25022015142636174m0500
type: Ontology
legacy code URI: /Users/max_neal/Dropbox/Semantic Project/Annotated CellML models/smith_crampin_2004/smith_crampin_2004.cellml
sem sim version: 0.2
has cell m ldocumentation: <documentation xmlns="http://cellml.org/tmp-documentation"> <articleinfo> Development of models of active ion transport for whole-cell modelling: cardiac sodium-potassium pump as a case study <author> <firstname>Alice</firstname> <surname>Boit</surname> <affiliation> <shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil> </affiliation> </author> </articleinfo> Model Status This CellML model runs in both OpenCell and COR. <sect1 id="sec_structure"> Model Structure ABSTRACT: This study presents a method for the reduction of biophysically-based kinetic models for the active transport of ions. A lumping scheme is presented which exploits the differences in timescales associated with fast and slow transitions between model states, while maintaining the thermodynamic properties of the model. The goal of this approach is to contribute to modelling of the effects of disturbances to metabolism, associated with ischaemic heart disease, on cardiac cell function. The approach is illustrated for the sodium-potassium pump in the myocyte. The lumping scheme is applied to produce a 4-state representation from the detailed 15-state model of Lauger and Apell, Eur. Biophys. J. 13 (1986) 309, for which the principles of free energy transduction are used to link the free energy released from ATP hydrolysis (deltaGATP) to the transition rates between states of the model. An iterative minimisation algorithm is implemented to determine the transition rate parameters based on the model fit to experimental data. Finally, the relationship between deltaGATP and pump cycling direction is investigated and compared with recent experimental findings. The original paper reference is cited below: Development of models of active ion transport for whole-cell modelling: cardiac sodium-potassium pump as a case study, N. P. Smith and E. J. Crampin, 2004, Progress in Biophysics and Molecular Biology PubMed ID: 15142754 <informalfigure float="0" id="fig_smith_crampin_state_d…
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/"> <rdf:Description rdf:about="http://www.cellml.org/cellml/1.0"> <dc:creator> <rdf:Description rdf:about="rdf:#bb0e207c-146d-4039-9f7c-d06ad25bd9c6"> <vCard:N> <rdf:Description rdf:about="rdf:#6ba26935-1582-4d2c-8d63-b5fe38631905"> <vCard:Other></vCard:Other> <vCard:Family>Boit</vCard:Family> <vCard:Given>Alice</vCard:Given> </rdf:Description> </vCard:N> <vCard:EMAIL> <j.0:internet rdf:about="rdf:#9a0073c8-2718-41c3-991a-5f3bb96b7e15"> <rdf:value>a.boit@auckland.ac.nz</rdf:value> </j.0:internet> </vCard:EMAIL> <vCard:ORG> <rdf:Description rdf:about="rdf:#bcf6b23d-9335-449b-83be-c2e0c4ac4d75"> <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:#93a24e90-c784-407e-8e0a-56b5e3ab32a5"> <dcterms:W3CDTF>2004-04-26T00:00:00+00:00</dcterms:W3CDTF> </rdf:Description> </dcterms:created> <cmeta:comment> <rdf:Description rdf:about="rdf:#59a55738-0e3b-48a0-9a7e-572dc6ab43fe"> <rdf:value></rdf:value> <dc:creator> <rdf:Description rdf:about="rdf:#6496b573-b950-4d87-9d53-de4874253a31"> <vCard:FN></vCard:FN> </rdf:Description> </dc:creator> </rdf:Description> </cmeta:comment> <dc:publisher>The University of Auckland, Auckland Bioengineering Institute</dc:publisher> </rdf:Description> <rdf:Description rdf:about="http://www.cellml.org/cellml/1.0#minus_alpha2"> <cmeta:comment> <rdf:Description rdf:about="rdf:#8f94dcfc-58fb-4b79-bfe5-545db58f0d46"> <rdf:value>Calculation of the reverse transition rate called minus_alpha2 from the 3rd to the second state.</rdf:value> </rdf:Desc…
model id: smith_2004
model name: smith_2004

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

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

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

Electrochemical potential
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Electrochemical potential

