- Author:
- Dewan Sarwar <sarwarcse@gmail.com>
- Date:
- 2019-01-31 16:34:20+13:00
- Desc:
- Testing with Max's suggested way of annotation for weinstein_1995_max model
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/584/rawfile/848b6a8fb585337adc4f3805c0ed682a6a5fd379/semgen_annotated_models/chang_fujita_2001_H_ATPase.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:semsim="http://www.bhi.washington.edu/SemSim#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="renal_H_ATPase_model" cmeta:id="renal_H_ATPase_model">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Mathematical Models of Ionic Transport in the Distal Tubule of the Rat</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>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.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>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 individual transporters, the model predictions are in agreement with free-flow micropuncture experiments in terms of HCO reabsorption rate in the normal state as well as under the high bicarbonate load. Although the model cannot simulate all of the microperfusion experiments, especially those that showed a flow-dependent increase in HCO reabsorption, the model is consistent with those microperfusion experiments that showed HCO reabsorption rates similar to those in the free-flow micropuncture experiments. We conclude that it is possible to develop a numerical model of the rat distal tubule that simulates acid-base transport, as well as basic solute and water transport, on the basis of tubular geometry, physical principles, and transporter kinetics. Such a model would provide a useful means of integrating detailed kinetic properties of transporters and predicting macroscopic transport characteristics of this nephron segment under physiological and pathophysiological settings.</para>
<para>The original paper reference is cited below:</para>
<para>
A numerical model of acid-base transport in rat distal tubule, Hangil Chang and Toshiro Fujita, 2001,
<emphasis>American Journal of Physiology</emphasis>
, 281, F222-F243.
<ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11457714&dopt=Abstract">PubMed ID: 11457714</ulink>
.
</para>
<informalfigure float="0" id="fig_reaction_diagram3">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction_diagram3</title>
</objectinfo>
<imagedata fileref="chang_2001c.png" />
</imageobject>
</mediaobject>
<caption>
Conceptual diagram of the H-ATPase. The transporter consists of two components: a transmembrane channel and an intracellular catalytic unit. Between these two components there is a buffer space known as the antechamber, in which hydrogen ions (H
<subscript>a</subscript>
) are in equilibrium with extracellular hydrogen ions (H) due to a large conductance of the transmembrane channel. Hydrogen ions are also moved between the antechamber and the cytosol via the catalytic unit. This ion transport is coupled to ATP hydrolysis/synthesis.
</caption>
</informalfigure>
<informalfigure float="0" id="fig_reaction_diagram4">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction_diagram4</title>
</objectinfo>
<imagedata fileref="chang_2001d.png" />
</imageobject>
</mediaobject>
<caption>State diagram of the catalytic unit of the H-ATPase. The catalytic unit (E) has two binding sites for H. Symbols with the asterisk (*) indicate conformations of the catalytic unit in which the binding sites face the cytosol, and symbols without the asterisk represent conformations in which the binding sites face the antechamber. Transition between the unloaded conformations is coupled with ATP synthesis/hydrolysis.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<units name="millivolt">
<unit prefix="milli" units="volt" />
</units>
<units name="millimolar">
<unit exponent="-1.0" units="litre" />
<unit prefix="milli" units="mole" />
</units>
<units name="coulomb_per_mole">
<unit units="coulomb" />
<unit exponent="-1.0" units="mole" />
</units>
<units name="first_order_rate_constant">
<unit exponent="-1.0" units="second" />
</units>
<units name="third_order_rate_constant">
<unit exponent="-1.0" units="second" />
<unit exponent="-2.0" units="millimolar" />
</units>
<units name="second_order_rate_constant">
<unit exponent="-1.0" units="second" />
<unit exponent="-1.0" units="millimolar" />
</units>
<units name="joule_per_mole_kelvin">
<unit units="joule" />
<unit exponent="-1.0" units="kelvin" />
<unit exponent="-1.0" units="mole" />
</units>
<component name="EH">
<variable cmeta:id="EH.EH2" name="EH2" public_interface="in" units="millimolar" />
<variable cmeta:id="EH.k2" name="k2" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH.k1" name="k1" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="EH.EH" name="EH" public_interface="out" units="millimolar" />
<variable cmeta:id="EH.E" name="E" public_interface="in" units="millimolar" />
<variable cmeta:id="EH.Ha" name="Ha" public_interface="in" units="millimolar" />
<variable cmeta:id="EH.k4" name="k4" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH.k3" name="k3" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="EH.time" name="time" public_interface="in" units="second" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<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>
</math>
</component>
<component name="EH2_">
