02042015230241746m0400
type: Ontology
legacy code URI: /Users/max_neal/_UW/SemGenGrant/Presentations/AucklandDemo/PHNmerge/origCellMLmodels/niederer_hunter_smith_2006.cellml.xml
sem sim version: 0.2
has cell m ldocumentation: <documentation xmlns="http://cellml.org/tmp-documentation"> Model Status This model is known to run in OpenCell and COR to reproduce the output shown in the publication. The units have been checked and they are consistent. <sect1 id="sec_structure"> Model Structure Abstract: The determinants of relaxation in cardiac muscle are poorly understood, yet compromised relaxation accompanies various pathologies and impaired pump function. In this study, we develop a model of active contraction to elucidate the relative importance of the [Ca2+]i transient magnitude, the unbinding of Ca2+ from troponin C (TnC), and the length-dependence of tension and Ca2+ sensitivity on relaxation. Using the framework proposed by one of our researchers, we extensively reviewed experimental literature, to quantitatively characterize the binding of Ca2+ to TnC, the kinetics of tropomyosin, the availability of binding sites, and the kinetics of crossbridge binding after perturbations in sarcomere length. Model parameters were determined from multiple experimental results and modalities (skinned and intact preparations) and model results were validated against data from length step, caged Ca2+, isometric twitches, and the half-time to relaxation with increasing sarcomere length experiments. A factorial analysis found that the [Ca2+]i transient and the unbinding of Ca2+ from TnC were the primary determinants of relaxation, with a fivefold greater effect than that of length-dependent maximum tension and twice the effect of tension-dependent binding of Ca2+ to TnC and length-dependent Ca2+ sensitivity. The affects of the [Ca2+]i transient and the unbinding rate of Ca2+ from TnC were tightly coupled with the effect of increasing either factor, depending on the reference [Ca2+]i transient and unbinding rate. <informalfigure float="0" id="fig_reaction_diagram"> <mediaobject> <imageobject> <objectinfo> model diagram </objectinfo> <imagedata fileref="niederer_2006.png" /> </imageobject> </mediaobject> S…
has cell m lrdf markup: <rdf:RDF xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:j.0="http://imc.org/vCard/3.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:ns7="http://www.cellml.org/metadata/simulation/1.0#"> <rdf:Description rdf:about="http://www.cellml.org/cellml/1.0"> <cmeta:modification> <rdf:Description rdf:about="rdf:#09f3904b-dd66-4a28-abac-7bb5cd351965"> <cmeta:modifier> <rdf:Description rdf:about="rdf:#7f8791df-4ef7-4dcc-963d-9a0480c65a43"> <vCard:N> <rdf:Description rdf:about="rdf:#5558142b-a43a-435c-aa8d-7da64599a4cc"> <vCard:Other>Richard</vCard:Other> <vCard:Family>Lawson</vCard:Family> <vCard:Given>James</vCard:Given> </rdf:Description> </vCard:N> </rdf:Description> </cmeta:modifier> <rdf:value>added cmeta id to T_0 variable</rdf:value> <dcterms:modified> <rdf:Description rdf:about="rdf:#a4cc9a49-f551-4ae0-8ce6-2c5513162628"> <dcterms:W3CDTF>2008-08-05T10:32:30+12:00</dcterms:W3CDTF> </rdf:Description> </dcterms:modified> </rdf:Description> </cmeta:modification> <dc:creator> <rdf:Description rdf:about="rdf:#e137d61c-82dc-4189-b9f0-29b66171c2e1"> <vCard:N> <rdf:Description rdf:about="rdf:#02fbf752-3e20-4809-818c-bd7725477072"> <vCard:Other></vCard:Other> <vCard:Family>Terkildsen</vCard:Family> <vCard:Given>Jonna</vCard:Given> </rdf:Description> </vCard:N> <vCard:EMAIL> <j.0:internet rdf:about="rdf:#53e5d308-54da-4612-80cc-b8391fe05593"> <rdf:value>j.terkildsen@auckland.ac.nz</rdf:value> </j.0:internet> </vCard:EMAIL> <vCard:ORG> <rdf:Description rdf:about="rdf:#ef3cf40f-3b42-4ed0-993c-730bdf918afc"> <vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit> <vCard:Orgname>The University of Auckland</vCard:Orgname> </rdf:Description> </vCard:ORG> </rdf:Description> </dc:creator> <dcterms:created> <rdf:Description rdf:about="rdf:#47b74e5d-97ed-4aaa-a687-07fd8f195b42">…
model id: niederer_2006
model name: niederer_2006

Chemical concentration
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Chemical concentration

Chemical concentration flow rate
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Chemical concentration flow rate

Surface normal tensile stress
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Surface normal tensile stress

Troponin C, slow skeletal and cardiac muscles (TN-C)
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Troponin C, slow skeletal and cardiac muscles (TN-C)

calcium(2+)
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: calcium(2+)

Cardiac myocyte
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Cardiac myocyte

Portion of cytosol
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Portion of cytosol

Composite physical entity
type: Class
subclass of: Physical entity
disjoint with: Custom physical entity
disjoint with: Reference physical entity
comment: A physical entity that is defined by linking multiple physical entity terms with structural relations.

Computation
type: Class
subclass of: Computational model component
disjoint with: Data structure
comment: A mathematical and/or logical expression that determines the value of a data structure.

