030938
constant: false
units: 460573
value: NaN
name: MC
type: Parameter

030948
constant: false
units: 460610
value: NaN
name: vsB
type: Parameter

460694
exponent: -1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

460742
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

030986
constant: true
units: 460658
value: 0.1
name: k8
type: Parameter

031016
constant: true
units: 460610
value: 0.3
name: V2P
type: Parameter

030944
constant: true
units: 460573
value: 1.0
name: KAC
type: Parameter

030996
constant: true
units: dimensionless
value: 4.0
name: m
type: Parameter

030954
constant: true
units: 460573
value: 0.4
name: KmB
type: Parameter

460585
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

030969
constant: false
units: 460573
value: NaN
name: BCP
type: Parameter

030965
constant: false
units: 460573
value: NaN
name: PCCP
type: Parameter

460658
unit: 460670
name: first_order_rate_constant
type: SBMLUnitsDef

030972
constant: false
units: 460573
value: NaN
name: BNP
type: Parameter

031023
constant: true
units: 460610
value: 0.1
name: V4PC
type: Parameter

030989
constant: true
units: 460658
value: 0.01
name: kdn
type: Parameter

030962
constant: false
units: 460573
value: NaN
name: PCC
type: Parameter

030992
constant: false
units: 460658
value: NaN
name: ksB
type: Parameter

030930
constant: false
units: 460573
value: NaN
name: MP
type: Parameter

460561
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

031002
constant: true
units: 460573
value: 0.3
name: Kdp
type: Parameter

460634
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

031017
constant: true
units: 460610
value: 0.1
name: V2PC
type: Parameter

030947
constant: false
units: 460573
value: NaN
name: MB
type: Parameter

030995
constant: false
units: 460658
value: NaN
name: ksP
type: Parameter

030953
constant: true
units: 460573
value: 0.8
name: KIB
type: Parameter

031007
constant: true
units: 460610
value: 1.0
name: V1B
type: Parameter

460610
unit: 460646
unit: 460634
unit: 460622
name: flux
type: SBMLUnitsDef

030957
constant: false
units: 460573
value: NaN
name: CC
type: Parameter

030981
constant: true
units: 460658
value: 0.4
name: k5
type: Parameter

030999
constant: true
units: 460610
value: 1.0
name: vstot
type: Parameter

030966
constant: false
units: 460573
value: NaN
name: PCNP
type: Parameter

030971
constant: false
units: 460573
value: NaN
name: BN
type: Parameter

030933
constant: true
units: 460658
value: 0.01
name: kdmp
type: Parameter

031022
constant: true
units: 460610
value: 0.2
name: V4B
type: Parameter

030950
constant: true
units: 460610
value: 0.2
name: vmB
type: Parameter

460718
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

031026
constant: true
units: 460610
value: 0.5
name: vdBN
type: Parameter

031013
constant: true
units: 460610
value: 0.1
name: V2B
type: Parameter

031008
constant: true
units: 460610
value: 0.6
name: V1C
type: Parameter

030975
constant: true
units: 460658
value: 0.8
name: k1
type: Parameter

031032
constant: true
units: 460610
value: 1.0
name: vdPCC
type: Parameter

460573
unit: 460597
unit: 460585
name: nanomolar
type: SBMLUnitsDef

030956
constant: false
units: 460573
value: NaN
name: PC
type: Parameter

030990
constant: true
units: 460658
value: 1.0
name: kstot
type: Parameter

030942
constant: true
units: 460658
value: 0.01
name: kdmc
type: Parameter

030977
constant: true
units: 460658
value: 0.2
name: k2
type: Parameter

030984
constant: true
units: 460682
value: 0.5
name: k7
type: Parameter

030998
constant: true
units: dimensionless
value: 4.0
name: n
type: Parameter

031004
constant: true
units: 460573
value: 0.1
name: Kp
type: Parameter

460682
unit: 460718
unit: 460706
unit: 460694
name: second_order_rate_constant
type: SBMLUnitsDef