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

inorganic phosphate
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: inorganic phosphate

sodium(1+)
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: sodium(1+)

potassium(1+)
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: potassium(1+)

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

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

Extracellular space
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Extracellular space

Human body
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Human body

Plasma membrane
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Plasma membrane

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.

proton
type: NamedIndividual
refers to: proton
is index entity for: CHEBI 24636 part of Portion of cytosol part of Cardiac myocyte
has physical property: Chemical concentration
part of: Portion of cytosol

inorganic phosphate
type: NamedIndividual
refers to: inorganic phosphate
is index entity for: CHEBI 24838 part of Portion of cytosol part of Cardiac myocyte
has physical property: Chemical concentration
part of: Portion of cytosol

sodium(1+)
type: NamedIndividual
refers to: sodium(1+)
is index entity for: CHEBI 29101 part of Portion of cytosol part of Cardiac myocyte
has physical property: Chemical concentration
part of: Portion of cytosol

sodium(1+)
type: NamedIndividual
refers to: sodium(1+)
is index entity for: CHEBI 29101 part of Extracellular space
part of: Extracellular space
has physical property: Chemical concentration

potassium(1+)
type: NamedIndividual
refers to: potassium(1+)
is index entity for: CHEBI 29103 part of Extracellular space
part of: Extracellular space
has physical property: Chemical concentration

potassium(1+)
type: NamedIndividual
refers to: potassium(1+)
is index entity for: CHEBI 29103 part of Portion of cytosol part of Cardiac myocyte
has physical property: Chemical concentration
part of: Portion of cytosol

MgATP(2-)
type: NamedIndividual
refers to: MgATP(2-)
is index entity for: CHEBI 30617 part of Portion of cytosol part of Cardiac myocyte
has physical property: Chemical concentration
part of: Portion of cytosol

Cardiac myocyte
type: NamedIndividual
refers to: Cardiac myocyte
has part: Plasma membrane
has part: Portion of cytosol

Extracellular space
type: NamedIndividual
refers to: Extracellular space
has part: sodium(1+)
has part: potassium(1+)

Human body
type: NamedIndividual
refers to: Human body
has physical property: Temperature

MgADP
type: NamedIndividual
type: Custom physical entity
comment: Magnesium-bound ADP
is index entity for: MgADP part of Portion of cytosol part of Cardiac myocyte
has physical property: Chemical concentration
part of: Portion of cytosol

NaK pump
type: NamedIndividual
type: Submodel
name: NaK_pump
has associated data structure: NaK pump.Vm
has associated data structure: NaK pump.alpha1
has associated data structure: NaK pump.alpha2
has associated data structure: NaK pump.alpha3
has associated data structure: NaK pump.alpha4
has associated data structure: NaK pump.body temp
has associated data structure: NaK pump.cH
has associated data structure: NaK pump.cK e
has associated data structure: NaK pump.cK i
has associated data structure: NaK pump.cMgADP
has associated data structure: NaK pump.cMgATP
has associated data structure: NaK pump.cNa e
has associated data structure: NaK pump.cNa i
has associated data structure: NaK pump.cPi
has associated data structure: NaK pump.cPi sum
has associated data structure: NaK pump.dG ATP
has associated data structure: NaK pump.dG K
has associated data structure: NaK pump.dG Na
has associated data structure: NaK pump.dG pump
has associated data structure: NaK pump.diagram sum
has associated data structure: NaK pump.dimless K e
has associated data structure: NaK pump.dimless K i
has associated data structure: NaK pump.dimless MgATP
has associated data structure: NaK pump.dimless Na e
has associated data structure: NaK pump.dimless Na i
has associated data structure: NaK pump.eq HPi
has associated data structure: NaK pump.eq KPi
has associated data structure: NaK pump.eq K e
has associated data structure: NaK pump.eq K i
has associated data structure: NaK pump.eq MgATP
has associated data structure: NaK pump.eq NaPi
has associated data structure: NaK pump.eq Na base e
has associated data structure: NaK pump.eq Na base i
has associated data structure: Faraday constant
has associated data structure: Gas constant
has associated data structure: NaK pump.k1
has associated data structure: NaK pump.k2
has associated data structure: NaK pump.k3
has associated data structure: NaK pump.k4
has associated data structure: NaK pump.minus alpha1
has associated data structure: NaK pump.minus alpha2
has associated data structure: NaK pump.minus alpha3
has associated data structure: NaK pump.minus alpha4
has associated data structure: NaK pump.minus k1
has associated data structure: NaK pump.minus k2
has associated data structure: NaK pump.minus k3
has associated data structure: NaK pump.minus k4
has associated data structure: NaK pump.net free energy
has associated data structure: NaK pump.partition factor
has associated data structure: NaK pump.v cyc
has computational component: NaK pump computation