Computational model component
type: Class
subclass of: SemSim component
disjoint with: Physical model component
comment: An element of a SemSim model that relates to the mathematical or logical representation of physical quantities or qualities.

Custom physical dependency
type: Class
subclass of: Physical dependency
disjoint with: Reference physical dependency
comment: A physical dependency defined in a specific SemSim model.

Custom physical entity
type: Class
subclass of: Physical entity
comment: A physical entity defined in a specific SemSim model.

Custom physical process
type: Class
subclass of: Physical process
comment: A physical process defined in a specific SemSim model.

Custom physical property
type: Class
subclass of: Physical property
disjoint with: Reference physical property
comment: A physical property defined in a specific SemSim model.

Data structure
type: Class
subclass of: Computational model component
comment: A computational element that stores numerical and/or logical information related to the model.

Decimal
type: Class
subclass of: Real
disjoint with: Integer
comment: A data structure whose value is limited to decimals.

Integer
type: Class
subclass of: Real
comment: A data structure whose value is limited to the whole numbers.

MMLchoice
type: Class
subclass of: Real
comment: A data structure unique to JSim's Mathematical Modeling Language (MML) used to set one or more model input values at runtime.

Physical dependency
type: Class
subclass of: Physical model component
disjoint with: Physical entity
disjoint with: Physical process
disjoint with: Physical property
comment: A quantitative relation between values of physical properties that occurs over a span of time and that determines the time-course of a physical process.

Physical entity
type: Class
subclass of: Physical model component
disjoint with: Physical process
disjoint with: Physical property
comment: A physics analytical entity that represents the material, energy, and/or information content of material or immaterial, space-occupying continuants.

Physical model component
type: Class
subclass of: SemSim component
comment: A SemSim model element used to represent, in whole or in part, the physical meaning of a computational element.

Physical process
type: Class
subclass of: Physical model component
disjoint with: Physical property
comment: A physical processural entity that is a flow, or the control of a flow, of energy and/or information amongst physical continuants that are participants in the physical process.

Physical property
type: Class
subclass of: Physical model component
comment: A physical attribute of an instance of a physical entity, an occurrence of a physical process, or a physical dependency that has a quantitative value that is measurable by a physical device or method, or is computable from such values.

Real
type: Class
subclass of: Data structure
comment: A data structure whose value is limited to the real numbers.

Reference physical dependency
type: Class
subclass of: Physical dependency
comment: A physical dependency that is defined using a term in an external knowledge resource.

Reference physical entity
type: Class
subclass of: Physical entity
comment: A physical entity that is defined using a term from an external knowledge resource.

Reference physical process
type: Class
subclass of: Physical process
comment: A physical process that is defined using a term in an external knowledge resource.

Reference physical property
type: Class
subclass of: Physical property
comment: A physical property that is defined using a term in an external knowledge resource.

Relational constraint
type: Class
subclass of: Computational model component
comment: A logical expression that constrains, but does not define, the value of a data structure. Example: x > 0.

SemSim component
type: Class
comment: A computational or physical element of a SemSim model.

Submodel
type: Class
subclass of: Physical model component
comment: A grouping of one or more data structures that comprise a computationally or physically distinct part of a model or submodel.

Unit of measurement
type: Class
subclass of: Computational model component
comment: A physical quantity chosen as a standard in terms of which other physical quantities may be expressed.

calcium(2+)
type: NamedIndividual
refers to: calcium(2+)
is index entity for: CHEBI 29108 part of fma66836 part of fma14067
part of: Portion of cytosol
has physical property: Chemical concentration

Calcium (2+) bound to troponin C
type: NamedIndividual
type: Custom physical entity
comment: Calcium (2+) ion bound to site II of troponin C
is index entity for: Calcium (2+) bound to troponin C part of fma66836 part of fma14067
part of: Portion of cytosol
has physical property: Chemical concentration

Cross Bridges
type: NamedIndividual
type: Submodel
name: Cross_Bridges
has associated data structure: Cross Bridges.A 1
has associated data structure: Cross Bridges.A 2
has associated data structure: Cross Bridges.A 3
has associated data structure: Cross Bridges.Q
has associated data structure: Cross Bridges.Q 1
has associated data structure: Cross Bridges.Q 2
has associated data structure: Cross Bridges.Q 3
has associated data structure: Cross Bridges.T 0
has associated data structure: Cross Bridges.Tension
has associated data structure: Cross Bridges.a
has associated data structure: Cross Bridges.alpha 1
has associated data structure: Cross Bridges.alpha 2
has associated data structure: Cross Bridges.alpha 3
has associated data structure: Cross Bridges.dExtensionRatiodt
has associated data structure: Time
has computational component: Cross Bridges computation

Cross Bridges.A 1
type: NamedIndividual
type: Decimal
has start value: -29
is solution domain: false
is discrete: false
is declared: true
comment: Weighting coefficient for process 1 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.A 1 property

Cross Bridges.A 2
type: NamedIndividual
type: Decimal
has start value: 138
is solution domain: false
is discrete: false
is declared: true
comment: Weighting coefficient for process 2 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.A 2 property

Cross Bridges.A 3
type: NamedIndividual
type: Decimal
has start value: 129
is discrete: false
is solution domain: false
is declared: true
comment: Weighting coefficient for process 3 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.A 3 property

Cross Bridges.Q
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Sum of the three exponential processes in the crossbridge dynamics fading memory model
is computational component for: Cross Bridges.Q property

