- Author:
- Dewan Sarwar <dsar941@UoA.auckland.ac.nz>
- Date:
- 2020-02-01 18:26:13+13:00
- Desc:
- adding some SEDML-based protocols for the model verification platform
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/267/rawfile/365b24f7c4bd35542064805f8f97c885bce4f490/SEDML/weinstein_1995_2A.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="weinstein_1995_2A" cmeta:id="Proximal_Tubule_NHE3">
<units name="mM_per_s">
<unit exponent="-1.0" units="second" />
<unit units="mM" />
</units>
<units name="cm2">
<unit exponent="2.0" prefix="centi" units="metre" />
</units>
<units name="nmol">
<unit prefix="nano" units="mole" />
</units>
<units name="cm">
<unit prefix="centi" units="metre" />
</units>
<units name="mM">
<unit exponent="-1.0" units="litre" />
<unit prefix="milli" units="mole" />
</units>
<units name="per_s">
<unit exponent="-1.0" units="second" />
</units>
<units name="nmol_per_s_per_cm2">
<unit units="nmol" />
<unit exponent="-1.0" units="cm2" />
<unit exponent="-1.0" units="second" />
</units>
<units name="umol">
<unit prefix="micro" units="mole" />
</units>
<units name="mmol">
<unit prefix="milli" units="mole" />
</units>
<units name="M">
<unit exponent="-1.0" units="litre" />
<unit units="mole" />
</units>
<units name="mmol_per_s_per_cm2">
<unit exponent="-1.0" units="cm2" />
<unit exponent="-1.0" units="second" />
<unit units="mmol" />
</units>
<component name="environment">
<variable cmeta:id="environment.time" name="time" public_interface="out" units="second" />
</component>
<component name="Concentrations">
<variable cmeta:id="Concentrations.C_ext_Na" initial_value="0.1" name="C_ext_Na" public_interface="out" units="mM" />
<variable cmeta:id="Concentrations.C_ext_H" name="C_ext_H" public_interface="out" units="mM" />
<variable cmeta:id="Concentrations.C_ext_NH4" initial_value="0" name="C_ext_NH4" public_interface="out" units="mM" />
<variable cmeta:id="Concentrations.C_int_Na" initial_value="0" name="C_int_Na" public_interface="out" units="mM" />
<variable cmeta:id="Concentrations.C_int_H" initial_value="1e-3" name="C_int_H" public_interface="out" units="mM" />
<variable cmeta:id="Concentrations.C_int_NH4" initial_value="0" name="C_int_NH4" public_interface="out" units="mM" />
<variable cmeta:id="Concentrations.time" name="time" public_interface="in" units="second" />
<variable cmeta:id="Concentrations.pH_ext" initial_value="6" name="pH_ext" units="dimensionless" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>pH_ext</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="per_s">2</cn>
</apply>
<apply>
<eq />
<ci>C_ext_H</ci>
<apply>
<times />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" type="e-notation" cellml:units="mM">
1
<sep />
3
</cn>
<apply>
<power />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">10</cn>
<apply>
<minus />
<ci>pH_ext</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="NHE3_Parameters">
<variable cmeta:id="NHE3_Parameters.XTxP0_NHE3_Na" initial_value="1.6e-3" name="XTxP0_NHE3_Na" public_interface="out" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3_Parameters.XTxP0_NHE3_H" initial_value="0.48e-3" name="XTxP0_NHE3_H" public_interface="out" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3_Parameters.XTxP0_NHE3_NH4" initial_value="1.6e-3" name="XTxP0_NHE3_NH4" public_interface="out" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3_Parameters.K_NHE3_Na" initial_value="30" name="K_NHE3_Na" public_interface="out" units="mM" />
<variable cmeta:id="NHE3_Parameters.K_NHE3_H" initial_value="72e-6" name="K_NHE3_H" public_interface="out" units="mM" />
