Views
Comparison of Simulated and Measured Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog
The CellML code.
<!-- FILE :baylor_model_b_2002.xml
CREATED : 1st November 2002
LAST MODIFIED : 9th April 2003
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/01/2002 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Baylor, Hollingworth and Chandler's 2002 model of the Ca2+-ATP binding reaction in skeletal myocytes.
CHANGES:
09/04/2003 - AAC - Added publication date information.
-->
<model xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns="http://www.cellml.org/cellml/1.0#" name="baylor_model_b_2002" cmeta:id="baylor_model_b_2002">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Calcium Sparks in Skeletal Muscle Fibers</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This is the original unchecked version of the model imported from the previous
CellML model repository, 24-Jan-2006.
</para>
<para>
This model describes Multistate reaction of Ca2+ and protein with fluo-3
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
The activation of Ca<superscript>2+</superscript> sparks is an essential step in cardiac excitation-contraction coupling. A Ca<superscript>2+</superscript> spark arises when sarcoplasmic reticulum (SR) Ca<superscript>2+</superscript>-release channels (ryanodine receptors, or RyRs) open, allowing Ca<superscript>2+</superscript> to diffuse out of the intracellular store, down its electrochemical gradient into the cytoplasm. The increase in intracellular calcium concentration ([Ca<superscript>2+</superscript>]<subscript>i</subscript>) is recognised as a Ca<superscript>2+</superscript> spark. After release, Ca<superscript>2+</superscript> diffuses through the cytoplasm and binds to buffers such as troponin, ATP, parvalbumin and the SR Ca<superscript>2+</superscript> pump.
</para>
<para>
In their 2002 paper, S.M. Baylor, S. Hollingworth and W.K. Chandler model Ca<superscript>2+</superscript> sparks in frog intact skeletal muscle fibers. The model calculates changes in the concentration of free Ca<superscript>2+</superscript> and of Ca<superscript>2+</superscript> bound to the buffers and to the Ca<superscript>2+</superscript> indicator fluo-3 (see <xref linkend="fig_reaction_diagram" /> below).
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.jgp.org/cgi/content/abstract/120/3/349">Comparison of Simulated and Measured Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog</ulink>, S.M. Baylor, S. Hollingworth and W.K. Chandler, 2002, <ulink url="http://www.jgp.org/">
<emphasis>Journal of General Physiology</emphasis>
</ulink>, 120, 349-368. (<ulink url="http://www.jgp.org/cgi/content/full/120/3/349">Full text</ulink> and <ulink url="http://www.jgp.org/cgi/reprint/120/3/349.pdf">PDF versions</ulink> of the article are available to subscribers on the Journal of General Physiology website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12198091&dopt=Abstract">PubMed ID: 12198091</ulink>
</para>
<para>
The raw CellML descriptions of the model can be downloaded in various formats as described in <xref linkend="sec_download_this_model" />.
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction_diagram</title>
</objectinfo>
<imagedata fileref="../images/baylor_model_2002/reaction_diagram.gif" />
</imageobject>
</mediaobject>
<caption>Schematic diagrams of the Ca<superscript>2+</superscript> binding reactions for various buffers and indicators: <emphasis role="bold">A</emphasis> The reaction of Ca<superscript>2+</superscript> with ATP in the presence of free Mg<superscript>2+</superscript>, <emphasis role="bold">B</emphasis> Reaction of Ca<superscript>2+</superscript> with protein (Pr) and fluo-3 (Fluo), <emphasis role="bold">C</emphasis> Competitive reaction of Ca<superscript>2+</superscript> and Mg<superscript>2+</superscript> with parvalbumin (Parv), <emphasis role="bold">D</emphasis> Binding reaction of Ca<superscript>2+</superscript> binding and transport by the sarcoplasmic reticulum Ca<superscript>2+</superscript> pump (E), <emphasis role="bold">E</emphasis> One-step reaction of Ca<superscript>2+</superscript> with Troponin (Trop), and <emphasis role="bold">F</emphasis> Two-step reaction of Ca<superscript>2+</superscript> with Troponin (Trop).</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<!--
Below, we define some additional units for association with variables and
constants within the model. The identifiers are fairly self-explanatory.