Cross Bridges.Q 1
type: NamedIndividual
type: Decimal
has start value: 0
is solution domain: false
is discrete: false
is declared: true
comment: Exponential process 1 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.Q 1 property

Cross Bridges.Q 2
type: NamedIndividual
type: Decimal
has start value: 0
is solution domain: false
is discrete: false
is declared: true
comment: Exponential process 2 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.Q 2 property

Cross Bridges.Q 3
type: NamedIndividual
type: Decimal
has start value: 0
is discrete: false
is solution domain: false
is declared: true
comment: Exponential process 3 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.Q 3 property

Cross Bridges.T 0
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: The isometric tension at a given intracellular calcium ion concentration and sarcomere length
is computational component for: Cross Bridges.T 0 property
has unit: UNIT N per mm2

Cross Bridges.Tension
type: NamedIndividual
type: Decimal
metadata ID: Cross_Bridges_Tension
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Active tension of cardiac myocyte
is computational component for: Surface normal tensile stress
has unit: UNIT N per mm2
mapped to: troponin.Tension

Surface normal tensile stress
type: NamedIndividual
refers to: Surface normal tensile stress
has computational component: Cross Bridges.Tension
physical property of: Cardiac myocyte

Cross Bridges.a
type: NamedIndividual
type: Decimal
has start value: 0.35
is discrete: false
is solution domain: false
is declared: true
comment: Curve-shaping constant for relationship between relative sarcomere velocity and relative tension
is computational component for: Cross Bridges.a property

Cross Bridges.alpha 1
type: NamedIndividual
type: Decimal
has start value: 0.03
is solution domain: false
is discrete: false
is declared: true
comment: Exponential rate constant for process 1 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.alpha 1 property
has unit: UNIT per ms

Cross Bridges.alpha 2
type: NamedIndividual
type: Decimal
has start value: 0.13
is discrete: false
is solution domain: false
is declared: true
comment: Exponential rate constant for process 2 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.alpha 2 property
has unit: UNIT per ms

Cross Bridges.alpha 3
type: NamedIndividual
type: Decimal
has start value: 0.625
is solution domain: false
is discrete: false
is declared: true
comment: Exponential rate constant for process 3 of the crossbridge kinetics fading memory model
is computational component for: Cross Bridges.alpha 3 property
has unit: UNIT per ms

Cross Bridges.dExtensionRatiodt
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Change in ExtensionRatio with respect to time
is computational component for: Cross Bridges.dExtensionRatiodt property
has unit: UNIT per ms

Time
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
refers to: http://bhi.washington.edu/OPB#OPB_01023
has cell m lpublic interface: in
is declared: true
comment: Temporal solution domain
is computational component for: Cross Bridges.time property
has unit: UNIT ms

Cross Bridges computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>Q</ci> <apply> <plus /> <ci>Q_1</ci> <ci>Q_2</ci> <ci>Q_3</ci> </apply> </apply> <apply> <eq /> <ci>Tension</ci> <piecewise> <piece> <apply> <divide /> <apply> <times /> <ci>T_0</ci> <apply> <plus /> <apply> <times /> <ci>a</ci> <ci>Q</ci> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </apply> </apply> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>Q</ci> </apply> </apply> <apply> <lt /> <ci>Q</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0</cn> </apply> </piece> <otherwise> <apply> <divide /> <apply> <times /> <ci>T_0</ci> <apply> <plus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <apply> <times /> <apply> <plus /> <ci>a</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> <ci>Q</ci> </apply> </apply> </apply> <apply> <plus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>Q</ci> </apply> </apply> </otherwise> </piecewise> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>Q_1</ci> </apply> <apply> <minus /> <apply> <times /> <ci>A_1</ci> <ci>dExtensionRatiodt</ci> </apply> <apply> <times /> <ci>alpha_1</ci> <ci>Q_1</ci> </apply> </apply> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>Q_2</ci> </apply> <apply> <minus /> <apply> <times /> <ci>A_2</ci> <ci>dExtensionRatiodt</ci> </apply> <apply> <times /> <ci>alpha_2</ci> <ci>Q_2</ci> </apply> </apply> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>Q_3</ci> </apply> <apply> <minus /> <apply> <times /> <ci>A_3</ci> <ci>dExtensionRatiodt</ci> </apply> <apply> <times /> <ci>alpha_3</ci> <ci>Q_3</ci> </apply> </apply> </apply>
is computational component for: Cross Bridges

Dissociation of troponin C bound to calcium
type: NamedIndividual
type: Custom physical process
comment: In this model, the formation of troponin C comes from the dissociation of the calcium (2+) / troponin C complex
has sink: calcium(2+)
has source: Calcium (2+) bound to troponin C
has sink: Troponin C, slow skeletal and cardiac muscles (TN-C)
has physical property: Chemical concentration flow rate

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: calcium(2+)
annotated source: Dissociation of troponin C bound to calcium

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated source: Dissociation of troponin C bound to calcium
annotated target: Troponin C, slow skeletal and cardiac muscles (TN-C)

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: Calcium (2+) bound to troponin C
annotated source: Dissociation of troponin C bound to calcium

Myofilaments
type: NamedIndividual
type: Submodel
name: Myofilaments
has associated data structure: Myofilaments.ExtensionRatio
has associated data structure: Myofilaments.dExtensionRatiodt
has associated data structure: Myofilaments.lambda
has associated data structure: Myofilaments.lambda prev
has associated data structure: Time
has computational component: Myofilaments computation