<variable cmeta:id="EH2_.k8" name="k8" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH2_.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="EH2_.EH2" name="EH2" public_interface="in" units="millimolar" />
<variable cmeta:id="EH2_.EH2_" name="EH2_" public_interface="out" units="millimolar" />
<variable cmeta:id="EH2_.H_" name="H_" public_interface="in" units="millimolar" />
<variable cmeta:id="EH2_.k12" name="k12" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH2_.EH_" name="EH_" public_interface="in" units="millimolar" />
<variable cmeta:id="EH2_.k11" name="k11" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH2_.k7" name="k7" public_interface="in" units="second_order_rate_constant" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<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>
</math>
</component>
<component name="E">
<variable cmeta:id="E.Ha" name="Ha" public_interface="in" units="millimolar" />
<variable cmeta:id="E.ADP_" name="ADP_" public_interface="in" units="millimolar" />
<variable cmeta:id="E.ATP_" name="ATP_" public_interface="in" units="millimolar" />
<variable cmeta:id="E.E_" name="E_" public_interface="in" units="millimolar" />
<variable cmeta:id="E.k2" name="k2" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="E.k1" name="k1" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="E.Pi_" name="Pi_" public_interface="in" units="millimolar" />
<variable cmeta:id="E.E" name="E" public_interface="out" units="millimolar" />
<variable cmeta:id="E.EH" name="EH" public_interface="in" units="millimolar" />
<variable cmeta:id="E.k10" name="k10" public_interface="in" units="third_order_rate_constant" />
<variable cmeta:id="E.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="E.k9" name="k9" public_interface="in" units="second_order_rate_constant" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<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>
</math>
</component>
<component name="E_">
<variable cmeta:id="E_.H_" name="H_" public_interface="in" units="millimolar" />
<variable cmeta:id="E_.k10" name="k10" public_interface="in" units="third_order_rate_constant" />
<variable cmeta:id="E_.ADP_" name="ADP_" public_interface="in" units="millimolar" />
<variable cmeta:id="E_.ATP_" name="ATP_" public_interface="in" units="millimolar" />
<variable cmeta:id="E_.E" name="E" public_interface="in" units="millimolar" />
<variable cmeta:id="E_.EH_" name="EH_" public_interface="in" units="millimolar" />
<variable cmeta:id="E_.E_" name="E_" public_interface="out" units="millimolar" />
<variable cmeta:id="E_.k5" name="k5" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="E_.k6" name="k6" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="E_.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="E_.k9" name="k9" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="E_.Pi_" name="Pi_" public_interface="in" units="millimolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<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>
</math>
</component>
<component name="EH_">
<variable cmeta:id="EH_.E_" name="E_" public_interface="in" units="millimolar" />
<variable cmeta:id="EH_.k5" name="k5" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="EH_.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="EH_.H_" name="H_" public_interface="in" units="millimolar" />
<variable cmeta:id="EH_.k8" name="k8" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH_.k7" name="k7" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="EH_.EH2_" name="EH2_" public_interface="in" units="millimolar" />
<variable cmeta:id="EH_.EH_" name="EH_" public_interface="out" units="millimolar" />
<variable cmeta:id="EH_.k6" name="k6" public_interface="in" units="first_order_rate_constant" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<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>
</math>
</component>
<component name="environment">
<variable cmeta:id="environment.time" name="time" public_interface="out" units="second" />
</component>
<component name="EH2">
<variable cmeta:id="EH2.EH" name="EH" public_interface="in" units="millimolar" />
<variable cmeta:id="EH2.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="EH2.EH2_" name="EH2_" public_interface="in" units="millimolar" />
<variable cmeta:id="EH2.k12" name="k12" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH2.k11" name="k11" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH2.k3" name="k3" public_interface="in" units="second_order_rate_constant" />
<variable cmeta:id="EH2.Ha" name="Ha" public_interface="in" units="millimolar" />
<variable cmeta:id="EH2.k4" name="k4" public_interface="in" units="first_order_rate_constant" />
<variable cmeta:id="EH2.EH2" name="EH2" public_interface="out" units="millimolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<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>
</math>
</component>
<component name="reaction_constants">
<variable cmeta:id="reaction_constants.R" name="R" units="joule_per_mole_kelvin" />
<variable cmeta:id="reaction_constants.T" name="T" units="kelvin" />
<variable cmeta:id="reaction_constants.k9" name="k9" public_interface="out" units="second_order_rate_constant" />
<variable cmeta:id="reaction_constants.Pi_" name="Pi_" public_interface="out" units="millimolar" />
<variable cmeta:id="reaction_constants.psi" name="psi" units="millivolt" />
