03032015122458800m0500
type: Ontology
legacy code URI: /Users/max_neal/Dropbox/Semantic Project/Annotated CellML models/chang_fujita_2001/chang_fujita_2001_H_ATPase.cellml
sem sim version: 0.2
has cell m ldocumentation: <documentation xmlns="http://cellml.org/tmp-documentation"> <articleinfo> Mathematical Models of Ionic Transport in the Distal Tubule of the Rat <author> <firstname>Catherine</firstname> <surname>Lloyd</surname> <affiliation> <shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil> </affiliation> </author> </articleinfo> Model Status This CellML model is a description of Chang and Fujita's 2001 mathematical model of a H-ATPase in the distal tubule of the rat: it is one component of an overall model of acid/base transport in a distal tubule. <sect1 id="sec_structure"> Model Structure ABSTRACT: The purpose of this study is to develop a numerical model that simulates acid-base transport in rat distal tubule. We have previously reported a model that deals with transport of Na(+), K(+), Cl(-), and water in this nephron segment (Chang H and Fujita T. Am J Physiol Renal Physiol 276: F931-F951, 1999). In this study, we extend our previous model by incorporating buffer systems, new cell types, and new transport mechanisms. Specifically, the model incorporates bicarbonate, ammonium, and phosphate buffer systems; has cell types corresponding to intercalated cells; and includes the Na/H exchanger, H-ATPase, and anion exchanger. Incorporation of buffer systems has required the following modifications of model equations: new model equations are introduced to represent chemical equilibria of buffer partners [e.g., pH = pK(a) + log(10) (NH(3)/NH(4))], and the formulation of mass conservation is extended to take into account interconversion of buffer partners. Furthermore, finite rates of H(2)CO(3)-CO(2) interconversion are taken into account in modeling the bicarbonate buffer system. Owing to this treatment, the model can simulate the development of disequilibrium pH in the distal tubular fluid. For each new transporter, a state diagram has been constructed to simulate its transport kinetics. With appropriate assignment of maximal transport rates for i…
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#renal_H_ATPase_model"> <cmeta:species>Rat</cmeta:species> <bqs:reference> <rdf:Description rdf:about="rdf:#ae6916fd-29d2-4763-a0ba-79ceec299157"> <bqs:JournalArticle> <rdf:Description rdf:about="rdf:#cd12d814-dc56-4756-825b-8bc1b2408625"> <bqs:last_page>F243</bqs:last_page> <dcterms:issued> <rdf:Description rdf:about="rdf:#6ca7c35d-64e6-4d14-bc97-937bd12069ce"> <dcterms:W3CDTF>2001-08</dcterms:W3CDTF> </rdf:Description> </dcterms:issued> <bqs:Journal> <rdf:Description rdf:about="rdf:#3a4bd135-2eb3-45c4-93ed-bad58aa3d1d2"> <dc:title>American Journal of Physiology</dc:title> </rdf:Description> </bqs:Journal> <bqs:first_page>F222</bqs:first_page> <bqs:volume>281</bqs:volume> <dc:title>A numerical model of acid-base transport in rat distal tubule</dc:title> <dc:creator> <rdf:Seq rdf:about="rdf:#5983efbf-2cf8-4d36-9de5-10ca91e31540"> <rdf:li> <bqs:Person rdf:about="rdf:#b07d2d63-b508-4b0d-9f19-90f956ba1108"> <vCard:N> <rdf:Description rdf:about="rdf:#08a1413b-bdd3-44d2-a58d-5e63804335c7"> <vCard:Family>Chang</vCard:Family> <vCard:Given>Hangil</vCard:Given> </rdf:Description> </vCard:N> </bqs:Person> </rdf:li> <rdf:li> <bqs:Person rdf:about="rdf:#d07e5835-41b3-4589-a6dc-1f166446c113"> <vCard:N> <rdf:Description rdf:about="rdf:#a4fdda4e-fb2d-486a-b0f9-52e630ad30f4"> <vCard:Family>Fujita</vCard:Family> <vCard:Given>Toshiro</vCard:Given> </rdf:Description> </vCard:N> </bqs:Person> </rdf:li> </rdf:Seq> </dc:creator> </rdf:Description> </bqs:JournalArticle> <bqs:Pubmed_id>11457714</bqs:Pubmed_id> </rdf:Description> </bqs:reference> <bqs:reference> <rdf:Description rdf:about="rdf:#25307320…
annotator name: Maxwell Neal
model name: renal_H_ATPase_model
model id: renal_H_ATPase_model

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

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

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

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

phosphate(3-)
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: phosphate(3-)

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

renal alpha-intercalated cell
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: renal alpha-intercalated cell

plasma membrane proton-transporting V-type ATPase, V1 domain
type: Class
subclass of: Custom physical entity

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

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

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.