Myofilaments.ExtensionRatio
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Sarcomere strain
is computational component for: Myofilaments.ExtensionRatio property

Myofilaments.dExtensionRatiodt
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Change in ExtensionRatio with respect to time
mapped to: Cross Bridges.dExtensionRatiodt
is computational component for: Myofilaments.dExtensionRatiodt property
has unit: UNIT per ms

Myofilaments.lambda
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Sarcomere strain, constrained to values between 0.8 and 1.15
is computational component for: Myofilaments.lambda property
mapped to: filament overlap.lambda
mapped to: tropomyosin.lambda

Myofilaments.lambda prev
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Mystery variable mathematically equal to sarcomere strain
is computational component for: Myofilaments.lambda prev property

Time
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
refers to: http://bhi.washington.edu/OPB#OPB_01023
has cell m lpublic interface: in
is declared: true
comment: Temporal solution domain
is computational component for: Myofilaments.time property
has unit: UNIT ms

Myofilaments computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>ExtensionRatio</ci> <piecewise> <piece> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <apply> <gt /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="ms">1000</cn> </apply> </piece> <otherwise> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </otherwise> </piecewise> </apply> <apply> <eq /> <ci>lambda_prev</ci> <ci>ExtensionRatio</ci> </apply> <apply> <eq /> <ci>dExtensionRatiodt</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_ms">0</cn> </apply> <apply> <eq /> <ci>lambda</ci> <piecewise> <piece> <ci>ExtensionRatio</ci> <apply> <and /> <apply> <gt /> <ci>ExtensionRatio</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.8</cn> </apply> <apply> <leq /> <ci>ExtensionRatio</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.15</cn> </apply> </apply> </piece> <piece> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.15</cn> <apply> <gt /> <ci>ExtensionRatio</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.15</cn> </apply> </piece> <otherwise> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.8</cn> </otherwise> </piecewise> </apply>
is computational component for: Myofilaments

Troponin C, slow skeletal and cardiac muscles (TN-C)
type: NamedIndividual
refers to: Troponin C, slow skeletal and cardiac muscles (TN-C)
is index entity for: P02591 part of fma66836 part of fma14067
part of: Portion of cytosol
has physical property: Chemical concentration

UNIT N per mm2
type: NamedIndividual
type: Unit of measurement
has computational code: N_per_mm2
unit for: Cross Bridges.T 0
unit for: Cross Bridges.Tension
has unit factor: UNIT metre
has unit factor: UNIT newton
unit for: isometric tension.T 0
unit for: isometric tension.T Base
unit for: length independent tension.T Base
unit for: length independent tension.T ref
unit for: troponin.T ref
unit for: troponin.Tension

Axiom
has unit factor exponent: -2.0
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT N per mm2
annotated target: UNIT metre

UNIT litre
type: NamedIndividual
type: Unit of measurement
has computational code: litre
is fundamental unit: true
unit factor for: UNIT mM

UNIT mM
type: NamedIndividual
type: Unit of measurement
has computational code: mM
has unit factor: UNIT litre
unit factor for: UNIT mM per ms
has unit factor: UNIT mole
unit factor for: UNIT per mM per ms
unit for: intracellular ion concentrations.Ca TRPN Max
unit for: intracellular ion concentrations.Ca b
unit for: intracellular ion concentrations.Ca i
unit for: intracellular ion concentrations.TRPN
unit for: tropomyosin.Ca 50
unit for: tropomyosin.Ca 50ref
unit for: tropomyosin.Ca TRPN 50
unit for: tropomyosin.Ca TRPN Max
unit for: tropomyosin.Ca b
unit for: troponin.Ca TRPN Max
unit for: troponin.Ca i
unit for: troponin.TRPN

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT mM
annotated target: UNIT mole

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT litre
annotated source: UNIT mM

UNIT mM per ms
type: NamedIndividual
type: Unit of measurement
has computational code: mM_per_ms
has unit factor: UNIT mM
has unit factor: UNIT second
unit for: intracellular ion concentrations.J TRPN
unit for: troponin.J TRPN

Axiom
has unit factor exponent: -1.0
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT mM per ms
annotated target: UNIT second

UNIT metre
type: NamedIndividual
type: Unit of measurement
has computational code: metre
is fundamental unit: true
unit factor for: UNIT N per mm2

UNIT mole
type: NamedIndividual
type: Unit of measurement
has computational code: mole
is fundamental unit: true
unit factor for: UNIT mM

UNIT ms
type: NamedIndividual
type: Unit of measurement
has computational code: ms
unit for: Time
has unit factor: UNIT second

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT ms
annotated target: UNIT second

UNIT newton
type: NamedIndividual
type: Unit of measurement
has computational code: newton
is fundamental unit: true
unit factor for: UNIT N per mm2

UNIT per mM per ms
type: NamedIndividual
type: Unit of measurement
has computational code: per_mM_per_ms
has unit factor: UNIT mM
has unit factor: UNIT second
unit for: tropomyosin.k on
unit for: troponin.k on

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT mM
annotated source: UNIT per mM per ms

Axiom
has unit factor exponent: -1.0
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT per mM per ms
annotated target: UNIT second