NaK pump.Vm
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
has cell m lprivate interface: out
is declared: true
comment: Membrane potential
is computational component for: Electrochemical potential
has unit: UNIT mV

Electrochemical potential
type: NamedIndividual
refers to: Electrochemical potential
has computational component: NaK pump.Vm
physical property of: Plasma membrane

NaK pump.alpha1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Apparent first-order forward rate constant for sodium-potassium exchanger transition from lumped states P1-P6 to state P7 of the Post-Albers cycle
is computational component for: NaK pump.alpha1 property
has unit: UNIT rate

NaK pump.alpha2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Apparent first-order forward rate constant for sodium-potassium exchanger transition from state P7 to lumped states P8-P13 of the Post-Albers cycle
is computational component for: NaK pump.alpha2 property
has unit: UNIT rate

NaK pump.alpha3
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Apparent first-order forward rate constant for sodium-potassium exchanger transition from lumped states P8-P13 to lumped states P14-P15 of the Post-Albers cycle
is computational component for: NaK pump.alpha3 property
has unit: UNIT rate

NaK pump.alpha4
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Apparent first-order forward rate constant for sodium-potassium exchanger transition from lumped states P14-P15 to lumped states P1-P6 of the Post-Albers cycle
is computational component for: NaK pump.alpha4 property
has unit: UNIT rate

NaK pump.body temp
type: NamedIndividual
type: Decimal
has start value: 310.
is solution domain: false
is discrete: false
has cell m lprivate interface: out
is declared: true
comment: Ambient temperature
is computational component for: Temperature
has unit: UNIT kelvin

Temperature
type: NamedIndividual
refers to: Temperature
physical property of: Human body
has computational component: NaK pump.body temp

NaK pump.cH
type: NamedIndividual
type: Decimal
has start value: 0.000081283
is discrete: false
is solution domain: false
is declared: true
comment: Intracellular proton concentration
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: NaK pump.cH

NaK pump.cK e
type: NamedIndividual
type: Decimal
has start value: 5.4
is solution domain: false
is discrete: false
is declared: true
comment: Extracellular potassium ion concentration
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: potassium(1+)
has computational component: NaK pump.cK e

NaK pump.cK i
type: NamedIndividual
type: Decimal
has start value: 140.
is solution domain: false
is discrete: false
is declared: true
comment: Intracellular potassium ion concentration
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: potassium(1+)
has computational component: NaK pump.cK i

NaK pump.cMgADP
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
has cell m lprivate interface: out
is declared: true
comment: Intracellular concentration of magnesium-bound ADP
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: MgADP
has computational component: NaK pump.cMgADP

NaK pump.cMgATP
type: NamedIndividual
type: Decimal
has start value: 9.8
is discrete: false
is solution domain: false
is declared: true
comment: Intracellular concentration of magnesium-bound ATP
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: MgATP(2-)
has computational component: NaK pump.cMgATP

NaK pump.cNa e
type: NamedIndividual
type: Decimal
has start value: 150.
is solution domain: false
is discrete: false
is declared: true
comment: Extracellular sodium ion concentration
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: sodium(1+)
has computational component: NaK pump.cNa e

NaK pump.cNa i
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
has cell m lprivate interface: out
is declared: true
comment: Intracellular sodium ion concentration
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: sodium(1+)
has computational component: NaK pump.cNa i

NaK pump.cPi
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Intracellular concentration of inorganic phosphate
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: inorganic phosphate
has computational component: NaK pump.cPi