<variable cmeta:id="NHE3_Parameters.K_NHE3_NH4" initial_value="0.027e3" name="K_NHE3_NH4" public_interface="out" units="mM" />
</component>
<component name="NHE3">
<variable cmeta:id="NHE3.C_ext_Na" name="C_ext_Na" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.C_ext_H" name="C_ext_H" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.C_ext_NH4" name="C_ext_NH4" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.C_int_Na" name="C_int_Na" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.C_int_H" name="C_int_H" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.C_int_NH4" name="C_int_NH4" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.XTxP0_NHE3_Na" name="XTxP0_NHE3_Na" public_interface="in" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.XTxP0_NHE3_H" name="XTxP0_NHE3_H" public_interface="in" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.XTxP0_NHE3_NH4" name="XTxP0_NHE3_NH4" public_interface="in" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.XTxP_NHE_Na" name="XTxP_NHE_Na" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.XTxP_NHE_H" name="XTxP_NHE_H" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.XTxP_NHE_NH4" name="XTxP_NHE_NH4" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.K_NHE3_Na" name="K_NHE3_Na" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.K_NHE3_H" name="K_NHE3_H" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.K_NHE3_NH4" name="K_NHE3_NH4" public_interface="in" units="mM" />
<variable cmeta:id="NHE3.alpha_ext_Na" name="alpha_ext_Na" units="dimensionless" />
<variable cmeta:id="NHE3.beta_ext_H" name="beta_ext_H" units="dimensionless" />
<variable cmeta:id="NHE3.gamma_ext_NH4" name="gamma_ext_NH4" units="dimensionless" />
<variable cmeta:id="NHE3.alpha_int_Na" name="alpha_int_Na" units="dimensionless" />
<variable cmeta:id="NHE3.beta_int_H" name="beta_int_H" units="dimensionless" />
<variable cmeta:id="NHE3.gamma_int_NH4" name="gamma_int_NH4" units="dimensionless" />
<variable cmeta:id="NHE3.sum_NHE3" name="sum_NHE3" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.J_NHE3_Na" name="J_NHE3_Na" public_interface="out" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.J_NHE3_H" name="J_NHE3_H" public_interface="out" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.J_NHE3_NH4" name="J_NHE3_NH4" public_interface="out" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.J_NHE3_Na_Max" name="J_NHE3_Na_Max" units="nmol_per_s_per_cm2" />
<variable cmeta:id="NHE3.plot_b" name="plot_b" units="dimensionless" />
<variable cmeta:id="NHE3.plot_a" name="plot_a" units="dimensionless" />
<variable cmeta:id="NHE3.K_H" name="K_H" units="dimensionless" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>alpha_ext_Na</ci>
<apply>
<divide />
<ci>C_ext_Na</ci>
<ci>K_NHE3_Na</ci>
</apply>
</apply>
<apply>
<eq />
<ci>beta_ext_H</ci>
<apply>
<divide />
<ci>C_ext_H</ci>
<ci>K_NHE3_H</ci>
</apply>
</apply>
<apply>
<eq />
<ci>gamma_ext_NH4</ci>
<apply>
<divide />
<ci>C_ext_NH4</ci>
<ci>K_NHE3_NH4</ci>
</apply>
</apply>
<apply>
<eq />
<ci>alpha_int_Na</ci>
<apply>
<divide />
<ci>C_int_Na</ci>
<ci>K_NHE3_Na</ci>
</apply>
</apply>
<apply>
<eq />
<ci>beta_int_H</ci>
<apply>
<divide />
<ci>C_int_H</ci>
<ci>K_NHE3_H</ci>
</apply>
</apply>
<apply>
<eq />
<ci>gamma_int_NH4</ci>
<apply>
<divide />
<ci>C_int_NH4</ci>
<ci>K_NHE3_NH4</ci>
</apply>
</apply>
<apply>
<eq />
<ci>XTxP_NHE_Na</ci>
<apply>
<divide />
<apply>
<times />
<ci>XTxP0_NHE3_Na</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn>
<ci>C_int_H</ci>
</apply>
<apply>
<plus />
<ci>C_int_H</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" type="e-notation" cellml:units="mM">