UNIT per ms
type: NamedIndividual
type: Unit of measurement
has computational code: per_ms
unit for: Cross Bridges.alpha 1
unit for: Cross Bridges.alpha 2
unit for: Cross Bridges.alpha 3
unit for: Cross Bridges.dExtensionRatiodt
unit for: Myofilaments.dExtensionRatiodt
has unit factor: UNIT second
unit for: tropomyosin.K 1
unit for: tropomyosin.K 2
unit for: tropomyosin.alpha 0
unit for: tropomyosin.alpha Tm
unit for: tropomyosin.alpha r1
unit for: tropomyosin.alpha r2
unit for: tropomyosin.beta Tm
unit for: tropomyosin.k Ref off
unit for: troponin.k Ref off
unit for: troponin.k off

Axiom
has unit factor exponent: -1.0
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT per ms
annotated target: UNIT second

UNIT second
type: NamedIndividual
type: Unit of measurement
has computational code: second
is fundamental unit: true
unit factor for: UNIT mM per ms
unit factor for: UNIT ms
unit factor for: UNIT per mM per ms
unit factor for: UNIT per ms

environment
type: NamedIndividual
type: Submodel
name: environment
has associated data structure: Time
has computational component: environment computation

Time
type: NamedIndividual
type: Decimal
metadata ID: environment_time
is solution domain: false
is discrete: false
refers to: http://bhi.washington.edu/OPB#OPB_01023
has cell m lpublic interface: out
is declared: true
comment: Temporal solution domain
mapped to: Time
has unit: UNIT ms
is computational component for: environment.time property

filament overlap
type: NamedIndividual
type: Submodel
name: filament_overlap
has associated data structure: filament overlap.beta 0
has associated data structure: filament overlap.lambda
has associated data structure: filament overlap.overlap
has computational component: filament overlap computation

filament overlap.beta 0
type: NamedIndividual
type: Decimal
has start value: 4.9
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Scaling factor (slope) for the relationship between lambda and T_0
is computational component for: filament overlap.beta 0 property
mapped to: tropomyosin.beta 0

filament overlap.lambda
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Sarcomere strain?
is computational component for: filament overlap.lambda property

filament overlap.overlap
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Sarcomere overlap?
is computational component for: filament overlap.overlap property
mapped to: isometric tension.overlap

filament overlap computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>overlap</ci> <apply> <plus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <apply> <times /> <ci>beta_0</ci> <apply> <minus /> <ci>lambda</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </apply> </apply> </apply> </apply>
is computational component for: filament overlap

Cardiac myocyte
type: NamedIndividual
refers to: Cardiac myocyte
has physical property: Surface normal tensile stress
has part: Portion of cytosol

Portion of cytosol
type: NamedIndividual
refers to: Portion of cytosol
has part: calcium(2+)
has part: Calcium (2+) bound to troponin C
has part: Troponin C, slow skeletal and cardiac muscles (TN-C)
part of: Cardiac myocyte
is index entity for: fma66836 part of fma14067

intracellular ion concentrations
type: NamedIndividual
type: Submodel
name: intracellular_ion_concentrations
has associated data structure: intracellular ion concentrations.Ca TRPN Max
has associated data structure: intracellular ion concentrations.Ca b
has associated data structure: intracellular ion concentrations.Ca i
has associated data structure: intracellular ion concentrations.J TRPN
has associated data structure: intracellular ion concentrations.TRPN
has associated data structure: Time
has computational component: intracellular ion concentrations computation

intracellular ion concentrations.Ca TRPN Max
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: The maximum concentration of calcium ions that can bind to site II on troponin C
has unit: UNIT mM
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: intracellular ion concentrations.Ca TRPN Max

intracellular ion concentrations.Ca b
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Concentration of calcium (2+) bound to troponin C
has unit: UNIT mM
is computational component for: Chemical concentration
mapped to: tropomyosin.Ca b

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Calcium (2+) bound to troponin C
has computational component: intracellular ion concentrations.Ca b

intracellular ion concentrations.Ca i
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
metadata ID: intracellular_ion_concentrations_Ca_i
has cell m lpublic interface: out
is declared: true
comment: Intracellular calcium (2+) concentration
has unit: UNIT mM
is computational component for: Chemical concentration
mapped to: troponin.Ca i

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium(2+)
has computational component: intracellular ion concentrations.Ca i

intracellular ion concentrations.J TRPN
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Intracellular troponin flux
has unit: UNIT mM per ms
is computational component for: Chemical concentration flow rate

Chemical concentration flow rate
type: NamedIndividual
refers to: Chemical concentration flow rate
physical property of: Dissociation of troponin C bound to calcium
has computational component: intracellular ion concentrations.J TRPN

intracellular ion concentrations.TRPN
type: NamedIndividual
type: Decimal
has start value: 0.067593139865
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Intracellular troponin concentration
has unit: UNIT mM
is computational component for: Chemical concentration
mapped to: troponin.TRPN

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Troponin C, slow skeletal and cardiac muscles (TN-C)
has computational component: intracellular ion concentrations.TRPN