NaK pump.cPi sum
type: NamedIndividual
type: Decimal
has start value: 4.2
is solution domain: false
is discrete: false
is declared: true
comment: Total intracellular concentration of bound and unbound inorganic phosphate
is computational component for: Chemical concentration
has unit: UNIT concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: NaK pump.cPi sum

NaK pump.dG ATP
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: The free energy of MgATP hydroysis
is computational component for: Chemical potential
has unit: UNIT energy

Chemical potential
type: NamedIndividual
refers to: Chemical potential
has computational component: NaK pump.dG ATP

NaK pump.dG K
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: The energy required to translocate a potassium ion from the extracellular environment to the intracellular cytosol
is computational component for: Chemical potential
has unit: UNIT energy

Chemical potential
type: NamedIndividual
refers to: Chemical potential
has computational component: NaK pump.dG K

NaK pump.dG Na
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: The energy required to translocate a sodium ion from the intracellular cytosol to the extracellular environment
is computational component for: Chemical potential
has unit: UNIT energy

Chemical potential
type: NamedIndividual
refers to: Chemical potential
has computational component: NaK pump.dG Na

NaK pump.dG pump
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Energy consumed for each pump cycle
is computational component for: Chemical potential
has unit: UNIT energy

Chemical potential
type: NamedIndividual
refers to: Chemical potential
has computational component: NaK pump.dG pump

NaK pump.diagram sum
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Convencience term for expressing equation that solves v_cyc
is computational component for: NaK pump.diagram sum property
has unit: UNIT rate diagram sum

NaK pump.dimless K e
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Convenience term that is the ratio of the extracellular potassium concentration to its equilibrium constant
is computational component for: NaK pump.dimless K e property

NaK pump.dimless K i
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Convenience term that is the ratio of the intracellular potassium concentration to its equilibrium constant
is computational component for: NaK pump.dimless K i property

NaK pump.dimless MgATP
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Convenience term that is the ratio of the intracellular MgATP concentration to its equilibrium constant
is computational component for: NaK pump.dimless MgATP property

NaK pump.dimless Na e
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Convenience term that is the ratio of the extracellular sodium concentration to its equilibrium constant
is computational component for: NaK pump.dimless Na e property

NaK pump.dimless Na i
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Convenience term that is the ratio of the intracellular sodium concentration to its equilibrium constant
is computational component for: NaK pump.dimless Na i property

NaK pump.eq HPi
type: NamedIndividual
type: Decimal
has start value: 0.000169
is solution domain: false
is discrete: false
is declared: true
comment: Equilibrium constant for dissociation of proton from inorganic phosphate
is computational component for: NaK pump.eq HPi property
has unit: UNIT concentration

NaK pump.eq KPi
type: NamedIndividual
type: Decimal
has start value: 292.
is discrete: false
is solution domain: false
is declared: true
comment: Equilibrium constant for dissociation of potassium ion from inorganic phosphate
is computational component for: NaK pump.eq KPi property
has unit: UNIT concentration

NaK pump.eq K e
type: NamedIndividual
type: Decimal
has start value: 0.213
is solution domain: false
is discrete: false
is declared: true
comment: Equilibrium constant for dissociation of potassium ion from extracellular-facing pump
is computational component for: NaK pump.eq K e property
has unit: UNIT concentration

NaK pump.eq K i
type: NamedIndividual
type: Decimal
has start value: 0.5
is discrete: false
is solution domain: false
is declared: true
comment: Equilibrium constant for dissociation of potassium ion from intracellular-facing pump
is computational component for: NaK pump.eq K i property
has unit: UNIT concentration

NaK pump.eq MgATP
type: NamedIndividual
type: Decimal
has start value: 2.51
is solution domain: false
is discrete: false
is declared: true
comment: Equilibrium constant for MgATP hydrolysis
is computational component for: NaK pump.eq MgATP property
has unit: UNIT concentration

NaK pump.eq NaPi
type: NamedIndividual
type: Decimal
has start value: 224.
is solution domain: false
is discrete: false
is declared: true
comment: Equilibrium constant for dissociation of sodium ion from inorganic phosphate
is computational component for: NaK pump.eq NaPi property
has unit: UNIT concentration