1
<sep />
-6
</cn>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>XTxP_NHE_H</ci>
<apply>
<divide />
<apply>
<times />
<ci>XTxP0_NHE3_H</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn>
<ci>C_int_H</ci>
</apply>
<apply>
<plus />
<ci>C_int_H</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" type="e-notation" cellml:units="mM">
1
<sep />
-6
</cn>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>XTxP_NHE_NH4</ci>
<apply>
<divide />
<apply>
<times />
<ci>XTxP0_NHE3_NH4</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn>
<ci>C_int_H</ci>
</apply>
<apply>
<plus />
<ci>C_int_H</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" type="e-notation" cellml:units="mM">
1
<sep />
-6
</cn>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>sum_NHE3</ci>
<apply>
<plus />
<apply>
<times />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<ci>alpha_ext_Na</ci>
<ci>beta_ext_H</ci>
<ci>gamma_ext_NH4</ci>
</apply>
<apply>
<plus />
<apply>
<times />
<ci>XTxP_NHE_Na</ci>
<ci>alpha_int_Na</ci>
</apply>
<apply>
<times />
<ci>XTxP_NHE_H</ci>
<ci>beta_int_H</ci>
</apply>
<apply>
<times />
<ci>XTxP_NHE_NH4</ci>
<ci>gamma_int_NH4</ci>
</apply>
</apply>
</apply>
<apply>
<times />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<ci>alpha_int_Na</ci>
<ci>beta_int_H</ci>
<ci>gamma_int_NH4</ci>
</apply>
<apply>
<plus />
<apply>
<times />
<ci>XTxP_NHE_Na</ci>
<ci>alpha_ext_Na</ci>
</apply>
<apply>
<times />
<ci>XTxP_NHE_H</ci>
<ci>beta_ext_H</ci>
</apply>
<apply>
<times />
<ci>XTxP_NHE_NH4</ci>
<ci>gamma_ext_NH4</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>J_NHE3_Na</ci>
<apply>
<plus />
<apply>
<times />
<apply>
<divide />
<apply>
<times />
<ci>XTxP_NHE_Na</ci>
<ci>XTxP_NHE_H</ci>
</apply>
<ci>sum_NHE3</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>alpha_ext_Na</ci>
<ci>beta_int_H</ci>
</apply>
<apply>
<times />
<ci>alpha_int_Na</ci>
<ci>beta_ext_H</ci>
</apply>
</apply>
</apply>
<apply>
<times />
<apply>
<divide />
<apply>
<times />
<ci>XTxP_NHE_Na</ci>
<ci>XTxP_NHE_NH4</ci>
</apply>
<ci>sum_NHE3</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>alpha_ext_Na</ci>
<ci>gamma_int_NH4</ci>
</apply>
<apply>
<times />
<ci>alpha_int_Na</ci>
<ci>gamma_ext_NH4</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>J_NHE3_H</ci>
<apply>
<plus />
<apply>
<times />
<apply>
<divide />
<apply>
<times />
<ci>XTxP_NHE_Na</ci>
<ci>XTxP_NHE_H</ci>
</apply>
<ci>sum_NHE3</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>alpha_int_Na</ci>
<ci>beta_ext_H</ci>
</apply>
<apply>
<times />
<ci>alpha_ext_Na</ci>
<ci>beta_int_H</ci>
</apply>
</apply>
</apply>
<apply>
<times />
<apply>
<divide />
<apply>
<times />
<ci>XTxP_NHE_H</ci>
<ci>XTxP_NHE_NH4</ci>
</apply>
<ci>sum_NHE3</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>beta_ext_H</ci>
<ci>gamma_int_NH4</ci>
</apply>
<apply>
<times />
<ci>beta_int_H</ci>
<ci>gamma_ext_NH4</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>J_NHE3_NH4</ci>
<apply>
<plus />
<apply>
<times />
<apply>
<divide />
<apply>
<times />
<ci>XTxP_NHE_Na</ci>
<ci>XTxP_NHE_NH4</ci>
</apply>
<ci>sum_NHE3</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>alpha_int_Na</ci>
<ci>gamma_ext_NH4</ci>
</apply>
<apply>
<times />
<ci>alpha_ext_Na</ci>
<ci>gamma_int_NH4</ci>
</apply>
</apply>
</apply>
<apply>
<times />
<apply>
<divide />
<apply>
<times />
<ci>XTxP_NHE_H</ci>
<ci>XTxP_NHE_NH4</ci>
</apply>
<ci>sum_NHE3</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>gamma_ext_NH4</ci>
<ci>beta_int_H</ci>
</apply>
<apply>
<times />
<ci>beta_ext_H</ci>