Time
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
refers to: http://bhi.washington.edu/OPB#OPB_01023
has cell m lpublic interface: in
is declared: true
comment: Temporal solution domain
has unit: UNIT ms
is computational component for: intracellular ion concentrations.time property

intracellular ion concentrations computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>Ca_b</ci> <apply> <minus /> <ci>Ca_TRPN_Max</ci> <ci>TRPN</ci> </apply> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>TRPN</ci> </apply> <ci>J_TRPN</ci> </apply> <apply> <eq /> <ci>Ca_i</ci> <piecewise> <piece> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1000</cn> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" type="e-notation" cellml:units="mM"> 1.8433 <sep /> -7 </cn> </apply> <apply> <lt /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="ms">1</cn> </apply> </piece> <piece> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1000</cn> <apply> <minus /> <apply> <plus /> <apply> <minus /> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="mM">1.055</cn> <apply> <power /> <apply> <divide /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="ms">1000</cn> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">3</cn> </apply> </apply> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="mM">0.03507</cn> <apply> <power /> <apply> <divide /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="ms">1000</cn> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> </apply> </apply> <apply> <divide /> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="mM">0.0003992</cn> <ci>time</ci> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="ms">1000</cn> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" type="e-notation" cellml:units="mM"> 1.356 <sep /> -6 </cn> </apply> </apply> <apply> <and /> <apply> <geq /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="ms">10</cn> </app…
is computational component for: intracellular ion concentrations

isometric tension
type: NamedIndividual
type: Submodel
name: isometric_tension
has associated data structure: isometric tension.T 0
has associated data structure: isometric tension.T Base
has associated data structure: isometric tension.overlap
has computational component: isometric tension computation

isometric tension.T 0
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
metadata ID: isometric_tension_T0
has cell m lpublic interface: out
is declared: true
comment: The isometric tension at a given intracellular calcium ion concentration and sarcomere length
mapped to: Cross Bridges.T 0
has unit: UNIT N per mm2
is computational component for: isometric tension.T 0 property

isometric tension.T Base
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Isometric tension of cell
has unit: UNIT N per mm2
is computational component for: isometric tension.T Base property

isometric tension.overlap
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
is computational component for: isometric tension.overlap property

isometric tension computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>T_0</ci> <apply> <times /> <ci>T_Base</ci> <ci>overlap</ci> </apply> </apply>
is computational component for: isometric tension

length independent tension
type: NamedIndividual
type: Submodel
name: length_independent_tension
has associated data structure: length independent tension.T Base
has associated data structure: length independent tension.T ref
has associated data structure: length independent tension.z
has associated data structure: length independent tension.z max
has computational component: length independent tension computation

length independent tension.T Base
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Isometric tension of cell
has unit: UNIT N per mm2
mapped to: isometric tension.T Base
is computational component for: length independent tension.T Base property

length independent tension.T ref
type: NamedIndividual
type: Decimal
has start value: 56.2
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Maximum tension at resting sarcomere length
has unit: UNIT N per mm2
is computational component for: length independent tension.T ref property
mapped to: troponin.T ref

length independent tension.z
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: The fraction of actin sites available for crossbridge binding
is computational component for: length independent tension.z property

length independent tension.z max
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: The fraction of actin sites available at full activation
is computational component for: length independent tension.z max property

length independent tension computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>T_Base</ci> <apply> <divide /> <apply> <times /> <ci>T_ref</ci> <ci>z</ci> </apply> <ci>z_max</ci> </apply> </apply>
is computational component for: length independent tension

thinfilaments
type: NamedIndividual
type: Submodel
name: thinfilaments
has computational component: thinfilaments computation

tropomyosin
type: NamedIndividual
type: Submodel
name: tropomyosin
has associated data structure: tropomyosin.Ca 50
has associated data structure: tropomyosin.Ca 50ref
has associated data structure: tropomyosin.Ca TRPN 50
has associated data structure: tropomyosin.Ca TRPN Max
has associated data structure: tropomyosin.Ca b
has associated data structure: tropomyosin.K 1
has associated data structure: tropomyosin.K 2
has associated data structure: tropomyosin.K z
has associated data structure: tropomyosin.alpha 0
has associated data structure: tropomyosin.alpha Tm
has associated data structure: tropomyosin.alpha r1
has associated data structure: tropomyosin.alpha r2
has associated data structure: tropomyosin.beta 0
has associated data structure: tropomyosin.beta 1
has associated data structure: tropomyosin.beta Tm
has associated data structure: tropomyosin.gamma trpn
has associated data structure: tropomyosin.k Ref off
has associated data structure: tropomyosin.k on
has associated data structure: tropomyosin.lambda
has associated data structure: tropomyosin.n Hill
has associated data structure: tropomyosin.n Rel
has associated data structure: Time
has associated data structure: tropomyosin.z
has associated data structure: tropomyosin.z max
has associated data structure: tropomyosin.z p
has computational component: tropomyosin computation

tropomyosin.Ca 50
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Concentration of free calcium (2+) at half-activation of maximum tension
has unit: UNIT mM
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: tropomyosin.Ca 50

tropomyosin.Ca 50ref
type: NamedIndividual
type: Decimal
has start value: 1.05e-3
is solution domain: false
is discrete: false
is declared: true
comment: Offset parameter for Ca_50 vs. lambda dependency
has unit: UNIT mM
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: tropomyosin.Ca 50ref

tropomyosin.Ca TRPN 50
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Calcium (2+) bound to TnC at half-activation of maximum tension
has unit: UNIT mM
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: tropomyosin.Ca TRPN 50

tropomyosin.Ca TRPN Max
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: The maximum concentration of calcium ions that can bind to site II on troponin C
has unit: UNIT mM
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: tropomyosin.Ca TRPN Max

tropomyosin.Ca b
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of calcium (2+) bound to troponin C
has unit: UNIT mM
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Calcium (2+) bound to troponin C
has computational component: tropomyosin.Ca b

tropomyosin.K 1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Linearization term for computing z_max
has unit: UNIT per ms
is computational component for: tropomyosin.K 1 property