<variable cmeta:id="reaction_constants.k7" name="k7" public_interface="out" units="second_order_rate_constant" />
<variable cmeta:id="reaction_constants.k8" name="k8" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="reaction_constants.k5" name="k5" public_interface="out" units="second_order_rate_constant" />
<variable cmeta:id="reaction_constants.ATP_" name="ATP_" public_interface="out" units="millimolar" />
<variable cmeta:id="reaction_constants.k6" name="k6" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="reaction_constants.k3" name="k3" public_interface="out" units="second_order_rate_constant" />
<variable cmeta:id="reaction_constants.k4" name="k4" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="reaction_constants.k1" name="k1" public_interface="out" units="second_order_rate_constant" />
<variable cmeta:id="reaction_constants.k2" name="k2" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="reaction_constants.F" name="F" units="coulomb_per_mole" />
<variable cmeta:id="reaction_constants.H" name="H" units="millimolar" />
<variable cmeta:id="reaction_constants.k12" name="k12" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="reaction_constants.ADP_" name="ADP_" public_interface="out" units="millimolar" />
<variable cmeta:id="reaction_constants.k11" name="k11" public_interface="out" units="first_order_rate_constant" />
<variable cmeta:id="reaction_constants.k10" name="k10" public_interface="out" units="third_order_rate_constant" />
<variable cmeta:id="reaction_constants.Ha" name="Ha" public_interface="out" units="millimolar" />
<variable cmeta:id="reaction_constants.H_" name="H_" public_interface="out" units="millimolar" />
<variable cmeta:id="reaction_constants.psi_" name="psi_" units="millivolt" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<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>
</math>
</component>
<connection>
<map_components component_1="EH_" component_2="EH2_" />
<map_variables variable_1="EH_" variable_2="EH_" />
</connection>
<connection>
<map_components component_1="EH2_" component_2="EH_" />
<map_variables variable_1="EH2_" variable_2="EH2_" />
</connection>
<connection>
<map_components component_1="environment" component_2="E" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="E" component_2="E_" />
<map_variables variable_1="E" variable_2="E" />
</connection>
<connection>
<map_components component_1="E_" component_2="EH_" />
<map_variables variable_1="E_" variable_2="E_" />
</connection>
<connection>
<map_components component_1="EH" component_2="E" />
<map_variables variable_1="EH" variable_2="EH" />
</connection>
<connection>
<map_components component_1="reaction_constants" component_2="E" />
<map_variables variable_1="k9" variable_2="k9" />
<map_variables variable_1="Pi_" variable_2="Pi_" />
<map_variables variable_1="ADP_" variable_2="ADP_" />
<map_variables variable_1="ATP_" variable_2="ATP_" />
<map_variables variable_1="k1" variable_2="k1" />
<map_variables variable_1="k2" variable_2="k2" />
<map_variables variable_1="Ha" variable_2="Ha" />
<map_variables variable_1="k10" variable_2="k10" />
</connection>
<connection>
<map_components component_1="environment" component_2="EH2" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="environment" component_2="E_" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="reaction_constants" component_2="E_" />
<map_variables variable_1="k5" variable_2="k5" />
<map_variables variable_1="k9" variable_2="k9" />
<map_variables variable_1="Pi_" variable_2="Pi_" />
<map_variables variable_1="ADP_" variable_2="ADP_" />
<map_variables variable_1="ATP_" variable_2="ATP_" />
<map_variables variable_1="H_" variable_2="H_" />
<map_variables variable_1="k6" variable_2="k6" />
<map_variables variable_1="k10" variable_2="k10" />
</connection>
<connection>
<map_components component_1="EH" component_2="EH2" />
<map_variables variable_1="EH" variable_2="EH" />
</connection>
<connection>
<map_components component_1="E_" component_2="E" />
<map_variables variable_1="E_" variable_2="E_" />
</connection>
<connection>
<map_components component_1="environment" component_2="EH" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="environment" component_2="EH2_" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="E" component_2="EH" />
<map_variables variable_1="E" variable_2="E" />
</connection>
<connection>
<map_components component_1="reaction_constants" component_2="EH_" />
<map_variables variable_1="k5" variable_2="k5" />
<map_variables variable_1="k7" variable_2="k7" />
<map_variables variable_1="k8" variable_2="k8" />
<map_variables variable_1="H_" variable_2="H_" />
<map_variables variable_1="k6" variable_2="k6" />
</connection>
<connection>
<map_components component_1="EH_" component_2="E_" />
<map_variables variable_1="EH_" variable_2="EH_" />
</connection>
<connection>
<map_components component_1="EH2" component_2="EH" />
<map_variables variable_1="EH2" variable_2="EH2" />
</connection>
<connection>
<map_components component_1="EH2" component_2="EH2_" />
<map_variables variable_1="EH2" variable_2="EH2" />
</connection>
<connection>
<map_components component_1="reaction_constants" component_2="EH2_" />
<map_variables variable_1="k11" variable_2="k11" />
<map_variables variable_1="k7" variable_2="k7" />