031010
constant: false
units: 460610
value: NaN
name: V1P
type: Parameter

031014
constant: true
units: 460610
value: 0.1
name: V2C
type: Parameter

MODEL0478895291
parameter: 030930
parameter: 031023
parameter: 030980
rule: 030926
parameter: 031025
parameter: 030965
units def: 460682
parameter: 030942
rule: 030911
parameter: 030977
parameter: 031014
parameter: 030954
parameter: 030968
units def: 460573
parameter: 030989
units def: 460658
parameter: 031001
type: SBMLModel
parameter: 030962
length unit: 222721
area units: area
rule: 030914
parameter: 031013
parameter: 030974
notes: This a model from the article: Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms. Leloup JC, Goldbeter A. J Theor Biol. 2004 Oct 21;230(4):541-62. 15363675 , Abstract: We extend the study of a computational model recently proposed for the mammalian circadian clock (Proc. Natl Acad. Sci. USA 100 (2003) 7051). The model, based on the intertwined positive and negative regulatory loops involving the Per, Cry, Bmal1, and Clock genes, can give rise to sustained circadian oscillations in conditions of continuous darkness. These limit cycle oscillations correspond to circadian rhythms autonomously generated by suprachiasmatic nuclei and by some peripheral tissues. By using different sets of parameter values producing circadian oscillations, we compare the effect of the various parameters and show that both the occurrence and the period of the oscillations are generally most sensitive to parameters related to synthesis or degradation of Bmal1 mRNA and BMAL1 protein. The mechanism of circadian oscillations relies on the formation of an inactive complex between PER and CRY and the activators CLOCK and BMAL1 that enhance Per and Cry expression. Bifurcation diagrams and computer simulations nevertheless indicate the possible existence of a second source of oscillatory behavior. Thus, sustained oscillations might arise from the sole negative autoregulation of Bmal1 expression. This second oscillatory mechanism may not be functional in physiological conditions, and its period need not necessarily be circadian. When incorporating the light-induced expression of the Per gene, the model accounts for entrainment of the oscillations by light-dark (LD) cycles. Long-term suppression of circadian oscillations by a single light pulse can occur in the model when a stable steady state coexists with a stable limit cycle. The phase of the oscillations upon entrainment in LD critically depends on the parameters that govern the level of CRY p…
parameter: 030951
rule: 030913
parameter: 031029
parameter: 030969
rule: 030922
rule: 030919
units def: 460549
parameter: 030986
rule: 030901
rule: 030907
parameter: 030998
parameter: 031010
parameter: 030931
parameter: 030971
parameter: 030990
compartment: 030891
rule: 030925
parameter: 031026
parameter: 030966
parameter: 030983
parameter: 030938
rule: 030910
parameter: 030978
rule: 030920
parameter: 030995
volume units: volume
substance units: substance
parameter: 031002
parameter: 030963
rule: 030895
rule: 030904
rule: 030899
parameter: 031004
parameter: 030935
rule: 030894
parameter: 030975
units def: 460610
rule: 030898
parameter: 031016
parameter: 030992
parameter: 031007
parameter: 030947
parameter: 030987
rule: 030928
parameter: 031022
parameter: 031019
parameter: 030959
rule: 030917
parameter: 030999
parameter: 030960
rule: 030905
parameter: 030941
parameter: 031034
parameter: 031011
parameter: 030932

030980
constant: true
units: 460658
value: 0.2
name: k4
type: Parameter

031025
constant: true
units: 460610
value: 1.0
name: vdBC
type: Parameter

030951
constant: true
units: 460658
value: 0.01
name: kdmb
type: Parameter

460646
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

031031
constant: true
units: 460610
value: 0.7
name: vdPC
type: Parameter

030936
constant: true
units: 460573
value: 0.3
name: KmP
type: Parameter

460730
unit: 460742
name: time
type: SBMLUnitsDef

030960
constant: false
units: 460573
value: NaN
name: CCP
type: Parameter

030974
constant: false
units: 460573
value: NaN
name: IN
type: Parameter

030932
constant: true
units: 460610
value: 1.1
name: vmP
type: Parameter

031029
constant: true
units: 460610
value: 0.8
name: vdIN
type: Parameter

030941
constant: true
units: 460610
value: 1.0
name: vmC
type: Parameter

460622
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

031019
constant: true
units: 460610
value: 1.0
name: V3B
type: Parameter

030993
constant: false
units: 460658
value: NaN
name: ksC
type: Parameter

030945
constant: true
units: 460573
value: 0.4
name: KmC
type: Parameter

030968
constant: false
units: 460573
value: NaN
name: BC
type: Parameter

460549
unit: 460561
name: hour
type: SBMLUnitsDef

030939
constant: false
units: 460610
value: NaN
name: vsC
type: Parameter

030987
constant: true
units: 460658
value: 0.01
name: kdnc
type: Parameter

031011
constant: false
units: 460610
value: NaN
name: V1PC
type: Parameter

030978
constant: true
units: 460682
value: 0.8
name: k3
type: Parameter

031005
constant: true
units: 460610
value: 0.6
name: Vphos
type: Parameter

030983
constant: true
units: 460658
value: 0.2
name: k6
type: Parameter

030959
constant: false
units: 460573
value: NaN
name: PCP
type: Parameter

460597
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

460670
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

031020
constant: false
units: 460610
value: NaN
name: V3PC
type: Parameter

030963
constant: false
units: 460573
value: NaN
name: PCN
type: Parameter

030935
constant: true
units: 460573
value: 0.7
name: KAP
type: Parameter

031034
constant: true
units: 460610
value: 1.0
name: vdPCN
type: Parameter

031028
constant: true
units: 460610
value: 0.7
name: vdCC
type: Parameter

031001
constant: true
units: 460573
value: 0.3
name: Kd
type: Parameter

030931
constant: false
units: 460610
value: NaN
name: vsP
type: Parameter

460706
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

030891
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0
type: Compartment