tropomyosin.K 2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Linearization term for computing z_max
has unit: UNIT per ms
is computational component for: tropomyosin.K 2 property

tropomyosin.K z
type: NamedIndividual
type: Decimal
has start value: 0.15
is discrete: false
is solution domain: false
is declared: true
comment: Fast relaxation rate parameter for computing z
is computational component for: tropomyosin.K z property

tropomyosin.alpha 0
type: NamedIndividual
type: Decimal
has start value: 8e-3
is solution domain: false
is discrete: false
is declared: true
comment: The monoexponential activation rate seen in caged calcium (2+) experiments. Used to compute z.
has unit: UNIT per ms
is computational component for: tropomyosin.alpha 0 property

tropomyosin.alpha Tm
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Intermediate term for first component of varaible z's ODE (equation 9 in reference paper)
has unit: UNIT per ms
is computational component for: tropomyosin.alpha Tm property

tropomyosin.alpha r1
type: NamedIndividual
type: Decimal
has start value: 2e-3
is solution domain: false
is discrete: false
is declared: true
comment: Slow relaxation rate parameter for computing z
has unit: UNIT per ms
is computational component for: tropomyosin.alpha r1 property

tropomyosin.alpha r2
type: NamedIndividual
type: Decimal
has start value: 1.75e-3
is discrete: false
is solution domain: false
is declared: true
comment: Fast relaxation rate parameter for computing z
has unit: UNIT per ms
is computational component for: tropomyosin.alpha r2 property

tropomyosin.beta 0
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Scaling factor (slope) for the relationship between lambda and T_0
is computational component for: tropomyosin.beta 0 property

tropomyosin.beta 1
type: NamedIndividual
type: Decimal
has start value: -4
is solution domain: false
is discrete: false
is declared: true
comment: Scaling parameter for Ca_50 vs. lambda dependency
is computational component for: tropomyosin.beta 1 property

tropomyosin.beta Tm
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Intermediate term for second component of variable z's ODE (equation 9 in reference paper)
has unit: UNIT per ms
is computational component for: tropomyosin.beta Tm property

tropomyosin.gamma trpn
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: A measure of the effect of tension on the unbinding rate of calcium (2+) from troponin C
is computational component for: tropomyosin.gamma trpn property

tropomyosin.k Ref off
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Rate of calcium (2+) unbinding from Troponin C in the absence of tension
has unit: UNIT per ms
is computational component for: tropomyosin.k Ref off property

tropomyosin.k on
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: The binding rate of calcium (2+) to troponin C site II
has unit: UNIT per mM per ms
is computational component for: tropomyosin.k on property

tropomyosin.lambda
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Sarcomere strain?
is computational component for: tropomyosin.lambda property

tropomyosin.n Hill
type: NamedIndividual
type: Decimal
has start value: 3
is discrete: false
is solution domain: false
is declared: true
comment: Analogous to the Hill coefficient in the steady-state force-calcium (2+) curve (F-pCa) and provides a phenomenological rep- resentation of the high cooperativity, due to nearest-neighbor interactions between tropomyosin and/or crossbridges, seen in the activation of tension in cardiac muscle
is computational component for: tropomyosin.n Hill property

tropomyosin.n Rel
type: NamedIndividual
type: Decimal
has start value: 3
is solution domain: false
is discrete: false
is declared: true
comment: Fast relaxation rate parameter for computing z
is computational component for: tropomyosin.n Rel property

Time
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
refers to: http://bhi.washington.edu/OPB#OPB_01023
has cell m lpublic interface: in
is declared: true
comment: Temporal solution domain
has unit: UNIT ms
is computational component for: tropomyosin.time property

tropomyosin.z
type: NamedIndividual
type: Decimal
has start value: 0.014417937837
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: The fraction of actin sites available for crossbridge binding as determined by thin filament kinetics
mapped to: length independent tension.z
is computational component for: tropomyosin.z property

tropomyosin.z max
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: the maximum fraction of available actin sites at a given sarcomere length
mapped to: length independent tension.z max
is computational component for: tropomyosin.z max property

tropomyosin.z p
type: NamedIndividual
type: Decimal
has start value: 0.85
is solution domain: false
is discrete: false
is declared: true
comment: Point around which the non-linear component of equation 9 in the paper (solving for dz/dt) is linearized to maintain an explicit formulation for the model
is computational component for: tropomyosin.z p property