NaK pump.eq Na base e
type: NamedIndividual
type: Decimal
has start value: 15.5
is discrete: false
is solution domain: false
is declared: true
comment: Equilibrium constant for dissociation of sodium ion from extracellular-facing pump when membrane potential is zero
is computational component for: NaK pump.eq Na base e property
has unit: UNIT concentration

NaK pump.eq Na base i
type: NamedIndividual
type: Decimal
has start value: 2.49
is solution domain: false
is discrete: false
is declared: true
comment: Equilibrium constant for dissociation of sodium ion from intracellular-facing pump when membrane potential is zero
is computational component for: NaK pump.eq Na base i property
has unit: UNIT concentration

Faraday constant
type: NamedIndividual
type: Decimal
has start value: 96485.
is discrete: false
is solution domain: false
refers to: http://bhi.washington.edu/OPB#OPB_00089
has cell m lprivate interface: out
is declared: true
comment: Faraday constant
is computational component for: NaK pump.faraday const property
has unit: UNIT faraday constant

Gas constant
type: NamedIndividual
type: Decimal
has start value: 8.314
is solution domain: false
is discrete: false
refers to: http://bhi.washington.edu/OPB#OPB_00410
has cell m lprivate interface: out
is declared: true
comment: Universal gas constant
is computational component for: NaK pump.gas const property
has unit: UNIT gas constant

NaK pump.k1
type: NamedIndividual
type: Decimal
has start value: 1050.
is discrete: false
is solution domain: false
is declared: true
comment: Forward rate constant for sodium-potassium exchanger transition from lumped states P1-P6 to state P7 of the Post-Albers cycle
is computational component for: NaK pump.k1 property
has unit: UNIT rate

NaK pump.k2
type: NamedIndividual
type: Decimal
has start value: 481.
is discrete: false
is solution domain: false
is declared: true
comment: Forward rate constant for sodium-potassium exchanger transition from state P7 to lumped states P8-P13 of the Post-Albers cycle
is computational component for: NaK pump.k2 property
has unit: UNIT rate

NaK pump.k3
type: NamedIndividual
type: Decimal
has start value: 2000.
is discrete: false
is solution domain: false
is declared: true
comment: Forward rate constant for sodium-potassium exchanger transition from lumped states P8-P13 to lumped states P14-P15 of the Post-Albers cycle
is computational component for: NaK pump.k3 property
has unit: UNIT rate

NaK pump.k4
type: NamedIndividual
type: Decimal
has start value: 320.
is discrete: false
is solution domain: false
is declared: true
comment: Forward rate constant for sodium-potassium exchanger transition from lumped states P14-P15 to lumped states P1-P6 of the Post-Albers cycle
is computational component for: NaK pump.k4 property
has unit: UNIT rate

NaK pump.minus alpha1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Psuedo-first-order backward rate constant for sodium-potassium exchanger transition from lumped states P1-P6 to state P7 of the Post-Albers cycle
is computational component for: NaK pump.minus alpha1 property
has unit: UNIT rate

NaK pump.minus alpha2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Psuedo-first-order backward rate constant for sodium-potassium exchanger transition from state P7 to lumped states P8-P13 of the Post-Albers cycle
is computational component for: NaK pump.minus alpha2 property
has unit: UNIT rate

NaK pump.minus alpha3
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Psuedo-first-order backward rate constant for sodium-potassium exchanger transition from lumped states P8-P13 to lumped states P14-P15 of the Post-Albers cycle
is computational component for: NaK pump.minus alpha3 property
has unit: UNIT rate

NaK pump.minus alpha4
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Psuedo-first-order backward rate constant for sodium-potassium exchanger transition from lumped states P14-P15 to lumped states P1-P6 of the Post-Albers cycle
is computational component for: NaK pump.minus alpha4 property
has unit: UNIT rate

NaK pump.minus k1
type: NamedIndividual
type: Decimal
has start value: 172.1
is discrete: false
is solution domain: false
is declared: true
comment: Backward rate constant for sodium-potassium exchanger transition from lumped states P1-P6 to state P7 of the Post-Albers cycle
is computational component for: NaK pump.minus k1 property
has unit: UNIT minus k1 rate