Antechamber-facing conformation of H-ATPase catalytic component
type: NamedIndividual
type: plasma membrane proton-transporting V-type ATPase, V1 domain
type: Custom physical entity
is index entity for: Antechamber-facing conformation of H-ATPase catalytic component part of CL 0005011 part of Late distal tubule
part of: renal alpha-intercalated cell
has physical property: Chemical concentration

Antechamber of H-ATPase
type: NamedIndividual
type: Custom physical entity
comment: The buffer space between the membrane and catalytic components of H-ATPase
is index entity for: Antechamber of H-ATPase part of CL 0005011 part of Late distal tubule
has part: proton
part of: renal alpha-intercalated cell

ATP
type: NamedIndividual
refers to: ATP
is index entity for: CHEBI 15422 part of Portion of cytosol part of CL 0005011 part of Late distal tubule
has physical property: Chemical concentration
part of: Portion of cytosol

ADP
type: NamedIndividual
refers to: ADP
is index entity for: CHEBI 16761 part of Portion of cytosol part of CL 0005011 part of Late distal tubule
has physical property: Chemical concentration
part of: Portion of cytosol

phosphate(3-)
type: NamedIndividual
refers to: phosphate(3-)
is index entity for: CHEBI 18367 part of Portion of cytosol part of CL 0005011 part of Late distal tubule
has physical property: Chemical concentration
part of: Portion of cytosol

proton
type: NamedIndividual
refers to: proton
is index entity for: CHEBI 24636 part of Portion of cytosol part of CL 0005011 part of Late distal tubule
has physical property: Chemical concentration
part of: Portion of cytosol

proton
type: NamedIndividual
refers to: proton
part of: Antechamber of H-ATPase
is index entity for: CHEBI 24636 part of Antechamber of H-ATPase part of CL 0005011 part of Late distal tubule
has physical property: Chemical concentration

proton
type: NamedIndividual
refers to: proton
is index entity for: CHEBI 24636 part of Portion of extracellular matrix part of Late distal tubule
part of: Portion of extracellular matrix
has physical property: Chemical concentration

renal alpha-intercalated cell
type: NamedIndividual
refers to: renal alpha-intercalated cell
has part: Antechamber-facing conformation of H-ATPase catalytic component
has part: Antechamber of H-ATPase
is index entity for: CL 0005011 part of Late distal tubule
has part: Cytosol-facing conformation of H-ATPase catalytic component
has part: Double proton-bound, antechamber-facing conformation of H-ATPase catalytic component
has part: Double proton-bound, cytosol-facing conformation of H-ATPase catalytic component
part of: Late distal tubule
has part: Portion of cytosol
has part: Proton-bound, antechamber-facing conformation of H-ATPase catalytic component
has part: Proton-bound, cytosol-facing conformation of H-ATPase catalytic component
has physical property: Electrical potential

Cytosol-facing conformation of H-ATPase catalytic component
type: NamedIndividual
type: plasma membrane proton-transporting V-type ATPase, V1 domain
type: Custom physical entity
part of: renal alpha-intercalated cell
is index entity for: Cytosol-facing conformation of H-ATPase catalytic component part of CL 0005011 part of Late distal tubule
has physical property: Chemical concentration

Double proton-bound, antechamber-facing conformation of H-ATPase catalytic component
type: NamedIndividual
type: Custom physical entity
part of: renal alpha-intercalated cell
is index entity for: Double proton-bound, antechamber-facing conformation of H-ATPase catalytic component part of CL 0005011 part of Late distal tubule
has physical property: Chemical concentration

Double proton-bound, cytosol-facing conformation of H-ATPase catalytic component
type: NamedIndividual
type: Custom physical entity
part of: renal alpha-intercalated cell
is index entity for: Double proton-bound, cytosol-facing conformation of H-ATPase catalytic component part of CL 0005011 part of Late distal tubule
has physical property: Chemical concentration

http://www.bhi.washington.edu/SemSim/03032015122458800m0500#E
type: NamedIndividual
type: Submodel
name: E
has associated data structure: E.ADP
has associated data structure: E.ATP
has associated data structure: E.E
has associated data structure: E.EH
has associated data structure: E.Ha
has associated data structure: E.Pi
has associated data structure: E.k1
has associated data structure: E.k10
has associated data structure: E.k2
has associated data structure: E.k9
has associated data structure: Time
has computational component: E computation