tropomyosin computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>K_2</ci> <apply> <times /> <apply> <divide /> <apply> <times /> <ci>alpha_r2</ci> <apply> <power /> <ci>z_p</ci> <ci>n_Rel</ci> </apply> </apply> <apply> <plus /> <apply> <power /> <ci>z_p</ci> <ci>n_Rel</ci> </apply> <apply> <power /> <ci>K_z</ci> <ci>n_Rel</ci> </apply> </apply> </apply> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <apply> <divide /> <apply> <times /> <ci>n_Rel</ci> <apply> <power /> <ci>K_z</ci> <ci>n_Rel</ci> </apply> </apply> <apply> <plus /> <apply> <power /> <ci>z_p</ci> <ci>n_Rel</ci> </apply> <apply> <power /> <ci>K_z</ci> <ci>n_Rel</ci> </apply> </apply> </apply> </apply> </apply> </apply> <apply> <eq /> <ci>K_1</ci> <apply> <divide /> <apply> <times /> <ci>alpha_r2</ci> <apply> <power /> <ci>z_p</ci> <apply> <minus /> <ci>n_Rel</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </apply> </apply> <ci>n_Rel</ci> <apply> <power /> <ci>K_z</ci> <ci>n_Rel</ci> </apply> </apply> <apply> <power /> <apply> <plus /> <apply> <power /> <ci>z_p</ci> <ci>n_Rel</ci> </apply> <apply> <power /> <ci>K_z</ci> <ci>n_Rel</ci> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> </apply> </apply> <apply> <eq /> <ci>z_max</ci> <apply> <divide /> <apply> <minus /> <apply> <divide /> <ci>alpha_0</ci> <apply> <power /> <apply> <divide /> <ci>Ca_TRPN_50</ci> <ci>Ca_TRPN_Max</ci> </apply> <ci>n_Hill</ci> </apply> </apply> <ci>K_2</ci> </apply> <apply> <plus /> <ci>alpha_r1</ci> <ci>K_1</ci> <apply> <divide /> <ci>alpha_0</ci> <apply> <power /> <apply> <divide /> <ci>Ca_TRPN_50</ci> <ci>Ca_TRPN_Max</ci> </apply> <ci>n_Hill</ci> </apply> </apply> </apply> </apply> </apply> <apply> <eq /> <ci>Ca_50</ci> <apply> <times /> <ci>Ca_50ref</ci> <apply> <plus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <apply> <times /> <ci>beta_1</ci> <apply> …
is computational component for: tropomyosin

troponin
type: NamedIndividual
type: Submodel
name: troponin
has associated data structure: troponin.Ca TRPN Max
has associated data structure: troponin.Ca i
has associated data structure: troponin.J TRPN
has associated data structure: troponin.TRPN
has associated data structure: troponin.T ref
has associated data structure: troponin.Tension
has associated data structure: troponin.gamma trpn
has associated data structure: troponin.k Ref off
has associated data structure: troponin.k off
has associated data structure: troponin.k on
has computational component: troponin computation

troponin.Ca TRPN Max
type: NamedIndividual
type: Decimal
has start value: 70e-3
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: The maximum concentration of calcium ions that can bind to site II on troponin C
has unit: UNIT mM
mapped to: intracellular ion concentrations.Ca TRPN Max
mapped to: tropomyosin.Ca TRPN Max
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: troponin.Ca TRPN Max

troponin.Ca i
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Intracellular calcium (2+) concentration
has unit: UNIT mM
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium(2+)
has computational component: troponin.Ca i

troponin.J TRPN
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Intracellular troponin flux
has unit: UNIT mM per ms
mapped to: intracellular ion concentrations.J TRPN
is computational component for: Chemical concentration flow rate

Chemical concentration flow rate
type: NamedIndividual
refers to: Chemical concentration flow rate
physical property of: Dissociation of troponin C bound to calcium
has computational component: troponin.J TRPN

troponin.TRPN
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Intracellular troponin concentration
has unit: UNIT mM
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Troponin C, slow skeletal and cardiac muscles (TN-C)
has computational component: troponin.TRPN

troponin.T ref
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Maximum tension at resting sarcomere length
has unit: UNIT N per mm2
is computational component for: troponin.T ref property

troponin.Tension
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Active tension of cardiac myocyte
has unit: UNIT N per mm2
is computational component for: Surface normal tensile stress

Surface normal tensile stress
type: NamedIndividual
refers to: Surface normal tensile stress
physical property of: Cardiac myocyte
has computational component: troponin.Tension

troponin.gamma trpn
type: NamedIndividual
type: Decimal
has start value: 2
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: A measure of the effect of tension on the unbinding rate of calcium (2+) from troponin C
mapped to: tropomyosin.gamma trpn
is computational component for: troponin.gamma trpn property

troponin.k Ref off
type: NamedIndividual
type: Decimal
has start value: 0.2
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Rate of calcium (2+) unbinding from Troponin C in the absence of tension
has unit: UNIT per ms
mapped to: tropomyosin.k Ref off
is computational component for: troponin.k Ref off property

troponin.k off
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: The unbinding rate of calcium (2+) from troponin C site II
has unit: UNIT per ms
is computational component for: troponin.k off property

troponin.k on
type: NamedIndividual
type: Decimal
has start value: 100
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: The binding rate of calcium (2+) to troponin C site II
has unit: UNIT per mM per ms
mapped to: tropomyosin.k on
is computational component for: troponin.k on property

troponin computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>k_off</ci> <piecewise> <piece> <apply> <times /> <ci>k_Ref_off</ci> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <apply> <divide /> <ci>Tension</ci> <apply> <times /> <ci>gamma_trpn</ci> <ci>T_ref</ci> </apply> </apply> </apply> </apply> <apply> <gt /> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <apply> <divide /> <ci>Tension</ci> <apply> <times /> <ci>gamma_trpn</ci> <ci>T_ref</ci> </apply> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.1</cn> </apply> </piece> <otherwise> <apply> <times /> <ci>k_Ref_off</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.1</cn> </apply> </otherwise> </piecewise> </apply> <apply> <eq /> <ci>J_TRPN</ci> <apply> <minus /> <apply> <times /> <apply> <minus /> <ci>Ca_TRPN_Max</ci> <ci>TRPN</ci> </apply> <ci>k_off</ci> </apply> <apply> <times /> <ci>Ca_i</ci> <ci>TRPN</ci> <ci>k_on</ci> </apply> </apply> </apply>
is computational component for: troponin