-->
<units name="micromolar">
<unit units="mole" prefix="micro" />
<unit units="litre" exponent="-1" />
</units>
<units name="molar">
<unit units="litre" exponent="-1" />
</units>
<units name="flux">
<unit units="micromolar" exponent="1" />
<unit units="second" exponent="-1" />
</units>
<units name="first_order_rate_constant">
<unit units="second" exponent="-1" />
</units>
<units name="second_order_rate_constant">
<unit units="molar" exponent="-1" />
<unit units="second" exponent="-1" />
</units>
<!--
The "environment" component is used to declare variables that are used by
all or most of the other components, in this case just "time".
-->
<component name="environment">
<variable units="second" public_interface="out" name="time" />
</component>
<!--
The following components describe all the reactants and products involved in
the reactions.
-->
<component cmeta:id="Ca" name="Ca">
<variable units="micromolar" public_interface="out" name="Ca" initial_value="0.05" />
<variable units="flux" public_interface="in" name="delta_Ca_rxn0" />
<variable units="flux" public_interface="in" name="delta_Ca_rxn3" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca</ci>
</apply>
<apply>
<plus />
<ci>delta_Ca_rxn0</ci>
<ci>delta_Ca_rxn3</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Fluo" name="Fluo">
<variable units="micromolar" public_interface="out" name="Fluo" initial_value="11.88" />
<variable units="flux" public_interface="in" name="delta_Fluo_rxn0" />
<variable units="flux" public_interface="in" name="delta_Fluo_rxn1" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Fluo</ci>
</apply>
<apply>
<plus />
<ci>delta_Fluo_rxn0</ci>
<ci>delta_Fluo_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Pr" name="Pr">
<variable units="micromolar" public_interface="out" name="Pr" initial_value="3000.0" />
<variable units="flux" public_interface="in" name="delta_Pr_rxn1" />
<variable units="flux" public_interface="in" name="delta_Pr_rxn2" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Pr</ci>
</apply>
<apply>
<plus />
<ci>delta_Pr_rxn1</ci>
<ci>delta_Pr_rxn2</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="PrFluo" name="PrFluo">
<variable units="micromolar" public_interface="out" name="PrFluo" initial_value="88.12" />
<variable units="flux" public_interface="in" name="delta_PrFluo_rxn1" />
<variable units="flux" public_interface="in" name="delta_PrFluo_rxn3" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>PrFluo</ci>
</apply>
<apply>
<plus />
<ci>delta_PrFluo_rxn1</ci>
<ci>delta_PrFluo_rxn3</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="CaFluo" name="CaFluo">
<variable units="micromolar" public_interface="out" name="CaFluo" />
<variable units="flux" public_interface="in" name="delta_CaFluo_rxn0" />
<variable units="flux" public_interface="in" name="delta_CaFluo_rxn2" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>CaFluo</ci>
</apply>
<apply>
<plus />
<ci>delta_CaFluo_rxn0</ci>
<ci>delta_CaFluo_rxn2</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="CaPrFluo" name="CaPrFluo">
<variable units="micromolar" public_interface="out" name="CaPrFluo" />
<variable units="flux" public_interface="in" name="delta_CaPrFluo_rxn2" />
<variable units="flux" public_interface="in" name="delta_CaPrFluo_rxn3" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>CaPrFluo</ci>
</apply>
<apply>
<plus />
<ci>delta_CaPrFluo_rxn2</ci>
<ci>delta_CaPrFluo_rxn3</ci>
</apply>
</apply>
</math>
</component>
<!--
The following components describe the reactions of the model.