E.ADP
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Cytosolic ADP concentration in type-A intercalated cells of late distal tubule
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: ADP
has computational component: E.ADP

E.ATP
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Cytosolic ATP concentration in type-A intercalated cells of late distal tubule
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: ATP
has computational component: E.ATP

E.E
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Concentration of antechamber-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
mapped to: EH.E
mapped to: E .E
has unit: UNIT millimolar

E.EH
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of proton-bound, antechamber-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: E.EH
physical property of: Proton-bound, antechamber-facing conformation of H-ATPase catalytic component

E.E
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of cytosol-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Cytosol-facing conformation of H-ATPase catalytic component
has computational component: E.E

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Antechamber-facing conformation of H-ATPase catalytic component
has computational component: E.E

E.Ha
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: H+ concentration in the antechamber between the membrane and catalytic components of H-ATPase
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: E.Ha

E.Pi
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Cytosolic phosphate(3-) concentration in type-A intercalated cells of late distal tubule
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: phosphate(3-)
has computational component: E.Pi

E.k1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component
is computational component for: E.k1 property
has unit: UNIT second order rate constant

E.k10
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing
is computational component for: E.k10 property
has unit: UNIT third order rate constant

E.k2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component
is computational component for: E.k2 property
has unit: UNIT first order rate constant

E.k9
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing
is computational component for: E.k9 property
has unit: UNIT second order rate constant

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: Time solution domain for simulation
is computational component for: E.time property
has unit: UNIT second

EH
type: NamedIndividual
type: Submodel
name: EH
has associated data structure: EH.E
has associated data structure: EH.EH
has associated data structure: EH.EH2
has associated data structure: EH.Ha
has associated data structure: EH.k1
has associated data structure: EH.k2
has associated data structure: EH.k3
has associated data structure: EH.k4
has associated data structure: Time
has computational component: EH computation

EH.E
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of antechamber-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

EH.EH
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Concentration of proton-bound, antechamber-facing conformation of H-ATPase catalytic component
mapped to: E.EH
is computational component for: Chemical concentration
mapped to: EH2.EH
has unit: UNIT millimolar

EH.EH2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of double proton-bound, antechamber-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Double proton-bound, antechamber-facing conformation of H-ATPase catalytic component
has computational component: EH.EH2

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: EH.EH
physical property of: Proton-bound, antechamber-facing conformation of H-ATPase catalytic component

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Antechamber-facing conformation of H-ATPase catalytic component
has computational component: EH.E

EH.Ha
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: H+ concentration in the antechamber between the membrane and catalytic components of H-ATPase
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: EH.Ha

EH.k1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component
is computational component for: EH.k1 property
has unit: UNIT second order rate constant

EH.k2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component
is computational component for: EH.k2 property
has unit: UNIT first order rate constant

EH.k3
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component
is computational component for: EH.k3 property
has unit: UNIT second order rate constant

EH.k4
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component
is computational component for: EH.k4 property
has unit: UNIT first order rate constant

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: Time solution domain for simulation
is computational component for: EH.time property
has unit: UNIT second

EH2
type: NamedIndividual
type: Submodel
name: EH2
has associated data structure: EH2.EH
has associated data structure: EH2.EH2
has associated data structure: EH2.Ha
has associated data structure: EH2.k11
has associated data structure: EH2.k12
has associated data structure: EH2.k3
has associated data structure: EH2.k4
has associated data structure: Time
has computational component: EH2 computation

EH2.EH
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of proton-bound, antechamber-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

EH2.EH2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Concentration of double proton-bound, antechamber-facing conformation of H-ATPase catalytic component
mapped to: EH.EH2
is computational component for: Chemical concentration
mapped to: EH2 .EH2
has unit: UNIT millimolar

EH2.EH2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of double proton-bound, cytosol-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Double proton-bound, cytosol-facing conformation of H-ATPase catalytic component
has computational component: EH2.EH2

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Double proton-bound, antechamber-facing conformation of H-ATPase catalytic component
has computational component: EH2.EH2

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: EH2.EH
physical property of: Proton-bound, antechamber-facing conformation of H-ATPase catalytic component

EH2.Ha
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: H+ concentration in the antechamber between the membrane and catalytic components of H-ATPase
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: EH2.Ha

EH2.k11
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing
is computational component for: EH2.k11 property
has unit: UNIT first order rate constant

