by: s10867-012-9264-x
reaction: COPASI31
species: COPASI9
reaction: COPASI40
species: COPASI18
reaction: COPASI34
parameter: COPASI25
species: COPASI6
reaction: COPASI43
parameter: COPASI28
area units: area
creator:
  ORG:
    orgname: Dept. of Bioinformatics Friedrich Schiller University Jena
  n:
    given: Ines
    family: Heiland
function def: COPASI49
reaction: COPASI35
species: COPASI3
species: COPASI4
substance units: 592510
reaction: COPASI38
parameter: COPASI22
parameter: COPASI21
name: Heiland2012_CircadianClock_C.reinhardtii
time units: 592485
species: COPASI8
function def: COPASI51
function def: COPASI50
function def: COPASI53
reaction: COPASI32
units def: 592485
curated: true
name: arhenius complexf temp var
rule: 182701
reaction: COPASI41
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
parameter: COPASI26
is version of: GO:0060086
compartment: 182351
parameter: COPASI29
species: COPASI2
name: arhenius mass action tempvar
name: arhenius michaelis menten temp var
reaction: COPASI36
occurs in: http://identifiers.org/taxonomy/3055
name: arhenius tranls temp var
reaction: COPASI39
parameter: COPASI23
is: MODEL1201130000
type: SBMLModel

COPASI36
name: C3_transl
fast: false
type: Reaction
is version of: GO:0006412
reactant: 592727
modifier: 592751
kinetic law: 592763
product: 592739
is: SBO:0000184
reversible: false

COPASI22
constant: true
value: 0.5
name: V_dephos
type: Parameter

592931
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

182676
value: 1.5
name: v
type: LocalParameter

182663
value: 0.1
name: v
type: LocalParameter

592835
stoichiometry: 1.0
species: COPASI10
type: SpeciesReference

182696
value: 4.0
name: Km
type: LocalParameter

COPASI7
boundary condition: false
initial amount: NaN
name: C1
type: Species
is: SBO:0000252
in compartment: 182351
initial concentration: 1.0
constant: false
is version of: A8J2S3
has only substance units: false

592497
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

COPASI35
kinetic law: 592715
product: 592703
reactant: 592691
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: C3_phos_degr
type: Reaction

COPASI42
kinetic law: 592991
product: 592979
reactant: 592967
is version of: GO:0016311
is: SBO:0000330
fast: false
reversible: false
name: C1_dephos
type: Reaction

COPASI25
constant: true
value: 24.0
name: entrperiod
type: Parameter

592583
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

592967
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

592655
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

592522
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

182697
value: 67000.0
name: E
type: LocalParameter

592703
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI6
has only substance units: false
boundary condition: true
constant: true
in compartment: 182351
initial concentration: 1.0
initial amount: NaN
name: C_3_pre
type: Species
is version of: A8J6K7
is: SBO:0000252

COPASI24
constant: true
value: 10.0
name: amplitude
type: Parameter

COPASI43
kinetic law: 593027
product: 593015
reactant: 593003
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: C1_phos_degr
type: Reaction

COPASI34
kinetic law: 592679
product: 592667
reactant: 592655
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: C3_degr
type: Reaction

182683
value: 67000.0
name: E
type: LocalParameter

592775
stoichiometry: 1.0
species: COPASI8
type: SpeciesReference

182694
value: 67000.0
name: E
type: LocalParameter

COPASI33
kinetic law: 592643
product: 592631
reactant: 592619
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: C3_mRNADegr
type: Reaction

592787
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

COPASI4
is version of: A8J6K7
type: Species
name: C_3
constant: false
has only substance units: false
in compartment: 182351
boundary condition: false
initial amount: NaN
is: SBO:0000252
initial concentration: 1.0

592510
unit: 592522
name: substance
type: SBMLUnitsDef

592871
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

182684
value: 10.0
name: v
type: LocalParameter

COPASI40
kinetic law: 592919
product: 592907
reactant: 592895
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: C1_degr
type: Reaction

COPASI27
constant: false
value: 84000.0
name: EAhigh
type: Parameter

592907
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

182665
value: 2.6
name: v
type: LocalParameter

COPASI32
reactant: 592571
is version of: GO:0009299
name: C3_transk
type: Reaction
product: 592583
modifier: 592595
kinetic law: 592607
fast: false
is: SBO:0000183
reversible: false

COPASI5
is version of: C00562
in compartment: 182351
boundary condition: false
constant: false
initial concentration: 1.0
is version of: A8J6K7
name: C_3_P
has only substance units: false
is: SBO:0000252
initial amount: NaN
type: Species

COPASI41
kinetic law: 592955
product: 592943
reactant: 592931
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: complexdegr
type: Reaction

593015
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI26
constant: false
value: 50000.0
name: EAlow
type: Parameter

592739
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

592823
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

182675
value: 0.2
name: Km
type: LocalParameter

COPASI31
kinetic law: 592559
product: 592547
reactant: 592535
is version of: GO:0016310
is: SBO:0000216
fast: false
reversible: false
name: C3_phos
type: Reaction

COPASI2
has only substance units: false
constant: true
initial amount: NaN
boundary condition: true
in compartment: 182351
name: C3_Gene
encodes: A8J6K7
type: Species
is: SBO:0000243
initial concentration: 1.0

COPASI21
constant: true
value: 1.0
name: v_phos
type: Parameter

592631
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

182686
value: 2.0
name: a
type: LocalParameter

COPASI29
constant: true
value: 60000.0
name: Ephos
type: Parameter

592859
stoichiometry: 1.0
species: COPASI7
type: SpeciesReference

182667
value: 0.4
name: k
type: LocalParameter

COPASI39
kinetic law: 592883
product: 592871
reactant: 592859
is version of: GO:0016310
is: SBO:0000216
fast: false
reversible: false
name: C1_phos
type: Reaction

182672
value: 2.0
name: Km
type: LocalParameter

182692
value: 20.0
name: v
type: LocalParameter

592547
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

COPASI30
constant: true
value: 67000.0
name: Edephos
type: Parameter

182351
is version of: GO:0005623
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: default
type: Compartment

COPASI10
is: SBO:0000297
type: Species
in compartment: 182351
has part: A8J2S3
boundary condition: false
has part: A8J6K7
initial amount: NaN
initial concentration: 1.0
name: c1c3complex
has only substance units: false
constant: false

592943
stoichiometry: 1.0
species: COPASI18
type: SpeciesReference

COPASI20
constant: false
value: 296.0
name: T2
type: Parameter

COPASI3
name: C3_mRNA
initial concentration: 1.0
type: Species
in compartment: 182351
boundary condition: false
encodes: A8J6K7
has only substance units: false
is: SBO:0000278
initial amount: NaN
constant: false

182687
value: 30.0
name: v
type: LocalParameter

592727
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI28
constant: true
value: 1.0
name: vphosdegr
type: Parameter

592811
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

592619
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

182673
value: 2.2
name: v
type: LocalParameter

593003
stoichiometry: 1.0
species: COPASI9
type: SpeciesReference

COPASI38
fast: false
kinetic law: 592847
type: Reaction
is: SBO:0000526
product: 592835
reactant: 592823
is version of: GO:0006461
reactant: 592811
reversible: false
name: complexformation