-->
<component name="reaction0">
<variable units="micromolar" public_interface="in" name="Ca" />
<variable units="micromolar" public_interface="in" name="Fluo" />
<variable units="micromolar" public_interface="in" name="CaFluo" />
<variable units="flux" public_interface="out" name="delta_Ca_rxn0" />
<variable units="flux" public_interface="out" name="delta_Fluo_rxn0" />
<variable units="flux" public_interface="out" name="delta_CaFluo_rxn0" />
<variable units="second_order_rate_constant" name="k0" initial_value="2.676E8" />
<variable units="first_order_rate_constant" name="k0_" initial_value="137.0" />
<variable units="flux" name="rate" />
<reaction reversible="yes">
<variable_ref variable="Ca">
<role role="reactant" direction="forward" delta_variable="delta_Ca_rxn0" stoichiometry="1" />
</variable_ref>
<variable_ref variable="Fluo">
<role role="reactant" direction="forward" delta_variable="delta_Fluo_rxn0" stoichiometry="1" />
</variable_ref>
<variable_ref variable="CaFluo">
<role role="product" direction="forward" delta_variable="delta_CaFluo_rxn0" stoichiometry="1" />
</variable_ref>
<variable_ref variable="rate">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>rate</ci>
<apply>
<plus />
<apply>
<times />
<ci>k0</ci>
<ci>Ca</ci>
<ci>Fluo</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k0_</ci>
<ci>CaFluo</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction1">
<variable units="micromolar" public_interface="in" name="Fluo" />
<variable units="micromolar" public_interface="in" name="Pr" />
<variable units="micromolar" public_interface="in" name="PrFluo" />
<variable units="flux" public_interface="out" name="delta_Fluo_rxn1" />
<variable units="flux" public_interface="out" name="delta_Pr_rxn1" />
<variable units="flux" public_interface="out" name="delta_PrFluo_rxn1" />
<variable units="second_order_rate_constant" name="k1" initial_value="1.149E7" />
<variable units="first_order_rate_constant" name="k1_" initial_value="4216.0" />
<variable units="flux" name="rate" />
<reaction reversible="yes">
<variable_ref variable="Fluo">
<role role="reactant" direction="forward" delta_variable="delta_Fluo_rxn1" stoichiometry="1" />
</variable_ref>
<variable_ref variable="Pr">
<role role="reactant" direction="forward" delta_variable="delta_Pr_rxn1" stoichiometry="1" />
</variable_ref>
<variable_ref variable="PrFluo">
<role role="product" direction="forward" delta_variable="delta_PrFluo_rxn1" stoichiometry="1" />
</variable_ref>
<variable_ref variable="rate">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>rate</ci>
<apply>
<plus />
<apply>
<times />
<ci>k1</ci>
<ci>Fluo</ci>
<ci>Pr</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k1_</ci>
<ci>PrFluo</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction2">
<variable units="micromolar" public_interface="in" name="CaFluo" />
<variable units="micromolar" public_interface="in" name="Pr" />
<variable units="micromolar" public_interface="in" name="CaPrFluo" />
<variable units="flux" public_interface="out" name="delta_CaFluo_rxn2" />
<variable units="flux" public_interface="out" name="delta_Pr_rxn2" />
<variable units="flux" public_interface="out" name="delta_CaPrFluo_rxn2" />
<variable units="second_order_rate_constant" name="k2" initial_value="1.149E7" />
<variable units="first_order_rate_constant" name="k2_" initial_value="15777.0" />
<variable units="flux" name="rate" />
<reaction reversible="yes">
<variable_ref variable="CaFluo">
<role role="reactant" direction="forward" delta_variable="delta_CaFluo_rxn2" stoichiometry="1" />
</variable_ref>
<variable_ref variable="Pr">
<role role="reactant" direction="forward" delta_variable="delta_Pr_rxn2" stoichiometry="1" />
</variable_ref>
<variable_ref variable="CaPrFluo">
<role role="product" direction="forward" delta_variable="delta_CaPrFluo_rxn2" stoichiometry="1" />
</variable_ref>
<variable_ref variable="rate">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>rate</ci>
<apply>
<plus />
<apply>
<times />
<ci>k2</ci>
<ci>CaFluo</ci>
<ci>Pr</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k2_</ci>
<ci>CaPrFluo</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction3">
<variable units="micromolar" public_interface="in" name="Ca" />
<variable units="micromolar" public_interface="in" name="PrFluo" />
<variable units="micromolar" public_interface="in" name="CaPrFluo" />
<variable units="flux" public_interface="out" name="delta_Ca_rxn3" />
<variable units="flux" public_interface="out" name="delta_PrFluo_rxn3" />