EH2.k12
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing
is computational component for: EH2.k12 property
has unit: UNIT first order rate constant

EH2.k3
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component
is computational component for: EH2.k3 property
has unit: UNIT second order rate constant

EH2.k4
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component
is computational component for: EH2.k4 property
has unit: UNIT first order rate constant

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: Time solution domain for simulation
is computational component for: EH2.time property
has unit: UNIT second

EH2
type: NamedIndividual
type: Submodel
name: EH2_
has associated data structure: EH2 .EH2
has associated data structure: EH2 .EH
has associated data structure: EH2 .H
has associated data structure: EH2 .k11
has associated data structure: EH2 .k12
has associated data structure: EH2 .k7
has associated data structure: EH2 .k8
has associated data structure: Time
has computational component: EH2 computation

EH2 .EH2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of double proton-bound, antechamber-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

EH2 .EH2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Concentration of double proton-bound, cytosol-facing conformation of H-ATPase catalytic component
mapped to: EH2.EH2
is computational component for: Chemical concentration
mapped to: EH .EH2
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Double proton-bound, cytosol-facing conformation of H-ATPase catalytic component
has computational component: EH2 .EH2

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Double proton-bound, antechamber-facing conformation of H-ATPase catalytic component
has computational component: EH2 .EH2

EH2 .EH
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of proton-bound, cytosol-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: EH2 .EH
physical property of: Proton-bound, cytosol-facing conformation of H-ATPase catalytic component

EH2 .H
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: H+ concentration in the cytosolic space
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: EH2 .H

EH2 .k11
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing
is computational component for: EH2 .k11 property
has unit: UNIT first order rate constant

EH2 .k12
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing
is computational component for: EH2 .k12 property
has unit: UNIT first order rate constant

EH2 .k7
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component
is computational component for: EH2 .k7 property
has unit: UNIT second order rate constant

EH2 .k8
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component
is computational component for: EH2 .k8 property
has unit: UNIT first order rate constant

Time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
refers to: http://bhi.washington.edu/OPB#OPB_01023
has cell m lpublic interface: in
is declared: true
comment: Time solution domain for simulation
is computational component for: EH2 .time property
has unit: UNIT second

EH2 computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>EH2_</ci> </apply> <apply> <minus /> <apply> <plus /> <apply> <times /> <ci>k7</ci> <ci>H_</ci> <ci>EH_</ci> </apply> <apply> <times /> <ci>k11</ci> <ci>EH2</ci> </apply> </apply> <apply> <plus /> <apply> <times /> <ci>k8</ci> <ci>EH2_</ci> </apply> <apply> <times /> <ci>k12</ci> <ci>EH2_</ci> </apply> </apply> </apply> </apply>
is computational component for: EH2

EH2 computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>EH2</ci> </apply> <apply> <minus /> <apply> <plus /> <apply> <times /> <ci>k3</ci> <ci>Ha</ci> <ci>EH</ci> </apply> <apply> <times /> <ci>k12</ci> <ci>EH2_</ci> </apply> </apply> <apply> <plus /> <apply> <times /> <ci>k4</ci> <ci>EH2</ci> </apply> <apply> <times /> <ci>k11</ci> <ci>EH2</ci> </apply> </apply> </apply> </apply>
is computational component for: EH2

EH
type: NamedIndividual
type: Submodel
name: EH_
has associated data structure: EH .EH2
has associated data structure: EH .EH
has associated data structure: EH .E
has associated data structure: EH .H
has associated data structure: EH .k5
has associated data structure: EH .k6
has associated data structure: EH .k7
has associated data structure: EH .k8
has associated data structure: Time
has computational component: EH computation

EH .EH2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of double proton-bound, cytosol-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Double proton-bound, cytosol-facing conformation of H-ATPase catalytic component
has computational component: EH .EH2

EH .EH
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Concentration of proton-bound, cytosol-facing conformation of H-ATPase catalytic component
mapped to: EH2 .EH
is computational component for: Chemical concentration
mapped to: E .EH
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: EH .EH
physical property of: Proton-bound, cytosol-facing conformation of H-ATPase catalytic component

EH .E
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of cytosol-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Cytosol-facing conformation of H-ATPase catalytic component
has computational component: EH .E

EH .H
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: H+ concentration in the cytosolic space
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: EH .H

EH .k5
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component
is computational component for: EH .k5 property
has unit: UNIT second order rate constant

EH .k6
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component
is computational component for: EH .k6 property
has unit: UNIT first order rate constant

