<?xml version="1.0"?>
<!-- FILE : rice_model2_2000_1_1_raw.xml
CREATED : 17th September 2003
LAST MODIFIED : 17th September 2003
AUTHOR : Catherine Lloyd
The Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.1 Specification and the
16/01/2002 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Rice et al's 2000
detailed model of ventricular cardiac myocytes. It simulates
action potentials, Ca2+-handling mechanisms and isometric force
generation by the myofilaments. Using the import and reuse
features of CellML 1.1 we embed these new mechanics within a
previously published ventricular myocyte model.
CHANGES:
-->
<model
name="rice_model2_1_1_2000"
xmlns="http://www.cellml.org/cellml/1.1#"
xmlns:cellml="http://www.cellml.org/cellml/1.1#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
xmlns:xlink="http://www.w3.org/1999/xlink">
<rdf:RDF xmlns:rdf="http://www.w3.org/2000/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.1#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
<!--
The following RDF block contains metadata that applies to this document
as a whole, as indicated by the empty about attribute on the
<rdf:Description> element.
-->
<rdf:Description rdf:about="">
<!--
The Model Builder Metadata. The Dublin Core "creator" element is used
to indicate the person who translated the model into CellML.
-->
<dc:creator rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Lloyd</vCard:Family>
<vCard:Given>Catherine</vCard:Given>
<vCard:Other>May</vCard:Other>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>c.lloyd@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet" />
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</dc:creator>
<!--
The Creation Date metadata. This is the date on which the model
was translated into CellML.
-->
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2003-09-17</dcterms:W3CDTF>
</dcterms:created>
<!--
The Modification History metadata. This lists the changes that have been
made to the document, who made the changes, and when they were made.
-->
<!-- The Publisher metadata. -->
<dc:publisher>
The University of Auckland, Bioengineering Institute
</dc:publisher>
</rdf:Description>
<!--
The following metadata refers to the model itself, as indicated by the
reference to the ID "rice_model2_2000", which is declared on the
<model> element.
-->
<rdf:Description rdf:about="#rice_model2_2000">
<!-- A human readable name for the model. -->
<dc:title>
Rice et al's 2000 detailed model of ventricular cardiac
myocytes
</dc:title>
<!-- A comment regarding the model. -->
<cmeta:comment rdf:parseType="Resource">
<rdf:value>
This is the CellML description of Rice et al's 2000 detailed model of
ventricular cardiac myocytes. It simulates action potentials,
Ca2+-handling mechanisms and isometric force generation by the
myofilaments. Using the import and reuse features of CellML 1.1 we
embed these new mechanics within a previously published ventricular
myocyte model.
</rdf:value>
<!-- The creator of the comment. -->
<dc:creator rdf:parseType="Resource">
<vCard:FN>Catherine Lloyd</vCard:FN>
</dc:creator>
</cmeta:comment>
<!-- This model is specific to cardiac muscle. -->
<cmeta:bio_entity>Cardiac Myocyte</cmeta:bio_entity>
<!--
The CellML Metadata Specification recommends that bibliographic metadata
is used to provide information about the original model reference. The
"identifier" attribute on the "BibliographicReference" class provides an
elegant way to identify a cited reference using a database identifier
such as Pubmed. All associated data such as author, journal title,
date, etc can be looked up on the database.