<variable units="flux" public_interface="out" name="delta_CaPrFluo_rxn3" />
<variable units="second_order_rate_constant" name="k3" initial_value="1.72E7" />
<variable units="first_order_rate_constant" name="k3_" initial_value="32.9" />
<variable units="flux" name="rate" />
<reaction reversible="yes">
<variable_ref variable="Ca">
<role role="reactant" direction="forward" delta_variable="delta_Ca_rxn3" stoichiometry="1" />
</variable_ref>
<variable_ref variable="PrFluo">
<role role="reactant" direction="forward" delta_variable="delta_PrFluo_rxn3" stoichiometry="1" />
</variable_ref>
<variable_ref variable="CaPrFluo">
<role role="product" direction="forward" delta_variable="delta_CaPrFluo_rxn3" stoichiometry="1" />
</variable_ref>
<variable_ref variable="rate">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>rate</ci>
<apply>
<plus />
<apply>
<times />
<ci>k3</ci>
<ci>Ca</ci>
<ci>PrFluo</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k3_</ci>
<ci>CaPrFluo</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<connection>
<map_components component_2="reaction0" component_1="Ca" />
<map_variables variable_2="Ca" variable_1="Ca" />
<map_variables variable_2="delta_Ca_rxn0" variable_1="delta_Ca_rxn0" />
</connection>
<connection>
<map_components component_2="reaction3" component_1="Ca" />
<map_variables variable_2="Ca" variable_1="Ca" />
<map_variables variable_2="delta_Ca_rxn3" variable_1="delta_Ca_rxn3" />
</connection>
<connection>
<map_components component_2="reaction0" component_1="Fluo" />
<map_variables variable_2="Fluo" variable_1="Fluo" />
<map_variables variable_2="delta_Fluo_rxn0" variable_1="delta_Fluo_rxn0" />
</connection>
<connection>
<map_components component_2="reaction1" component_1="Fluo" />
<map_variables variable_2="Fluo" variable_1="Fluo" />
<map_variables variable_2="delta_Fluo_rxn1" variable_1="delta_Fluo_rxn1" />
</connection>
<connection>
<map_components component_2="reaction1" component_1="Pr" />
<map_variables variable_2="Pr" variable_1="Pr" />
<map_variables variable_2="delta_Pr_rxn1" variable_1="delta_Pr_rxn1" />
</connection>
<connection>
<map_components component_2="reaction2" component_1="Pr" />
<map_variables variable_2="Pr" variable_1="Pr" />
<map_variables variable_2="delta_Pr_rxn2" variable_1="delta_Pr_rxn2" />
</connection>
<connection>
<map_components component_2="reaction1" component_1="PrFluo" />
<map_variables variable_2="PrFluo" variable_1="PrFluo" />
<map_variables variable_2="delta_PrFluo_rxn1" variable_1="delta_PrFluo_rxn1" />
</connection>
<connection>
<map_components component_2="reaction3" component_1="PrFluo" />
<map_variables variable_2="PrFluo" variable_1="PrFluo" />
<map_variables variable_2="delta_PrFluo_rxn3" variable_1="delta_PrFluo_rxn3" />
</connection>
<connection>
<map_components component_2="reaction0" component_1="CaFluo" />
<map_variables variable_2="CaFluo" variable_1="CaFluo" />
<map_variables variable_2="delta_CaFluo_rxn0" variable_1="delta_CaFluo_rxn0" />
</connection>
<connection>
<map_components component_2="reaction2" component_1="CaFluo" />
<map_variables variable_2="CaFluo" variable_1="CaFluo" />
<map_variables variable_2="delta_CaFluo_rxn2" variable_1="delta_CaFluo_rxn2" />
</connection>
<connection>
<map_components component_2="reaction2" component_1="CaPrFluo" />
<map_variables variable_2="CaPrFluo" variable_1="CaPrFluo" />
<map_variables variable_2="delta_CaPrFluo_rxn2" variable_1="delta_CaPrFluo_rxn2" />
</connection>
<connection>
<map_components component_2="reaction3" component_1="CaPrFluo" />
<map_variables variable_2="CaPrFluo" variable_1="CaPrFluo" />
<map_variables variable_2="delta_CaPrFluo_rxn3" variable_1="delta_CaPrFluo_rxn3" />
</connection>
<connection>
<map_components component_2="environment" component_1="Ca" />
<map_variables variable_2="time" variable_1="time" />
</connection>
<connection>
<map_components component_2="environment" component_1="Fluo" />
<map_variables variable_2="time" variable_1="time" />
</connection>
<connection>
<map_components component_2="environment" component_1="Pr" />
<map_variables variable_2="time" variable_1="time" />
</connection>
<connection>
<map_components component_2="environment" component_1="PrFluo" />
<map_variables variable_2="time" variable_1="time" />
</connection>
<connection>
CREATED : 1st November 2002
LAST MODIFIED : 9th April 2003
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/01/2002 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Baylor, Hollingworth and Chandler's 2002 model of the Ca2+-ATP binding reaction in skeletal myocytes.