<map_variables variable_1="k8" variable_2="k8" />
<map_variables variable_1="H_" variable_2="H_" />
<map_variables variable_1="k12" variable_2="k12" />
</connection>
<connection>
<map_components component_1="EH2_" component_2="EH2" />
<map_variables variable_1="EH2_" variable_2="EH2_" />
</connection>
<connection>
<map_components component_1="environment" component_2="EH_" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="reaction_constants" component_2="EH2" />
<map_variables variable_1="k11" variable_2="k11" />
<map_variables variable_1="k3" variable_2="k3" />
<map_variables variable_1="Ha" variable_2="Ha" />
<map_variables variable_1="k4" variable_2="k4" />
<map_variables variable_1="k12" variable_2="k12" />
</connection>
<connection>
<map_components component_1="reaction_constants" component_2="EH" />
<map_variables variable_1="k1" variable_2="k1" />
<map_variables variable_1="k2" variable_2="k2" />
<map_variables variable_1="k3" variable_2="k3" />
<map_variables variable_1="Ha" variable_2="Ha" />
<map_variables variable_1="k4" variable_2="k4" />
</connection>
<rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#" xmlns:j.0="http://imc.org/vCard/3.0#">
<rdf:Description rdf:about="#E.Ha">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_8">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_5">
<ro:part_of>
<rdf:Description rdf:about="#entity_6">
<ro:part_of>
<rdf:Description rdf:about="#entity_1">
<ro:part_of>
<rdf:Description rdf:about="#entity_2">
<dcterms:description>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.</dcterms:description>
<semsim:name>Late distal tubule</semsim:name>
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/cl/CL:0005011" />
</rdf:Description>
</ro:part_of>
<dcterms:description>The buffer space between the membrane and catalytic components of H-ATPase</dcterms:description>
<semsim:name>Antechamber of H-ATPase</semsim:name>
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:24636" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>H+ concentration in the antechamber between the membrane and catalytic components of H-ATPase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.H">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_34">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_16">
<ro:part_of>
<rdf:Description rdf:about="#entity_15">
<ro:part_of rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:9672" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:24636" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Extracellular H+ concentration</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.EH_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_19">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_10">
<ro:part_of rdf:resource="#entity_1" />
<semsim:name>Proton-bound, cytosol-facing conformation of H-ATPase catalytic component</semsim:name>
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.k10">
<dcterms:description>Backward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k12">
<dcterms:description>Backward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.ADP_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_16">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_11">
<ro:part_of>
<rdf:Description rdf:about="#entity_9">
<ro:part_of rdf:resource="#entity_1" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:66836" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:16761" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic ADP concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k3">
<dcterms:description>Forward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.EH2_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_27">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_7">
<ro:part_of rdf:resource="#entity_1" />
<semsim:name>Double proton-bound, cytosol-facing conformation of H-ATPase catalytic component</semsim:name>
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of double proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.ATP_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_17">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_12">
<ro:part_of rdf:resource="#entity_9" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:15422" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic ATP concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.k8">
<dcterms:description>Backward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.H_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_6">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_8">
<ro:part_of rdf:resource="#entity_9" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:24636" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>H+ concentration in the cytosolic space</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.Ha">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_36">
<semsim:physicalPropertyOf rdf:resource="#entity_5" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>H+ concentration in the antechamber between the membrane and catalytic components of H-ATPase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.Pi_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_21">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_14">
<ro:part_of rdf:resource="#entity_9" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/chebi/CHEBI:18367" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic phosphate(3-) concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.k11">