EH .k7
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component
is computational component for: EH .k7 property
has unit: UNIT second order rate constant

EH .k8
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component
is computational component for: EH .k8 property
has unit: UNIT first order rate constant

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: Time solution domain for simulation
is computational component for: EH .time property
has unit: UNIT second

EH computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>EH_</ci> </apply> <apply> <minus /> <apply> <plus /> <apply> <times /> <ci>k5</ci> <ci>H_</ci> <ci>E_</ci> </apply> <apply> <times /> <ci>k8</ci> <ci>EH2_</ci> </apply> </apply> <apply> <plus /> <apply> <times /> <ci>k6</ci> <ci>EH_</ci> </apply> <apply> <times /> <ci>k7</ci> <ci>H_</ci> <ci>EH_</ci> </apply> </apply> </apply> </apply>
is computational component for: EH

EH computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>EH</ci> </apply> <apply> <minus /> <apply> <plus /> <apply> <times /> <ci>k1</ci> <ci>Ha</ci> <ci>E</ci> </apply> <apply> <times /> <ci>k4</ci> <ci>EH2</ci> </apply> </apply> <apply> <plus /> <apply> <times /> <ci>k2</ci> <ci>EH</ci> </apply> <apply> <times /> <ci>k3</ci> <ci>Ha</ci> <ci>EH</ci> </apply> </apply> </apply> </apply>
is computational component for: EH

E
type: NamedIndividual
type: Submodel
name: E_
has associated data structure: E .ADP
has associated data structure: E .ATP
has associated data structure: E .E
has associated data structure: E .EH
has associated data structure: E .H
has associated data structure: E .Pi
has associated data structure: E .k10
has associated data structure: E .k5
has associated data structure: E .k6
has associated data structure: E .k9
has associated data structure: Time
has computational component: E computation

E .ADP
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Cytosolic ADP concentration in type-A intercalated cells of late distal tubule
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: ADP
has computational component: E .ADP

E .ATP
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Cytosolic ATP concentration in type-A intercalated cells of late distal tubule
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: ATP
has computational component: E .ATP

E .E
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of antechamber-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

E .EH
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Concentration of proton-bound, cytosol-facing conformation of H-ATPase catalytic component
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: E .EH
physical property of: Proton-bound, cytosol-facing conformation of H-ATPase catalytic component

E .E
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Concentration of cytosol-facing conformation of H-ATPase catalytic component
mapped to: E.E
mapped to: EH .E
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Cytosol-facing conformation of H-ATPase catalytic component
has computational component: E .E

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: Antechamber-facing conformation of H-ATPase catalytic component
has computational component: E .E

E .H
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: H+ concentration in the cytosolic space
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: E .H

E .Pi
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Cytosolic phosphate(3-) concentration in type-A intercalated cells of late distal tubule
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: phosphate(3-)
has computational component: E .Pi

E .k10
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing
is computational component for: E .k10 property
has unit: UNIT third order rate constant

E .k5
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component
is computational component for: E .k5 property
has unit: UNIT second order rate constant

E .k6
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Backward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component
is computational component for: E .k6 property
has unit: UNIT first order rate constant

E .k9
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Forward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing
is computational component for: E .k9 property
has unit: UNIT second order rate constant

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: Time solution domain for simulation
is computational component for: E .time property
has unit: UNIT second

E computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>E_</ci> </apply> <apply> <minus /> <apply> <plus /> <apply> <times /> <ci>k9</ci> <ci>ATP_</ci> <ci>E</ci> </apply> <apply> <times /> <ci>k6</ci> <ci>EH_</ci> </apply> </apply> <apply> <plus /> <apply> <times /> <ci>k5</ci> <ci>H_</ci> <ci>E_</ci> </apply> <apply> <times /> <ci>k10</ci> <ci>ADP_</ci> <ci>Pi_</ci> <ci>E_</ci> </apply> </apply> </apply> </apply>
is computational component for: E

E computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>E</ci> </apply> <apply> <minus /> <apply> <plus /> <apply> <times /> <ci>k10</ci> <ci>ADP_</ci> <ci>Pi_</ci> <ci>E_</ci> </apply> <apply> <times /> <ci>k2</ci> <ci>EH</ci> </apply> </apply> <apply> <plus /> <apply> <times /> <ci>k1</ci> <ci>Ha</ci> <ci>E</ci> </apply> <apply> <times /> <ci>k9</ci> <ci>ATP_</ci> <ci>E</ci> </apply> </apply> </apply> </apply>
is computational component for: http://www.bhi.washington.edu/SemSim/03032015122458800m0500#E