CHANGES:
09/04/2003 - AAC - Added publication date information.
-->
<model xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns="http://www.cellml.org/cellml/1.0#" name="baylor_model_b_2002" cmeta:id="baylor_model_b_2002">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Calcium Sparks in Skeletal Muscle Fibers</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This is the original unchecked version of the model imported from the previous
CellML model repository, 24-Jan-2006.
</para>
<para>
This model describes Multistate reaction of Ca2+ and protein with fluo-3
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
The activation of Ca<superscript>2+</superscript> sparks is an essential step in cardiac excitation-contraction coupling. A Ca<superscript>2+</superscript> spark arises when sarcoplasmic reticulum (SR) Ca<superscript>2+</superscript>-release channels (ryanodine receptors, or RyRs) open, allowing Ca<superscript>2+</superscript> to diffuse out of the intracellular store, down its electrochemical gradient into the cytoplasm. The increase in intracellular calcium concentration ([Ca<superscript>2+</superscript>]<subscript>i</subscript>) is recognised as a Ca<superscript>2+</superscript> spark. After release, Ca<superscript>2+</superscript> diffuses through the cytoplasm and binds to buffers such as troponin, ATP, parvalbumin and the SR Ca<superscript>2+</superscript> pump.
</para>
<para>
In their 2002 paper, S.M. Baylor, S. Hollingworth and W.K. Chandler model Ca<superscript>2+</superscript> sparks in frog intact skeletal muscle fibers. The model calculates changes in the concentration of free Ca<superscript>2+</superscript> and of Ca<superscript>2+</superscript> bound to the buffers and to the Ca<superscript>2+</superscript> indicator fluo-3 (see <xref linkend="fig_reaction_diagram" /> below).
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.jgp.org/cgi/content/abstract/120/3/349">Comparison of Simulated and Measured Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog</ulink>, S.M. Baylor, S. Hollingworth and W.K. Chandler, 2002, <ulink url="http://www.jgp.org/">
<emphasis>Journal of General Physiology</emphasis>
</ulink>, 120, 349-368. (<ulink url="http://www.jgp.org/cgi/content/full/120/3/349">Full text</ulink> and <ulink url="http://www.jgp.org/cgi/reprint/120/3/349.pdf">PDF versions</ulink> of the article are available to subscribers on the Journal of General Physiology website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12198091&dopt=Abstract">PubMed ID: 12198091</ulink>
</para>
<para>
The raw CellML descriptions of the model can be downloaded in various formats as described in <xref linkend="sec_download_this_model" />.
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction_diagram</title>
</objectinfo>
<imagedata fileref="../images/baylor_model_2002/reaction_diagram.gif" />
</imageobject>
</mediaobject>
<caption>Schematic diagrams of the Ca<superscript>2+</superscript> binding reactions for various buffers and indicators: <emphasis role="bold">A</emphasis> The reaction of Ca<superscript>2+</superscript> with ATP in the presence of free Mg<superscript>2+</superscript>, <emphasis role="bold">B</emphasis> Reaction of Ca<superscript>2+</superscript> with protein (Pr) and fluo-3 (Fluo), <emphasis role="bold">C</emphasis> Competitive reaction of Ca<superscript>2+</superscript> and Mg<superscript>2+</superscript> with parvalbumin (Parv), <emphasis role="bold">D</emphasis> Binding reaction of Ca<superscript>2+</superscript> binding and transport by the sarcoplasmic reticulum Ca<superscript>2+</superscript> pump (E), <emphasis role="bold">E</emphasis> One-step reaction of Ca<superscript>2+</superscript> with Troponin (Trop), and <emphasis role="bold">F</emphasis> Two-step reaction of Ca<superscript>2+</superscript> with Troponin (Trop).</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<!--
Below, we define some additional units for association with variables and
constants within the model. The identifiers are fairly self-explanatory.
-->
<units name="micromolar">
<unit units="mole" prefix="micro" />
<unit units="litre" exponent="-1" />
</units>
<units name="molar">
<unit units="litre" exponent="-1" />
</units>
<units name="flux">
<unit units="micromolar" exponent="1" />
<unit units="second" exponent="-1" />
</units>
<units name="first_order_rate_constant">
<unit units="second" exponent="-1" />
</units>
<units name="second_order_rate_constant">
<unit units="molar" exponent="-1" />
<unit units="second" exponent="-1" />
</units>
<!--
The "environment" component is used to declare variables that are used by
all or most of the other components, in this case just "time".
