BIOMD0000000411
type: SBMLModel
species: COPASI10
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
parameter: COPASI30
reaction: COPASI37
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
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
function def: COPASI49
reaction: COPASI35
species: COPASI3
species: COPASI4
substance units: 592510
reaction: COPASI38
creator:
  ORG:
    orgname: Dept. of Bioinformatics Friedrich Schiller University Jena
  n:
    given: Ines
    family: Heiland
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
parameter: COPASI26
is version of: GO:0060086
compartment: 182351
parameter: COPASI29
species: COPASI2
name: arhenius mass action tempvar
name: arhenius michaelis menten temp var
created:
  W3 CDTF: Mon Apr 02 16:49:46 BST 2012
reaction: COPASI36
occurs in: http://identifiers.org/taxonomy/3055
name: arhenius tranls temp var
reaction: COPASI39
modified:
  W3 CDTF: Mon May 14 14:51:57 BST 2012
parameter: COPASI23
is: MODEL1201130000

COPASI10
type: Species
is: SBO:0000297
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

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

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

182672
type: LocalParameter
value: 2.0
name: Km

182670
type: LocalParameter
value: 3.0
name: v

592631
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

COPASI18
type: Species
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

592619
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

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

592510
type: SBMLUnitsDef
unit: 592522
name: substance

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

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

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

592979
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

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

592967
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

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

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

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

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

182683
type: LocalParameter
value: 67000.0
name: E

182680
type: LocalParameter
value: 19.0
name: v

592787
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

592775
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

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

COPASI5
type: Species
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

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

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

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

182663
type: LocalParameter
value: 0.1
name: v

592547
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

592535
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI4
type: Species
is version of: A8J6K7
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

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

182691
type: LocalParameter
value: 2.0
name: Km

182688
type: LocalParameter
value: 67000.0
name: E

182687
type: LocalParameter
value: 30.0
name: v

592907
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

592895
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

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

182675
type: LocalParameter
value: 0.2
name: Km

182673
type: LocalParameter
value: 2.2
name: v

592667
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

592655
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

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

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

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

182698
type: LocalParameter
value: 1.0
name: Km

182697
type: LocalParameter
value: 67000.0
name: E

593015
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

593003
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

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

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

182678
type: LocalParameter
value: 1.4
name: Km

182676
type: LocalParameter
value: 1.5
name: v

592703
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

592691
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

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

182686
type: LocalParameter
value: 2.0
name: a

182684
type: LocalParameter
value: 10.0
name: v

592835
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

592823
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

592811
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

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

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

592485
type: SBMLUnitsDef
unit: 592497
name: time

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

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

592571
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

592583
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

182669
type: LocalParameter
value: 2.0
name: h

182667
type: LocalParameter
value: 0.4
name: k

182665
type: LocalParameter
value: 2.6
name: v

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

182696
type: LocalParameter
value: 4.0
name: Km

182694
type: LocalParameter
value: 67000.0
name: E

182692
type: LocalParameter
value: 20.0
name: v

592943
type: SpeciesReference
stoichiometry: 1.0
species: COPASI18

592931
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

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

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

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

592727
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

182679
type: LocalParameter
value: 5.0
name: v

592739
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

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

592871
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

592859
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

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