Late distal tubule
type: NamedIndividual
type: Custom physical entity
comment: The authors distinguish between "early" and "late" segments of the distal tubule. The early segment is the distal convoluted tubule, the late segment is composed of the connecting tubule and the initial collecting tubule.
has part: renal alpha-intercalated cell
has part: Portion of extracellular matrix
has physical property: Temperature

Portion of cytosol
type: NamedIndividual
refers to: Portion of cytosol
has part: ATP
has part: ADP
has part: phosphate(3-)
has part: proton
part of: renal alpha-intercalated cell
is index entity for: Portion of cytosol part of CL 0005011 part of Late distal tubule

Portion of extracellular matrix
type: NamedIndividual
refers to: Portion of extracellular matrix
has part: proton
part of: Late distal tubule
is index entity for: Portion of extracellular matrix part of Late distal tubule
has physical property: Electrical potential

Proton-bound, antechamber-facing conformation of H-ATPase catalytic component
type: NamedIndividual
type: Custom physical entity
part of: renal alpha-intercalated cell
has physical property: Chemical concentration
is index entity for: Proton-bound, antechamber-facing conformation of H-ATPase catalytic component part of CL 0005011 part of Late distal tubule

Proton-bound, cytosol-facing conformation of H-ATPase catalytic component
type: NamedIndividual
type: Custom physical entity
part of: renal alpha-intercalated cell
has physical property: Chemical concentration
is index entity for: Proton-bound, cytosol-facing conformation of H-ATPase catalytic component part of CL 0005011 part of Late distal tubule

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

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

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

UNIT first order rate constant
type: NamedIndividual
type: Unit of measurement
has computational code: first_order_rate_constant
unit for: E.k2
unit for: EH.k2
unit for: EH.k4
unit for: EH2.k11
unit for: EH2.k12
unit for: EH2.k4
unit for: EH2 .k11
unit for: EH2 .k12
unit for: EH2 .k8
unit for: EH .k6
unit for: EH .k8
unit for: E .k6
has unit factor: UNIT second
unit for: reaction constants.k11
unit for: reaction constants.k12
unit for: reaction constants.k2
unit for: reaction constants.k4
unit for: reaction constants.k6
unit for: reaction constants.k8

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

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

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

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT joule per mole kelvin
annotated target: UNIT mole

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT joule per mole kelvin
annotated target: UNIT kelvin

UNIT kelvin
type: NamedIndividual
type: Unit of measurement
has computational code: kelvin
is fundamental unit: true
unit factor for: UNIT joule per mole kelvin
unit for: reaction constants.T

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

UNIT millimolar
type: NamedIndividual
type: Unit of measurement
has computational code: millimolar
unit for: E.ADP
unit for: E.ATP
unit for: E.E
unit for: E.EH
unit for: E.Ha
unit for: E.Pi
unit for: EH.E
unit for: EH.EH
unit for: EH.EH2
unit for: EH.Ha
unit for: EH2.EH
unit for: EH2.EH2
unit for: EH2.Ha
unit for: EH2 .EH2
unit for: EH2 .EH
unit for: EH2 .H
unit for: EH .EH2
unit for: EH .EH
unit for: EH .E
unit for: EH .H
unit for: E .ADP
unit for: E .ATP
unit for: E .E
unit for: E .EH
unit for: E .H
unit for: E .Pi
has unit factor: UNIT litre
has unit factor: UNIT mole
unit factor for: UNIT second order rate constant
unit factor for: UNIT third order rate constant
unit for: reaction constants.ADP
unit for: reaction constants.ATP
unit for: reaction constants.H
unit for: reaction constants.Ha
unit for: reaction constants.Pi

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

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

UNIT millivolt
type: NamedIndividual
type: Unit of measurement
has computational code: millivolt
has unit factor: UNIT volt
unit for: reaction constants.psi

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

UNIT mole
type: NamedIndividual
type: Unit of measurement
has computational code: mole
is fundamental unit: true
unit factor for: UNIT coulomb per mole
unit factor for: UNIT joule per mole kelvin
unit factor for: UNIT millimolar

UNIT second
type: NamedIndividual
type: Unit of measurement
has computational code: second
is fundamental unit: true
unit for: Time
unit factor for: UNIT first order rate constant
unit factor for: UNIT second order rate constant
unit factor for: UNIT third order rate constant