<dcterms:description>Forward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.EH">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_26">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_3">
<ro:part_of rdf:resource="#entity_1" />
<semsim:name>Proton-bound, antechamber-facing conformation of H-ATPase catalytic component</semsim:name>
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.time">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_01023" />
<dcterms:description>Time solution domain for simulation</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.E_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_22">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_13">
<ro:part_of rdf:resource="#entity_1" />
<semsim:name>Cytosol-facing conformation of H-ATPase catalytic component</semsim:name>
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.EH2_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_24">
<semsim:physicalPropertyOf rdf:resource="#entity_7" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of double proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k4">
<dcterms:description>Backward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.ATP_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_10">
<semsim:physicalPropertyOf rdf:resource="#entity_12" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic ATP concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k10">
<dcterms:description>Backward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.F">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00089" />
<dcterms:description>Faraday constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.E">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_13">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_4">
<ro:part_of rdf:resource="#entity_1" />
<semsim:name>Antechamber-facing conformation of H-ATPase catalytic component</semsim:name>
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.k4">
<dcterms:description>Backward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.k5">
<dcterms:description>Forward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.time">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_01023" />
<dcterms:description>Time solution domain for simulation</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.k12">
<dcterms:description>Backward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k5">
<dcterms:description>Forward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.Ha">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf rdf:resource="#entity_5" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>H+ concentration in the antechamber between the membrane and catalytic components of H-ATPase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.k3">
<dcterms:description>Forward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.ADP_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_9">
<semsim:physicalPropertyOf rdf:resource="#entity_11" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic ADP concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k11">
<dcterms:description>Forward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.k6">
<dcterms:description>Backward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.H_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_23">
<semsim:physicalPropertyOf rdf:resource="#entity_8" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>H+ concentration in the cytosolic space</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k6">
<dcterms:description>Backward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.EH2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_29">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_0">
<ro:part_of rdf:resource="#entity_1" />
<semsim:name>Double proton-bound, antechamber-facing conformation of H-ATPase catalytic component</semsim:name>
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of double proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.E">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_18">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.k4">
<dcterms:description>Backward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.EH2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_4">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of double proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.E_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_11">
<semsim:physicalPropertyOf rdf:resource="#entity_13" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.EH2">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_0">
<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of double proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.k8">
<dcterms:description>Backward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.time">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_01023" />
<dcterms:description>Time solution domain for simulation</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.EH_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_25">
<semsim:physicalPropertyOf rdf:resource="#entity_10" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.time">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_01023" />