-->
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>10710361</bqs:Pubmed_id>
<bqs:JournalArticle rdf:parseType="Resource">
<dc:creator>
<rdf:Seq>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Rice</vCard:Family>
<vCard:Given>John</vCard:Given>
<vCard:Other>Jeremy</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Jafri</vCard:Family>
<vCard:Given>M</vCard:Given>
<vCard:Other>Saleet</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
<rdf:li rdf:parseType="Resource">
<bqs:Person rdf:parseType="Resource">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Winslow</vCard:Family>
<vCard:Given>Raimond</vCard:Given>
<vCard:Other>L</vCard:Other>
</vCard:N>
</bqs:Person>
</rdf:li>
</rdf:Seq>
</dc:creator>
<dc:title>
Modeling short-term interval-force relations in cardiac muscle
</dc:title>
<dcterms:issued rdf:parseType="Resource">
<dcterms:W3CDTF>2000-03</dcterms:W3CDTF>
</dcterms:issued>
<bqs:Journal rdf:parseType="Resource">
<dc:title>
American Journal of Physiology: Heart and Circulatory Physiology
</dc:title>
</bqs:Journal>
<bqs:volume>278</bqs:volume>
<bqs:first_page>H913</bqs:first_page>
<bqs:last_page>H931</bqs:last_page>
</bqs:JournalArticle>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
<import xlink:href="http://www.cellml.org/examples/models/jafri_rice_winslow_model_1998.xml">
<units name="millisecond" units_ref="millisecond" />
<units name="per_millisecond" units_ref="per_millisecond" />
<units name="per_second" units_ref="per_second" />
<units name="millivolt" units_ref="millivolt" />
<units name="cm2" units_ref="cm2" />
<units name="micro_litre" units_ref="micro_litre" />
<units name="millimolar" units_ref="millimolar" />
<units name="micromolar" units_ref="micromolar" />
<units name="micromolar_per_second" units_ref="micromolar_per_second" />
<units name="micromolar_per_millisecond" units_ref="micromolar_per_millisecond" />
<units name="per_micromolar_per_second" units_ref="per_micromolar_per_second" />
<units name="per_micromolar3_per_millisecond" units_ref="per_micromolar3_per_millisecond" />
<units name="per_micromolar4_per_millisecond" units_ref="per_micromolar4_per_millisecond" />
<units name="microA_per_microF" units_ref="microA_per_microF" />
<units name="coulomb_per_millimole" units_ref="coulomb_per_millimole" />
<component name="environment" component_ref="environment" />
<component name="membrane" component_ref="membrane" />
<component name="fast_sodium_current" component_ref="fast_sodium_current" />
<component name="L_type_Ca_channel" component_ref="L_type_Ca_channel" />
<component name="time_dependent_potassium_current" component_ref="time_dependent_potassium_current" />
<component name="Na_Ca_exchanger" component_ref="Na_Ca_exchanger" />
<component name="time_independent_potassium_current" component_ref="time_independent_potassium_current" />
<component name="plateau_potassium_current" component_ref="plateau_potassium_current" />
<component name="sarcolemmal_calcium_pump" component_ref="sarcolemmal_calcium_pump" />
<component name="sodium_background_current" component_ref="sodium_background_current" />
<component name="calcium_background_current" component_ref="calcium_background_current" />
<component name="sodium_potassium_pump" component_ref="sodium_potassium_pump" />
<component name="non_specific_calcium_activated_current" component_ref="non_specific_calcium_activated_current" />
</import>
<!-- Below, we define some additional units. -->
<units name="micrometre">
<unit prefix="micro" units="metre" />
</units>
<units name="N_per_mm2">
<unit units="newton" />
<unit prefix="milli" units="metre" exponent="-2" />
</units>
<!-- New Components. -->
<component name="cell_geometry">
<variable name="A_cap" public_interface="out" initial_value="1.534E-4" units="cm2" />
<variable name="V_myo" public_interface="out" initial_value="25.84E-6" units="micro_litre" />
<variable name="V_JSR" public_interface="out" initial_value="0.16E-6" units="micro_litre" />
<variable name="V_NSR" public_interface="out" initial_value="1.40E-6" units="micro_litre" />
<variable name="V_SS" public_interface="out" initial_value="0.495E-6" units="micro_litre" />
</component>
<component name="RyR_channel_states">
<variable name="P_O1" public_interface="out" initial_value="0.428917E-3" units="dimensionless" />
<variable name="P_O2" public_interface="out" initial_value="0.487455E-9" units="dimensionless" />
<variable name="P_C1" initial_value="0.637931" units="dimensionless" />