UNIT second order rate constant
type: NamedIndividual
type: Unit of measurement
has computational code: second_order_rate_constant
unit for: E.k1
unit for: E.k9
unit for: EH.k1
unit for: EH.k3
unit for: EH2.k3
unit for: EH2 .k7
unit for: EH .k5
unit for: EH .k7
unit for: E .k5
unit for: E .k9
has unit factor: UNIT millimolar
has unit factor: UNIT second
unit for: reaction constants.k1
unit for: reaction constants.k3
unit for: reaction constants.k5
unit for: reaction constants.k7
unit for: reaction constants.k9

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

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

UNIT third order rate constant
type: NamedIndividual
type: Unit of measurement
has computational code: third_order_rate_constant
unit for: E.k10
unit for: E .k10
has unit factor: UNIT millimolar
has unit factor: UNIT second
unit for: reaction constants.k10

Axiom
has unit factor exponent: -2.0
annotated property: hasUnitFactor
annotated target: UNIT millimolar
annotated source: UNIT third order rate constant

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

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

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

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: out
is declared: true
comment: Time solution domain for simulation
mapped to: Time
has unit: UNIT second
is computational component for: environment.time property

reaction constants
type: NamedIndividual
type: Submodel
name: reaction_constants
has associated data structure: reaction constants.ADP
has associated data structure: reaction constants.ATP
has associated data structure: Faraday constant
has associated data structure: reaction constants.H
has associated data structure: reaction constants.Ha
has associated data structure: reaction constants.Pi
has associated data structure: Gas constant
has associated data structure: reaction constants.T
has associated data structure: reaction constants.k1
has associated data structure: reaction constants.k10
has associated data structure: reaction constants.k11
has associated data structure: reaction constants.k12
has associated data structure: reaction constants.k2
has associated data structure: reaction constants.k3
has associated data structure: reaction constants.k4
has associated data structure: reaction constants.k5
has associated data structure: reaction constants.k6
has associated data structure: reaction constants.k7
has associated data structure: reaction constants.k8
has associated data structure: reaction constants.k9
has associated data structure: reaction constants.psi
has computational component: reaction constants computation

reaction constants.ADP
type: NamedIndividual
type: Decimal
has start value: 1.0
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Cytosolic ADP concentration in type-A intercalated cells of late distal tubule
mapped to: E.ADP
mapped to: E .ADP
has unit: UNIT millimolar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: ADP
has computational component: reaction constants.ADP

reaction constants.ATP
type: NamedIndividual
type: Decimal
has start value: 1.0
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Cytosolic ATP concentration in type-A intercalated cells of late distal tubule
mapped to: E.ATP
mapped to: E .ATP
has unit: UNIT millimolar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: ATP
has computational component: reaction constants.ATP

Faraday constant
type: NamedIndividual
type: Decimal
has start value: 96500.0
is discrete: false
is solution domain: false
refers to: http://bhi.washington.edu/OPB#OPB_00089
is declared: true
comment: Faraday constant
has unit: UNIT coulomb per mole
is computational component for: reaction constants.F property

reaction constants.H
type: NamedIndividual
type: Decimal
has start value: 1.0
is discrete: false
is solution domain: false
is declared: true
comment: Extracellular H+ concentration
has unit: UNIT millimolar
is computational component for: Chemical concentration

reaction constants.H
type: NamedIndividual
type: Decimal
has start value: 1.0
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: H+ concentration in the cytosolic space
mapped to: EH2 .H
mapped to: EH .H
mapped to: E .H
has unit: UNIT millimolar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: reaction constants.H

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: reaction constants.H

reaction constants.Ha
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: H+ concentration in the antechamber between the membrane and catalytic components of H-ATPase
mapped to: E.Ha
mapped to: EH.Ha
mapped to: EH2.Ha
has unit: UNIT millimolar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: proton
has computational component: reaction constants.Ha

reaction constants.Pi
type: NamedIndividual
type: Decimal
has start value: 1.0
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Cytosolic phosphate(3-) concentration in type-A intercalated cells of late distal tubule
mapped to: E.Pi
mapped to: E .Pi
has unit: UNIT millimolar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: phosphate(3-)
has computational component: reaction constants.Pi

Gas constant
type: NamedIndividual
type: Decimal
has start value: 8.314
is discrete: false
is solution domain: false
refers to: http://bhi.washington.edu/OPB#OPB_00410
is declared: true
comment: Gas constant
has unit: UNIT joule per mole kelvin
is computational component for: reaction constants.R property

reaction constants.T
type: NamedIndividual
type: Decimal
has start value: 310.0
is discrete: false
is solution domain: false
is declared: true
comment: Ambient temperature
has unit: UNIT kelvin
is computational component for: Temperature