<dcterms:description>Time solution domain for simulation</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.Ha">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_28">
<semsim:physicalPropertyOf rdf:resource="#entity_5" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>H+ concentration in the antechamber between the membrane and catalytic components of H-ATPase</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.k11">
<dcterms:description>Forward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k7">
<dcterms:description>Forward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.k10">
<dcterms:description>Backward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.EH">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_1">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.k2">
<dcterms:description>Backward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="http://www.cellml.org/cellml/1.0" dc:title="H-ATPase">
<dc:publisher>The University of Auckland, Auckland Bioengineering Institute</dc:publisher>
<cmeta:comment>
<rdf:Description rdf:about="rdf:#6178f046-fbaf-4065-9f92-f172a5230666" rdf:value="">
<dc:creator rdf:resource="rdf:#c29cc0b6-14f4-4866-84c0-f9fd689980db" vCard:FN="" />
</rdf:Description>
</cmeta:comment>
<dcterms:created rdf:resource="rdf:#df754649-a053-4044-a5b2-6caf16dd5350" dcterms:W3CDTF="2007-05-29T00:00:00+00:00" />
<dc:creator>
<rdf:Description rdf:about="rdf:#bd9ee214-d7c0-4738-9b8f-aa6dbb2fc0e5">
<vCard:ORG>
<rdf:Description rdf:about="rdf:#1874a94e-ffba-42b8-b3b9-91ee526a18b7">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
</rdf:Description>
</vCard:ORG>
<vCard:EMAIL rdf:resource="rdf:#6d779a8c-1830-4c79-b105-a26f6a24de90" rdf:value="c.lloyd@auckland.ac.nz" rdf:type="http://imc.org/vCard/3.0#internet" />
<vCard:N rdf:resource="rdf:#a5a71012-dc0b-43fb-9da5-73558f9d8700" vCard:Given="Catherine" vCard:Family="Lloyd" vCard:Other="May" />
</rdf:Description>
</dc:creator>
<cmeta:modification>
<rdf:Description rdf:about="rdf:#35902352-7cc0-4181-bf07-f1f73e90956b">
<dcterms:modified rdf:resource="rdf:#525c17d9-ad8f-425f-9732-3468096c2fcc" dcterms:W3CDTF="2007-06-05T09:56:00+12:00" />
<rdf:value>The new version of this model has been re-coded to remove the reaction element and replace it with a simple MathML description of the model reaction kinetics. This is thought to be truer to the original publication, and information regarding the enzyme kinetics etc will later be added to the metadata through use of an ontology. 

The model runs in the PCEnv simulator but gives a flat output.</rdf:value>
<cmeta:modifier>
<rdf:Description rdf:about="rdf:#d88da72b-8a46-453b-adbe-3f53e7be8036">
<vCard:N rdf:resource="rdf:#7abcf947-9092-4800-9056-bf5da0cbeb2d" vCard:Given="Catherine" vCard:Family="Lloyd" vCard:Other="May" />
</rdf:Description>
</cmeta:modifier>
</rdf:Description>
</cmeta:modification>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.ADP_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_35">
<semsim:physicalPropertyOf rdf:resource="#entity_11" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic ADP concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.ATP_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_33">
<semsim:physicalPropertyOf rdf:resource="#entity_12" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic ATP concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.Pi_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_12">
<semsim:physicalPropertyOf rdf:resource="#entity_14" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic phosphate(3-) concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#chang_fujita_2001_H_ATPase" semsim:modelId="renal_H_ATPase_model" semsim:AnnotatorContactInfo="maxneal@gmail.com" semsim:modelName="renal_H_ATPase_model">
<semsim:AnnotatorName>Maxwell Neal</semsim:AnnotatorName>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.k7">
<dcterms:description>Forward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.Pi_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_31">
<semsim:physicalPropertyOf rdf:resource="#entity_14" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Cytosolic phosphate(3-) concentration in type-A intercalated cells of late distal tubule</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2.k12">
<dcterms:description>Backward rate constant for conformational change of double proton-bound H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.k1">
<dcterms:description>Forward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k8">
<dcterms:description>Backward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.k3">
<dcterms:description>Forward rate constant for proton binding to the proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="http://www.cellml.org/cellml/1.0#renal_H_ATPase_model" cmeta:species="Rat">
<dc:title>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.</dc:title>
<cmeta:bio_entity>Renal Distal Tubule</cmeta:bio_entity>
<cmeta:comment>
<rdf:Description rdf:about="rdf:#9e6c1010-5605-4a78-9992-5403125ce223">
<dc:creator>
<rdf:Description rdf:about="rdf:#92dbb897-b5d4-4696-b11c-ad6b55d5332f">
<vCard:FN>Catherine Lloyd</vCard:FN>
</rdf:Description>
</dc:creator>
<rdf:value>This is the CellML 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.