<variable name="P_C2" initial_value="0.361643" units="dimensionless" />
<variable name="k_a_plus" initial_value="0.01215" units="per_micromolar4_per_millisecond" />
<variable name="k_a_minus" initial_value="0.1425" units="per_millisecond" />
<variable name="k_b_plus" initial_value="0.00405" units="per_micromolar3_per_millisecond" />
<variable name="k_b_minus" initial_value="1.930" units="per_millisecond" />
<variable name="k_c_plus" initial_value="0.010" units="per_millisecond" />
<variable name="k_c_minus" initial_value="0.0008" units="per_millisecond" />
<variable name="n" initial_value="4.0" units="dimensionless" />
<variable name="m" initial_value="3.0" units="dimensionless" />
<variable name="time" public_interface="in" units="millisecond" />
<variable name="Ca_SS" public_interface="in" units="millimolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="P_C1_diff_eq"><eq />
<apply><diff />
<bvar><ci> time </ci></bvar>
<ci> P_C1 </ci>
</apply>
<apply><plus />
<apply><times />
<apply><minus />
<ci> k_a_plus </ci>
</apply>
<apply><power />
<ci> Ca_SS </ci>
<ci> n </ci>
</apply>
<ci> P_C1 </ci>
</apply>
<apply><times />
<ci> k_a_minus </ci>
<ci> P_O1 </ci>
</apply>
</apply>
</apply>
<apply id="P_O1_diff_eq"><eq />
<apply><diff />
<bvar><ci> time </ci></bvar>
<ci> P_O1 </ci>
</apply>
<apply><plus />
<apply><minus />
<apply><times />
<ci> k_a_plus </ci>
<apply><power />
<ci> Ca_SS </ci>
<ci> n </ci>
</apply>
<ci> P_C1 </ci>
</apply>
<apply><plus />
<apply><times />
<ci> k_a_minus </ci>
<ci> P_O1 </ci>
</apply>
<apply><times />
<ci> k_b_plus </ci>
<apply><power />
<ci> Ca_SS </ci>
<ci> m </ci>
</apply>
<ci> P_O1 </ci>
</apply>
<apply><times />
<ci> k_c_plus </ci>
<ci> P_O1 </ci>
</apply>
</apply>
</apply>
<apply><times />
<ci> k_b_minus </ci>
<ci> P_O2 </ci>
</apply>
<apply><times />
<ci> k_c_minus </ci>
<ci> P_C2 </ci>
</apply>
</apply>
</apply>
<apply id="P_O2_diff_eq"><eq />
<apply><diff />
<bvar><ci> time </ci></bvar>
<ci> P_O2 </ci>
</apply>
<apply><minus />
<apply><times />
<ci> k_b_plus </ci>
<apply><power />
<ci> Ca_SS </ci>
<ci> m </ci>
</apply>
<ci> P_O1 </ci>
</apply>
<apply><times />
<ci> k_b_minus </ci>
<ci> P_O2 </ci>
</apply>
</apply>
</apply>
<apply id="P_C2_diff_eq"><eq />
<apply><diff />
<bvar><ci> time </ci></bvar>
<ci> P_C2 </ci>
</apply>
<apply><minus />
<apply><times />
<ci> k_c_plus </ci>
<ci> P_O1 </ci>
</apply>
<apply><times />
<ci> k_c_minus </ci>
<ci> P_C2 </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="SERCA_pump">
<variable name="J_up" public_interface="out" units="micromolar_per_millisecond" />
<variable name="k_fb" initial_value="0.24" units="micromolar" />
<variable name="k_rb" initial_value="1.64" units="millimolar" />
<variable name="fb" initial_value="0.292" units="micromolar_per_second" />
<variable name="rb" initial_value="0.311" units="micromolar_per_second" />
<variable name="Vmax_f" units="micromolar_per_second" />
<variable name="Vmax_r" units="micromolar_per_second" />
<variable name="n_fb" initial_value="1.4" units="dimensionless" />
<variable name="n_rb" units="dimensionless" />
<variable name="time" public_interface="in" units="millisecond" />
<variable name="Ca_NSR" public_interface="in" units="micromolar" />
<variable name="Cai" public_interface="in" units="micromolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_up_calculation"><eq />
<ci> J_up </ci>
<apply><divide />
<apply><minus />
<apply><times />
<ci> Vmax_f </ci>
<ci> fb </ci>
</apply>
<apply><times />
<ci> Vmax_r </ci>
<ci> rb </ci>
</apply>
</apply>
<apply><plus />
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci> fb </ci>
<ci> rb </ci>
</apply>
</apply>
</apply>
<apply id="fb_calculation"><eq />
<ci> fb </ci>
<apply><power />
<apply><divide />
<ci> Cai </ci>
<ci> k_fb </ci>
</apply>
<ci> n_fb </ci>
</apply>
</apply>
<apply id="rb_calculation"><eq />
<ci> rb </ci>
<apply><power />
<apply><divide />
<ci> Ca_NSR </ci>
<ci> k_rb </ci>
</apply>
<ci> n_rb </ci>
</apply>
</apply>
</math>
</component>
<component name="intracellular_Ca_fluxes">
<variable name="J_rel" public_interface="out" units="micromolar_per_millisecond" />
<variable name="J_trpn" public_interface="out" units="micromolar_per_millisecond" />
<variable name="J_tr" public_interface="out" units="micromolar_per_millisecond" />
<variable name="J_xfer" public_interface="out" units="micromolar_per_millisecond" />
<variable name="v1" initial_value="3.6" units="per_millisecond" />
<variable name="tau_tr" initial_value="0.5747" units="millisecond" />