Temperature
type: NamedIndividual
refers to: Temperature
physical property of: Late distal tubule
has computational component: reaction constants.T

reaction constants.k1
type: NamedIndividual
type: Decimal
has start value: 8.33E9
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Forward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component
mapped to: E.k1
mapped to: EH.k1
has unit: UNIT second order rate constant
is computational component for: reaction constants.k1 property

reaction constants.k10
type: NamedIndividual
type: Decimal
has start value: 1.80E5
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Backward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing
mapped to: E.k10
mapped to: E .k10
has unit: UNIT third order rate constant
is computational component for: reaction constants.k10 property

reaction constants.k11
type: NamedIndividual
type: Decimal
has start value: 5.00E2
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Forward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing
mapped to: EH2.k11
mapped to: EH2 .k11
has unit: UNIT first order rate constant
is computational component for: reaction constants.k11 property

reaction constants.k12
type: NamedIndividual
type: Decimal
has start value: 1.00E2
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Backward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing
mapped to: EH2.k12
mapped to: EH2 .k12
has unit: UNIT first order rate constant
is computational component for: reaction constants.k12 property

reaction constants.k2
type: NamedIndividual
type: Decimal
has start value: 1.00E3
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Backward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component
mapped to: E.k2
mapped to: EH.k2
has unit: UNIT first order rate constant
is computational component for: reaction constants.k2 property

reaction constants.k3
type: NamedIndividual
type: Decimal
has start value: 8.33E9
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Forward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component
mapped to: EH.k3
mapped to: EH2.k3
has unit: UNIT second order rate constant
is computational component for: reaction constants.k3 property

reaction constants.k4
type: NamedIndividual
type: Decimal
has start value: 1.00E4
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Backward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component
mapped to: EH.k4
mapped to: EH2.k4
has unit: UNIT first order rate constant
is computational component for: reaction constants.k4 property

reaction constants.k5
type: NamedIndividual
type: Decimal
has start value: 2.5E10
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Forward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component
mapped to: EH .k5
mapped to: E .k5
has unit: UNIT second order rate constant
is computational component for: reaction constants.k5 property

reaction constants.k6
type: NamedIndividual
type: Decimal
has start value: 1.0E3
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Backward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component
mapped to: EH .k6
mapped to: E .k6
has unit: UNIT first order rate constant
is computational component for: reaction constants.k6 property

reaction constants.k7
type: NamedIndividual
type: Decimal
has start value: 2.5E10
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Forward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component
mapped to: EH2 .k7
mapped to: EH .k7
has unit: UNIT second order rate constant
is computational component for: reaction constants.k7 property

reaction constants.k8
type: NamedIndividual
type: Decimal
has start value: 2.5E2
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Backward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component
mapped to: EH2 .k8
mapped to: EH .k8
has unit: UNIT first order rate constant
is computational component for: reaction constants.k8 property

reaction constants.k9
type: NamedIndividual
type: Decimal
has start value: 1.00E9
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Forward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing
mapped to: E.k9
mapped to: E .k9
has unit: UNIT second order rate constant
is computational component for: reaction constants.k9 property

reaction constants.psi
type: NamedIndividual
type: Decimal
has start value: 1.0
is discrete: false
is solution domain: false
is declared: true
comment: Extracellular electrical potential
has unit: UNIT millivolt
is computational component for: Electrical potential

reaction constants.psi
type: NamedIndividual
type: Decimal
has start value: -89.6
is discrete: false
is solution domain: false
is declared: true
comment: Intraceullar electrical potential
has unit: UNIT millivolt
is computational component for: Electrical potential

Electrical potential
type: NamedIndividual
refers to: Electrical potential
physical property of: renal alpha-intercalated cell
has computational component: reaction constants.psi

Electrical potential
type: NamedIndividual
refers to: Electrical potential
physical property of: Portion of extracellular matrix
has computational component: reaction constants.psi

reaction constants computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>Ha</ci> <apply> <times /> <ci>H</ci> <apply> <exp /> <apply> <divide /> <apply> <times /> <ci>F</ci> <apply> <plus /> <ci>psi</ci> <ci>psi_</ci> </apply> </apply> <apply> <times /> <ci>R</ci> <ci>T</ci> </apply> </apply> </apply> </apply> </apply>
is computational component for: reaction constants