NaK pump.minus k2
type: NamedIndividual
type: Decimal
has start value: 40.1
is discrete: false
is solution domain: false
is declared: true
comment: Backward rate constant for sodium-potassium exchanger transition from state P7 to lumped states P8-P13 of the Post-Albers cycle
is computational component for: NaK pump.minus k2 property
has unit: UNIT rate

NaK pump.minus k3
type: NamedIndividual
type: Decimal
has start value: 79287.1
is solution domain: false
is discrete: false
is declared: true
comment: Backward rate constant for sodium-potassium exchanger transition from lumped states P8-P13 to lumped states P14-P15 of the Post-Albers cycle
is computational component for: NaK pump.minus k3 property
has unit: UNIT minus k3 rate

NaK pump.minus k4
type: NamedIndividual
type: Decimal
has start value: 40.1
is discrete: false
is solution domain: false
is declared: true
comment: Backward rate constant for sodium-potassium exchanger transition from lumped states P14-P15 to lumped states P1-P6 of the Post-Albers cycle
is computational component for: NaK pump.minus k4 property
has unit: UNIT rate

NaK pump.net free energy
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: The net free energy of a sodium-potassium pump cycle
is computational component for: NaK pump.net free energy property
has unit: UNIT energy
mapped to: interface.net free energy

NaK pump.partition factor
type: NamedIndividual
type: Decimal
has start value: -0.031288692380984445
is solution domain: false
is discrete: false
is declared: true
comment: Factor for determining how voltage dependence is partitioned between the intra- and extracellular sodium ion dissociation reactions
is computational component for: NaK pump.partition factor property

NaK pump.v cyc
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Steady-state cycle rate of sodium-potassium pump
is computational component for: NaK pump.v cyc property
has unit: UNIT rate
mapped to: interface.v cyc

NaK pump computation
type: NamedIndividual
type: Computation
has math ML: <apply id="cPi"> <eq /> <ci>cPi</ci> <apply> <divide /> <ci>cPi_sum</ci> <apply> <plus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1.0</cn> <apply> <divide /> <ci>cK_i</ci> <ci>eq_KPi</ci> </apply> <apply> <divide /> <ci>cH</ci> <ci>eq_HPi</ci> </apply> <apply> <divide /> <ci>cNa_i</ci> <ci>eq_NaPi</ci> </apply> </apply> </apply> </apply> <apply id="dG_Na_calc"> <eq /> <ci>dG_Na</ci> <apply> <minus /> <apply> <times /> <ci>gas_const</ci> <ci>body_temp</ci> <apply> <ln /> <apply> <divide /> <ci>cNa_e</ci> <ci>cNa_i</ci> </apply> </apply> </apply> <apply> <times /> <ci>faraday_const</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.001</cn> <ci>Vm</ci> </apply> </apply> </apply> <apply id="dG_K_calc"> <eq /> <ci>dG_K</ci> <apply> <plus /> <apply> <times /> <ci>gas_const</ci> <ci>body_temp</ci> <apply> <ln /> <apply> <divide /> <ci>cK_i</ci> <ci>cK_e</ci> </apply> </apply> </apply> <apply> <times /> <ci>faraday_const</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.001</cn> <ci>Vm</ci> </apply> </apply> </apply> <apply id="dG_pump_calc"> <eq /> <ci>dG_pump</ci> <apply> <plus /> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2.0</cn> <ci>dG_K</ci> </apply> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">3.0</cn> <ci>dG_Na</ci> </apply> </apply> </apply> <apply id="dG_ATP_calc"> <eq /> <ci>dG_ATP</ci> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="energy">-29600.</cn> <apply> <times /> <ci>gas_const</ci> <ci>body_temp</ci> <apply> <ln /> <apply> <divide /> <ci>cMgATP</ci> <apply> <times /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_concentration">0.001</cn> <ci>cMgADP</ci> <ci>cPi</ci> </apply> </apply> </apply> </apply> </apply> </apply> <apply id="net_free_energy_calc"> <eq /> <ci>ne…
is computational component for: NaK pump