-->
<component name="environment">
<variable units="second" public_interface="out" name="time" />
</component>
<!--
The following components describe all the reactants and products involved in
the reactions.
-->
<component cmeta:id="Ca" name="Ca">
<variable units="micromolar" public_interface="out" name="Ca" initial_value="0.05" />
<variable units="flux" public_interface="in" name="delta_Ca_rxn0" />
<variable units="flux" public_interface="in" name="delta_Ca_rxn3" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca</ci>
</apply>
<apply>
<plus />
<ci>delta_Ca_rxn0</ci>
<ci>delta_Ca_rxn3</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Fluo" name="Fluo">
<variable units="micromolar" public_interface="out" name="Fluo" initial_value="11.88" />
<variable units="flux" public_interface="in" name="delta_Fluo_rxn0" />
<variable units="flux" public_interface="in" name="delta_Fluo_rxn1" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Fluo</ci>
</apply>
<apply>
<plus />
<ci>delta_Fluo_rxn0</ci>
<ci>delta_Fluo_rxn1</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Pr" name="Pr">
<variable units="micromolar" public_interface="out" name="Pr" initial_value="3000.0" />
<variable units="flux" public_interface="in" name="delta_Pr_rxn1" />
<variable units="flux" public_interface="in" name="delta_Pr_rxn2" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>Pr</ci>
</apply>
<apply>
<plus />
<ci>delta_Pr_rxn1</ci>
<ci>delta_Pr_rxn2</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="PrFluo" name="PrFluo">
<variable units="micromolar" public_interface="out" name="PrFluo" initial_value="88.12" />
<variable units="flux" public_interface="in" name="delta_PrFluo_rxn1" />
<variable units="flux" public_interface="in" name="delta_PrFluo_rxn3" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>PrFluo</ci>
</apply>
<apply>
<plus />
<ci>delta_PrFluo_rxn1</ci>
<ci>delta_PrFluo_rxn3</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="CaFluo" name="CaFluo">
<variable units="micromolar" public_interface="out" name="CaFluo" />
<variable units="flux" public_interface="in" name="delta_CaFluo_rxn0" />
<variable units="flux" public_interface="in" name="delta_CaFluo_rxn2" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>CaFluo</ci>
</apply>
<apply>
<plus />
<ci>delta_CaFluo_rxn0</ci>
<ci>delta_CaFluo_rxn2</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="CaPrFluo" name="CaPrFluo">
<variable units="micromolar" public_interface="out" name="CaPrFluo" />
<variable units="flux" public_interface="in" name="delta_CaPrFluo_rxn2" />
<variable units="flux" public_interface="in" name="delta_CaPrFluo_rxn3" />
<variable units="second" public_interface="in" name="time" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>time</ci>
</bvar>
<ci>CaPrFluo</ci>
</apply>
<apply>
<plus />
<ci>delta_CaPrFluo_rxn2</ci>
<ci>delta_CaPrFluo_rxn3</ci>
</apply>
</apply>
</math>
</component>
<!--
The following components describe the reactions of the model.