<variable name="tau_xfer" initial_value="9.09" units="millisecond" />
<variable name="HTRPN_tot" public_interface="in" units="micromolar" />
<variable name="LTRPN_tot" public_interface="in" units="micromolar" />
<variable name="HTRPNCa" public_interface="in" units="millimolar" />
<variable name="LTRPNCa" public_interface="in" units="millimolar" />
<variable name="k_htrpn_plus" public_interface="in" units="per_micromolar_per_second" />
<variable name="k_htrpn_minus" public_interface="in" units="per_second" />
<variable name="k_ltrpn_plus" public_interface="in" units="per_micromolar_per_second" />
<variable name="k_ltrpn_minus" public_interface="in" units="per_micromolar_per_second" />
<variable name="time" public_interface="in" units="millisecond" />
<variable name="P_O1" public_interface="in" units="dimensionless" />
<variable name="P_O2" public_interface="in" units="dimensionless" />
<variable name="Cai" public_interface="in" units="micromolar" />
<variable name="Ca_SS" public_interface="in" units="millimolar" />
<variable name="Ca_NSR" public_interface="in" units="micromolar" />
<variable name="Ca_JSR" public_interface="in" units="millimolar" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_rel_calculation"><eq />
<ci> J_rel </ci>
<apply><times />
<ci> v1 </ci>
<apply><plus />
<ci> P_O1 </ci>
<ci> P_O2 </ci>
</apply>
<apply><minus />
<ci> Ca_JSR </ci>
<ci> Ca_SS </ci>
</apply>
</apply>
</apply>
<apply id="J_tr_calculation"><eq />
<ci> J_tr </ci>
<apply><divide />
<apply><minus />
<ci> Ca_NSR </ci>
<ci> Ca_JSR </ci>
</apply>
<ci> tau_tr </ci>
</apply>
</apply>
<apply id="J_xfer_calculation"><eq />
<ci> J_xfer </ci>
<apply><divide />
<apply><minus />
<ci> Ca_SS </ci>
<ci> Cai </ci>
</apply>
<ci> tau_xfer </ci>
</apply>
</apply>
<apply id="J_trpn_calculation"><eq />
<ci> J_trpn </ci>
<apply><plus />
<apply><times />
<ci> k_htrpn_plus </ci>
<ci> Cai </ci>
<apply><minus />
<apply><minus />
<ci> HTRPN_tot </ci>
<ci> HTRPNCa </ci>
</apply>
<apply><times />
<ci> k_htrpn_minus </ci>
<ci> HTRPNCa </ci>
</apply>
</apply>
</apply>
<apply><times />
<ci> k_ltrpn_plus </ci>
<ci> Cai </ci>
<apply><minus />
<apply><minus />
<ci> LTRPN_tot </ci>
<ci> LTRPNCa </ci>
</apply>
<apply><times />
<ci> k_ltrpn_minus </ci>
<ci> LTRPNCa </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="intracellular_ionic_concentrations">
<variable name="Nai" public_interface="out" units="millimolar" />
<variable
name="Nao" public_interface="out"
initial_value="140.0" units="millimolar" />
<variable name="Ki" public_interface="out" units="millimolar" />
<variable
name="Ko" public_interface="out"
initial_value="5.4" units="millimolar" />
<variable name="Cai" public_interface="out" units="millimolar" />
<variable
name="Cao" public_interface="out"
initial_value="1.8" units="millimolar" />
<variable name="Ca_SS" public_interface="out" units="millimolar" />
<variable name="Ca_NSR" public_interface="out" units="millimolar" />
<variable name="Ca_JSR" public_interface="out" units="millimolar" />
<variable name="betai" units="dimensionless" />
<variable name="beta_SS" units="dimensionless" />
<variable name="beta_JSR" units="dimensionless" />
<variable name="K_mCMDN" initial_value="2.38" units="micromolar" />
<variable name="K_mCSQN" initial_value="0.8" units="millimolar" />
<variable name="CSQN_tot" initial_value="15.0" units="millimolar" />
<variable name="CMDN_tot" initial_value="50.0" units="micromolar" />
<variable name="time" public_interface="in" units="millisecond" />
<variable name="J_rel" public_interface="in" units="micromolar_per_millisecond" />
<variable name="J_up" public_interface="in" units="micromolar_per_millisecond" />
<variable name="J_tr" public_interface="in" units="micromolar_per_millisecond" />
<variable name="J_xfer" public_interface="in" units="micromolar_per_millisecond" />
<variable name="J_trpn" public_interface="in" units="micromolar_per_millisecond" />
<variable name="F" public_interface="in" units="coulomb_per_millimole" />
<variable name="i_Na" public_interface="in" units="microA_per_microF" />
<variable name="i_Na_b" public_interface="in" units="microA_per_microF" />
<variable name="i_ns_Na" public_interface="in" units="microA_per_microF" />
<variable name="i_NaCa" public_interface="in" units="microA_per_microF" />
<variable name="i_NaK" public_interface="in" units="microA_per_microF" />
<variable name="i_Ca" public_interface="in" units="microA_per_microF" />
<variable name="i_p_Ca" public_interface="