Plasma membrane
type: NamedIndividual
refers to: Plasma membrane
part of: Cardiac myocyte
has physical property: Electrochemical potential
is index entity for: Plasma membrane part of Cardiac myocyte

Portion of cytosol
type: NamedIndividual
refers to: Portion of cytosol
has part: proton
has part: inorganic phosphate
has part: sodium(1+)
has part: potassium(1+)
has part: MgATP(2-)
part of: Cardiac myocyte
has part: MgADP
is index entity for: Portion of cytosol part of Cardiac myocyte

UNIT concentration
type: NamedIndividual
type: Unit of measurement
has computational code: concentration
unit for: NaK pump.cH
unit for: NaK pump.cK e
unit for: NaK pump.cK i
unit for: NaK pump.cMgADP
unit for: NaK pump.cMgATP
unit for: NaK pump.cNa e
unit for: NaK pump.cNa i
unit for: NaK pump.cPi
unit for: NaK pump.cPi sum
unit for: NaK pump.eq HPi
unit for: NaK pump.eq KPi
unit for: NaK pump.eq K e
unit for: NaK pump.eq K i
unit for: NaK pump.eq MgATP
unit for: NaK pump.eq NaPi
unit for: NaK pump.eq Na base e
unit for: NaK pump.eq Na base i
has unit factor: UNIT litre
has unit factor: UNIT mole
unit for: interface.cMgADP
unit for: interface.cNa i

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

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

UNIT coulomb
type: NamedIndividual
type: Unit of measurement
has computational code: coulomb
is fundamental unit: true
unit factor for: UNIT faraday constant

UNIT energy
type: NamedIndividual
type: Unit of measurement
has computational code: energy
unit for: NaK pump.dG ATP
unit for: NaK pump.dG K
unit for: NaK pump.dG Na
unit for: NaK pump.dG pump
unit for: NaK pump.net free energy
has unit factor: UNIT joule
has unit factor: UNIT mole
unit for: interface.net free energy

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT energy
annotated target: UNIT mole

UNIT faraday constant
type: NamedIndividual
type: Unit of measurement
has computational code: faraday_constant
unit for: Faraday constant
has unit factor: UNIT coulomb
has unit factor: UNIT mole

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT faraday constant
annotated target: UNIT mole

UNIT gas constant
type: NamedIndividual
type: Unit of measurement
has computational code: gas_constant
unit for: Gas constant
has unit factor: UNIT joule
has unit factor: UNIT kelvin
has unit factor: UNIT mole

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT gas constant
annotated target: UNIT kelvin

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT gas constant
annotated target: UNIT mole

UNIT joule
type: NamedIndividual
type: Unit of measurement
has computational code: joule
is fundamental unit: true
unit factor for: UNIT energy
unit factor for: UNIT gas constant

UNIT kelvin
type: NamedIndividual
type: Unit of measurement
has computational code: kelvin
is fundamental unit: true
unit for: NaK pump.body temp
unit factor for: UNIT gas constant

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

UNIT mM
type: NamedIndividual
type: Unit of measurement
has computational code: mM
unit factor for: UNIT minus k1 rate
unit factor for: UNIT minus k3 rate
has unit factor: UNIT mole

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

UNIT mV
type: NamedIndividual
type: Unit of measurement
has computational code: mV
unit for: NaK pump.Vm
has unit factor: UNIT volt
unit for: interface.Vm

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT mV
annotated target: UNIT volt

UNIT minus k1 rate
type: NamedIndividual
type: Unit of measurement
has computational code: minus_k1_rate
unit for: NaK pump.minus k1
has unit factor: UNIT mM
has unit factor: UNIT second

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT minus k1 rate
annotated target: UNIT second

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT mM
annotated source: UNIT minus k1 rate

UNIT minus k3 rate
type: NamedIndividual
type: Unit of measurement
has computational code: minus_k3_rate
unit for: NaK pump.minus k3
has unit factor: UNIT mM
has unit factor: UNIT second

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT minus k3 rate
annotated target: UNIT second

Axiom
has unit factor exponent: -2.0
annotated property: hasUnitFactor
annotated target: UNIT mM
annotated source: UNIT minus k3 rate