-->
<component name="reaction0">
<variable units="micromolar" public_interface="in" name="Ca" />
<variable units="micromolar" public_interface="in" name="Fluo" />
<variable units="micromolar" public_interface="in" name="CaFluo" />
<variable units="flux" public_interface="out" name="delta_Ca_rxn0" />
<variable units="flux" public_interface="out" name="delta_Fluo_rxn0" />
<variable units="flux" public_interface="out" name="delta_CaFluo_rxn0" />
<variable units="second_order_rate_constant" name="k0" initial_value="2.676E8" />
<variable units="first_order_rate_constant" name="k0_" initial_value="137.0" />
<variable units="flux" name="rate" />
<reaction reversible="yes">
<variable_ref variable="Ca">
<role role="reactant" direction="forward" delta_variable="delta_Ca_rxn0" stoichiometry="1" />
</variable_ref>
<variable_ref variable="Fluo">
<role role="reactant" direction="forward" delta_variable="delta_Fluo_rxn0" stoichiometry="1" />
</variable_ref>
<variable_ref variable="CaFluo">
<role role="product" direction="forward" delta_variable="delta_CaFluo_rxn0" stoichiometry="1" />
</variable_ref>
<variable_ref variable="rate">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>rate</ci>
<apply>
<plus />
<apply>
<times />
<ci>k0</ci>
<ci>Ca</ci>
<ci>Fluo</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k0_</ci>
<ci>CaFluo</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction1">
<variable units="micromolar" public_interface="in" name="Fluo" />
<variable units="micromolar" public_interface="in" name="Pr" />
<variable units="micromolar" public_interface="in" name="PrFluo" />
<variable units="flux" public_interface="out" name="delta_Fluo_rxn1" />
<variable units="flux" public_interface="out" name="delta_Pr_rxn1" />
<variable units="flux" public_interface="out" name="delta_PrFluo_rxn1" />
<variable units="second_order_rate_constant" name="k1" initial_value="1.149E7" />
<variable units="first_order_rate_constant" name="k1_" initial_value="4216.0" />
<variable units="flux" name="rate" />
<reaction reversible="yes">
<variable_ref variable="Fluo">
<role role="reactant" direction="forward" delta_variable="delta_Fluo_rxn1" stoichiometry="1" />
</variable_ref>
<variable_ref variable="Pr">
<role role="reactant" direction="forward" delta_variable="delta_Pr_rxn1" stoichiometry="1" />
</variable_ref>
<variable_ref variable="PrFluo">
<role role="product" direction="forward" delta_variable="delta_PrFluo_rxn1" stoichiometry="1" />
</variable_ref>
<variable_ref variable="rate">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>rate</ci>
<apply>
<plus />
<apply>
<times />
<ci>k1</ci>
<ci>Fluo</ci>
<ci>Pr</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k1_</ci>
<ci>PrFluo</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction2">
<variable units="micromolar" public_interface="in" name="CaFluo" />
<variable units="micromolar" public_interface="in" name="Pr" />
<variable units="micromolar" public_interface="in" name="CaPrFluo" />
<variable units="flux" public_interface="out" name="delta_CaFluo_rxn2" />
<variable units="flux" public_interface="out" name="delta_Pr_rxn2" />
<variable units="flux" public_interface="out" name="delta_CaPrFluo_rxn2" />
<variable units="second_order_rate_constant" name="k2" initial_value="1.149E7" />
<variable units="first_order_rate_constant" name="k2_" initial_value="15777.0" />
<variable units="flux" name="rate" />
<reaction reversible="yes">
<variable_ref variable="CaFluo">
<role role="reactant" direction="forward" delta_variable="delta_CaFluo_rxn2" stoichiometry="1" />
</variable_ref>
<variable_ref variable="Pr">
<role role="reactant" direction="forward" delta_variable="delta_Pr_rxn2" stoichiometry="1" />
</variable_ref>
<variable_ref variable="CaPrFluo">
<role role="product" direction="forward" delta_variable="delta_CaPrFluo_rxn2" stoichiometry="1" />
</variable_ref>
<variable_ref variable="rate">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>rate</ci>
<apply>
<plus />
<apply>
<times />
<ci>k2</ci>
<ci>CaFluo</ci>
<ci>Pr</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k2_</ci>
<ci>CaPrFluo</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<component name="reaction3">
<variable units="micromolar" public_interface="in" name="Ca" />
<variable units="micromolar" public_interface="in" name="PrFluo" />
<variable units="micromolar" public_interface="in" name="CaPrFluo" />
<variable units="flux" public_interface="out" name="delta_Ca_rxn3" />