<ci>gamma_int_NH4</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>J_NHE3_Na_Max</ci>
<apply>
<divide />
<apply>
<times />
<ci>XTxP_NHE_Na</ci>
<ci>XTxP_NHE_H</ci>
</apply>
<apply>
<plus />
<ci>XTxP_NHE_Na</ci>
<ci>XTxP_NHE_H</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>plot_a</ci>
<apply>
<divide />
<ci>J_NHE3_Na</ci>
<ci>J_NHE3_Na_Max</ci>
</apply>
</apply>
<apply>
<eq />
<ci>plot_b</ci>
<apply>
<divide />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<ci>plot_a</ci>
</apply>
</apply>
<apply>
<eq />
<ci>K_H</ci>
<apply>
<divide />
<apply>
<plus />
<apply>
<times />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<ci>alpha_ext_Na</ci>
</apply>
<ci>beta_int_H</ci>
</apply>
<apply>
<divide />
<apply>
<times />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<ci>beta_int_H</ci>
</apply>
<ci>alpha_ext_Na</ci>
<ci>XTxP_NHE_Na</ci>
</apply>
<ci>XTxP_NHE_H</ci>
</apply>
</apply>
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn>
<apply>
<times />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn>
<ci>beta_int_H</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="Concentrations" component_2="NHE3" />
<map_variables variable_1="C_int_Na" variable_2="C_int_Na" />
<map_variables variable_1="C_ext_NH4" variable_2="C_ext_NH4" />
<map_variables variable_1="C_ext_H" variable_2="C_ext_H" />
<map_variables variable_1="C_int_H" variable_2="C_int_H" />
<map_variables variable_1="C_ext_Na" variable_2="C_ext_Na" />
<map_variables variable_1="C_int_NH4" variable_2="C_int_NH4" />
</connection>
<connection>
<map_components component_1="environment" component_2="Concentrations" />
<map_variables variable_1="time" variable_2="time" />
</connection>
<connection>
<map_components component_1="NHE3_Parameters" component_2="NHE3" />
<map_variables variable_1="K_NHE3_Na" variable_2="K_NHE3_Na" />
<map_variables variable_1="K_NHE3_NH4" variable_2="K_NHE3_NH4" />
<map_variables variable_1="XTxP0_NHE3_H" variable_2="XTxP0_NHE3_H" />
<map_variables variable_1="XTxP0_NHE3_Na" variable_2="XTxP0_NHE3_Na" />
<map_variables variable_1="K_NHE3_H" variable_2="K_NHE3_H" />
<map_variables variable_1="XTxP0_NHE3_NH4" variable_2="XTxP0_NHE3_NH4" />
</connection>
<rdf:RDF xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#">
<rdf:Description rdf:about="#NHE3.C_ext_Na">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_0">
<ro:part_of>
<rdf:Description rdf:about="#entity_1">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:74550" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:29101" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of Na+ in the portion of renal filtrate in proximal convoluted tubule compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NHE3.C_int_Na">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_4">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_2">
<ro:part_of>
<rdf:Description rdf:about="#entity_3">
<ro:part_of>
<rdf:Description rdf:about="#entity_4">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:70973" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/fma/FMA:66836" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:29101" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>Concentration of Na+ in the portion of cytosol in epithelial cell of proximal tubule compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Concentrations.pH_ext">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_2">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_5">
<ro:part_of rdf:resource="#entity_1" />
<semsim:hasPhysicalDefinition rdf:resource="https://identifiers.org/chebi/CHEBI:82715" />
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