UNIT mole
type: NamedIndividual
type: Unit of measurement
has computational code: mole
is fundamental unit: true
unit factor for: UNIT concentration
unit factor for: UNIT energy
unit factor for: UNIT faraday constant
unit factor for: UNIT gas constant
unit factor for: UNIT mM

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

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

UNIT rate
type: NamedIndividual
type: Unit of measurement
has computational code: rate
unit for: NaK pump.alpha1
unit for: NaK pump.alpha2
unit for: NaK pump.alpha3
unit for: NaK pump.alpha4
unit for: NaK pump.k1
unit for: NaK pump.k2
unit for: NaK pump.k3
unit for: NaK pump.k4
unit for: NaK pump.minus alpha1
unit for: NaK pump.minus alpha2
unit for: NaK pump.minus alpha3
unit for: NaK pump.minus alpha4
unit for: NaK pump.minus k2
unit for: NaK pump.minus k4
unit for: NaK pump.v cyc
has unit factor: UNIT second
unit for: interface.v cyc

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT rate
annotated target: UNIT second

UNIT rate diagram sum
type: NamedIndividual
type: Unit of measurement
has computational code: rate_diagram_sum
unit for: NaK pump.diagram sum
has unit factor: UNIT second

Axiom
has unit factor exponent: -3.0
annotated property: hasUnitFactor
annotated source: UNIT rate diagram sum
annotated target: UNIT second

UNIT second
type: NamedIndividual
type: Unit of measurement
has computational code: second
is fundamental unit: true
unit factor for: UNIT minus k1 rate
unit factor for: UNIT minus k3 rate
unit factor for: UNIT ms
unit factor for: UNIT rate
unit factor for: UNIT rate diagram sum

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

interface
type: NamedIndividual
type: Submodel
name: interface
includes submodel: NaK pump
has associated data structure: interface.Vm
has associated data structure: interface.cMgADP
has associated data structure: interface.cNa i
has associated data structure: interface.net free energy
has associated data structure: Time
has associated data structure: interface.v cyc
has computational component: interface computation

Axiom
submodel subsumption type: encapsulation
annotated property: includesSubmodel
annotated target: NaK pump
annotated source: interface

interface.Vm
type: NamedIndividual
type: Decimal
has start value: -150
is solution domain: false
is discrete: false
has cell m lprivate interface: out
is declared: true
comment: Membrane potential
mapped to: NaK pump.Vm
has unit: UNIT mV
is computational component for: Electrochemical potential

Electrochemical potential
type: NamedIndividual
refers to: Electrochemical potential
physical property of: Plasma membrane
has computational component: interface.Vm

interface.cMgADP
type: NamedIndividual
type: Decimal
has start value: 0.01
is discrete: false
is solution domain: false
has cell m lprivate interface: out
is declared: true
comment: Intracellular concentration of magnesium-bound ADP
mapped to: NaK pump.cMgADP
has unit: UNIT concentration
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: MgADP
has computational component: interface.cMgADP

interface.cNa i
type: NamedIndividual
type: Decimal
has start value: 50.
is solution domain: false
is discrete: false
has cell m lprivate interface: out
is declared: true
comment: Intracellular sodium ion concentration
mapped to: NaK pump.cNa i
has unit: UNIT concentration
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: sodium(1+)
has computational component: interface.cNa i

interface.net free energy
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lprivate interface: in
has cell m lpublic interface: out
is declared: true
comment: The net free energy of a sodium-potassium pump cycle
has unit: UNIT energy
is computational component for: interface.net free energy 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 lprivate interface: out
is declared: true
comment: Time domain for simulation
has unit: UNIT ms
is computational component for: interface.time property

interface.v cyc
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lprivate interface: in
has cell m lpublic interface: out
is declared: true
comment: Steady-state cycle rate of sodium-potassium pump
has unit: UNIT rate
is computational component for: interface.v cyc property

interface computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>Vm</ci> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="mV_per_ms">1.0</cn> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>cMgADP</ci> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="concentration_per_ms">0.0</cn> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>cNa_i</ci> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="concentration_per_ms">0.0</cn> </apply>
is computational component for: interface