These models can be run in PCEnv but they give a flat output. I suspect they need to be embedded within a whole cell model in order to give a reasonable output.</rdf:value>
</rdf:Description>
</cmeta:comment>
<bqs:reference>
<rdf:Description rdf:about="rdf:#25307320-acfc-4d52-b152-79c3b61ae355">
<dc:subject>
<rdf:Description rdf:about="rdf:#8efd9e1e-2923-41fc-b13b-f5703584df68" bqs:subject_type="keyword">
<rdf:value>
<rdf:Bag rdf:about="rdf:#35acf3e3-18b1-4518-bde2-8cfd8c7ee1ed">
<rdf:li>kidney</rdf:li>
<rdf:li>electrophysiology</rdf:li>
<rdf:li>distal tubule</rdf:li>
<rdf:li>renal</rdf:li>
<rdf:li>acid-base transport</rdf:li>
<rdf:li>ion transport</rdf:li>
</rdf:Bag>
</rdf:value>
</rdf:Description>
</dc:subject>
</rdf:Description>
</bqs:reference>
<bqs:reference>
<rdf:Description rdf:about="rdf:#ae6916fd-29d2-4763-a0ba-79ceec299157" bqs:Pubmed_id="11457714">
<bqs:JournalArticle>
<rdf:Description rdf:about="rdf:#cd12d814-dc56-4756-825b-8bc1b2408625" bqs:volume="281" bqs:first_page="F222" bqs:last_page="F243">
<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:resource="rdf:#08a1413b-bdd3-44d2-a58d-5e63804335c7" vCard:Given="Hangil" vCard:Family="Chang" />
</bqs:Person>
</rdf:li>
<rdf:li>
<bqs:Person rdf:about="rdf:#d07e5835-41b3-4589-a6dc-1f166446c113">
<vCard:N rdf:resource="rdf:#a4fdda4e-fb2d-486a-b0f9-52e630ad30f4" vCard:Given="Toshiro" vCard:Family="Fujita" />
</bqs:Person>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title>A numerical model of acid-base transport in rat distal tubule</dc:title>
<bqs:Journal>
<rdf:Description rdf:about="rdf:#3a4bd135-2eb3-45c4-93ed-bad58aa3d1d2">
<dc:title>American Journal of Physiology</dc:title>
</rdf:Description>
</bqs:Journal>
<dcterms:issued rdf:resource="rdf:#6ca7c35d-64e6-4d14-bc97-937bd12069ce" dcterms:W3CDTF="2001-08" />
</rdf:Description>
</bqs:JournalArticle>
</rdf:Description>
</bqs:reference>
</rdf:Description>
<rdf:Description rdf:about="#E.k9">
<dcterms:description>Forward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#environment.time">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_01023" />
<dcterms:description>Time solution domain for simulation</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.E_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_20">
<semsim:physicalPropertyOf rdf:resource="#entity_13" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.psi">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_32">
<semsim:physicalPropertyOf rdf:resource="#entity_15" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00506" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Extracellular electrical potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.k5">
<dcterms:description>Forward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.k9">
<dcterms:description>Forward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.EH">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_14">
<semsim:physicalPropertyOf rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of proton-bound, antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.R">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00410" />
<dcterms:description>Gas constant</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E.k2">
<dcterms:description>Backward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k9">
<dcterms:description>Forward rate constant for conformational change of H-ATPase catalytic component from antechamber-facing to cytosol-facing</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.EH2_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_5">
<semsim:physicalPropertyOf rdf:resource="#entity_7" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of double proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.time">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_01023" />
<dcterms:description>Time solution domain for simulation</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k1">
<dcterms:description>Forward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.psi_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_38">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_17">
<ro:part_of rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/cl/CL:0005011" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00506" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Intraceullar electrical potential</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.E">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_2">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.k6">
<dcterms:description>Backward rate constant for proton binding to cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.H_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_37">
<semsim:physicalPropertyOf rdf:resource="#entity_8" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>H+ concentration in the cytosolic space</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.time">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_01023" />
<dcterms:description>Time solution domain for simulation</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.T">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_30">
<semsim:physicalPropertyOf rdf:resource="#entity_2" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00293" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Ambient temperature</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#E_.H_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_15">
<semsim:physicalPropertyOf rdf:resource="#entity_8" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>H+ concentration in the cytosolic space</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH2_.EH_">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_7">
<semsim:physicalPropertyOf rdf:resource="#entity_10" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#reaction_constants.k2">
<dcterms:description>Backward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH.k1">
<dcterms:description>Forward rate constant for proton binding to antechamber-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#EH_.k7">
<dcterms:description>Forward rate constant for proton binding to the proton-bound, cytosol-facing conformation of H-ATPase catalytic component</dcterms:description>
</rdf:Description>
</rdf:RDF>
</model>