<variable units="flux" public_interface="out" name="delta_PrFluo_rxn3" />
<variable units="flux" public_interface="out" name="delta_CaPrFluo_rxn3" />
<variable units="second_order_rate_constant" name="k3" initial_value="1.72E7" />
<variable units="first_order_rate_constant" name="k3_" initial_value="32.9" />
<variable units="flux" name="rate" />
<reaction reversible="yes">
<variable_ref variable="Ca">
<role role="reactant" direction="forward" delta_variable="delta_Ca_rxn3" stoichiometry="1" />
</variable_ref>
<variable_ref variable="PrFluo">
<role role="reactant" direction="forward" delta_variable="delta_PrFluo_rxn3" stoichiometry="1" />
</variable_ref>
<variable_ref variable="CaPrFluo">
<role role="product" direction="forward" delta_variable="delta_CaPrFluo_rxn3" stoichiometry="1" />
</variable_ref>
<variable_ref variable="rate">
<role role="rate">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>rate</ci>
<apply>
<plus />
<apply>
<times />
<ci>k3</ci>
<ci>Ca</ci>
<ci>PrFluo</ci>
</apply>
<apply>
<minus />
<apply>
<times />
<ci>k3_</ci>
<ci>CaPrFluo</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</role>
</variable_ref>
</reaction>
</component>
<connection>
<map_components component_2="reaction0" component_1="Ca" />
<map_variables variable_2="Ca" variable_1="Ca" />
<map_variables variable_2="delta_Ca_rxn0" variable_1="delta_Ca_rxn0" />
</connection>
<connection>
<map_components component_2="reaction3" component_1="Ca" />
<map_variables variable_2="Ca" variable_1="Ca" />
<map_variables variable_2="delta_Ca_rxn3" variable_1="delta_Ca_rxn3" />
</connection>
<connection>
<map_components component_2="reaction0" component_1="Fluo" />
<map_variables variable_2="Fluo" variable_1="Fluo" />
<map_variables variable_2="delta_Fluo_rxn0" variable_1="delta_Fluo_rxn0" />
</connection>
<connection>
<map_components component_2="reaction1" component_1="Fluo" />
<map_variables variable_2="Fluo" variable_1="Fluo" />
<map_variables variable_2="delta_Fluo_rxn1" variable_1="delta_Fluo_rxn1" />
</connection>
<connection>
<map_components component_2="reaction1" component_1="Pr" />
<map_variables variable_2="Pr" variable_1="Pr" />
<map_variables variable_2="delta_Pr_rxn1" variable_1="delta_Pr_rxn1" />
</connection>
<connection>
<map_components component_2="reaction2" component_1="Pr" />
<map_variables variable_2="Pr" variable_1="Pr" />
<map_variables variable_2="delta_Pr_rxn2" variable_1="delta_Pr_rxn2" />
</connection>
<connection>
<map_components component_2="reaction1" component_1="PrFluo" />
<map_variables variable_2="PrFluo" variable_1="PrFluo" />
<map_variables variable_2="delta_PrFluo_rxn1" variable_1="delta_PrFluo_rxn1" />
</connection>
<connection>
<map_components component_2="reaction3" component_1="PrFluo" />
<map_variables variable_2="PrFluo" variable_1="PrFluo" />
<map_variables variable_2="delta_PrFluo_rxn3" variable_1="delta_PrFluo_rxn3" />
</connection>
<connection>
<map_components component_2="reaction0" component_1="CaFluo" />
<map_variables variable_2="CaFluo" variable_1="CaFluo" />
<map_variables variable_2="delta_CaFluo_rxn0" variable_1="delta_CaFluo_rxn0" />
</connection>
<connection>
<map_components component_2="reaction2" component_1="CaFluo" />
<map_variables variable_2="CaFluo" variable_1="CaFluo" />
<map_variables variable_2="delta_CaFluo_rxn2" variable_1="delta_CaFluo_rxn2" />
</connection>
<connection>
<map_components component_2="reaction2" component_1="CaPrFluo" />
<map_variables variable_2="CaPrFluo" variable_1="CaPrFluo" />
<map_variables variable_2="delta_CaPrFluo_rxn2" variable_1="delta_CaPrFluo_rxn2" />
</connection>
<connection>
<map_components component_2="reaction3" component_1="CaPrFluo" />
<map_variables variable_2="CaPrFluo" variable_1="CaPrFluo" />
<map_variables variable_2="delta_CaPrFluo_rxn3" variable_1="delta_CaPrFluo_rxn3" />
</connection>
<connection>
<map_components component_2="environment" component_1="Ca" />
<map_variables variable_2="time" variable_1="time" />
</connection>
<connection>
<map_components component_2="environment" component_1="Fluo" />
<map_variables variable_2="time" variable_1="time" />
</connection>
<connection>
<map_components component_2="environment" component_1="Pr" />
<map_variables variable_2="time" variable_1="time" />
</connection>
<connection>
<map_components component_2="environment" component_1="PrFluo" />
<map_variables variable_2="time" variable_1="time" />
</connection>
<connection>