Location: Yamaguchi, Takaki, Matsubara, Yasuhara, Suga, 1996 @ 7a42a2b99b0b / yamaguchi_takaki_matsubara_yasuhara_suga_1996.cellml

Author:

rcai987 <devnull@localhost>

Date:

2014-12-18 12:35:31+13:00

Desc:

Added some annotations to yamaguchi_takaki_mastubara_yashura_... model

Permanent Source URI:

https://staging.physiomeproject.org/workspace/yamaguchi_takaki_matsubara_yasuhara_suga_1996/rawfile/7a42a2b99b0b62beff8b5daf8995bebfbe2681db/yamaguchi_takaki_matsubara_yasuhara_suga_1996.cellml

<?xml version="1.0"?>
<!--
This CellML file was generated on 1/07/2008 at 4:39:09 at p.m. using:

COR (0.9.31.979)
Copyright 2002-2008 Dr Alan Garny
http://COR.physiol.ox.ac.uk/ - COR@physiol.ox.ac.uk

CellML 1.0 was used to generate this model
http://www.CellML.org/
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xml:base="file:///H:/yamaguchi_takaki_matsubara_yasuhara_suga_1996/yamaguchi_takaki_matsubara_yasuhara_suga_1996.cellml" cmeta:id="yamaguchi_takaki_matsubara_yasuhara_suga_1996" name="yamaguchi_takaki_matsubara_yasuhara_suga_1996">
  <documentation xmlns="http://cellml.org/tmp-documentation">
		<article>
			<articleinfo>
				<title>Constancy and variability of contractile efficiency as a function of calcium and cross-bridge kinetics: simulation</title>
				<author>
					<firstname>Geoffrey</firstname>
					<surname>Nunns</surname>
					<affiliation>
						<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
					</affiliation>
				</author>
			</articleinfo>
			<section id="sec_status">
				<title>Model Status</title>
				<para>
        This model is known to run in both OpenCell and COR. It recreates the published results for the simulation, except in the case of FTI_end, FLA_max and ATP, because CellML cannot compute finite integrals or maximums of functions. These values are instead estimated based on graphs, but must be re-estimated for different initial conditions. The parameters for this model are the control values. 
          </para>
			</section>
			<sect1 id="sec_structure">
				<title>Model Structure</title>
				<para>
Abstract: We simulated myocardial Ca2+ (Ca) and cross-bridge (CB) kinetics to get insight into the experimentally observed constancy and variability of cardiac contractile efficiency in generating total mechanical energy under various inotropic and pathological conditions. The simulation consisted of a Ca transient, Ca association and dissociation rate constants of troponin C, and CB on and off rate constants. We evaluated sarcomere isometric twitch contractions at a constant muscle length. We assumed that each CB cycle hydrolyzes one ATP and that the force-length area (FLA) quantifies the total mechanical energy generated by CB cycles in a twitch contraction. FLA is a linear version of pressure-volume area, which quantifies the total mechanical energy of cardiac twitch contraction and correlates linearly with cardiac oxygen consumption (H. Suga, Physiol. Rev. 70: 247-277, 1990). The simulation shows that the contractile efficiency varies with changes in the Ca transient and Ca and CB kinetics except when they simultaneously speed up or slow down proportionally. These results point to possible mechanisms underlying the constancy and variability of cardiac contractile efficiency.    
</para>
				<para>
The original paper reference is cited below:
</para>
				<para>Constancy and variability of contractile efficiency as a function of calcium and cross-bridge kinetics: simulation, Hiroki Yamaguchi, Miyako Takaki, Hiromi Matsubara, Shingo Yasuhara, and Hiroyuki Suga,  1996, <emphasis>American Journal of Physiology</emphasis>, 270, H1501-1508.  <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8967394  &amp;dopt=Abstract">PubMed ID: 8967394   </ulink>
				</para>
				
				<informalfigure float="0" id="fig_reaction_diagram">
					<mediaobject>
						<imageobject>
							<objectinfo>
								<title>model diagram</title>
							</objectinfo>
							<imagedata fileref="yamaguchi_1996.png"/>
						</imageobject>
					</mediaobject>
					<caption>Schematic diagram showing the calcium kinetics between transient calcium (Ca2+), and troponin C (Tn), and cross bridge kinetics (CB).</caption>
				</informalfigure>
				
			</sect1>
		</article>
	</documentation>   
   
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      <unit units="meter"/>
      <unit exponent="-1" units="second"/>
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      <unit units="force"/>
      <unit units="meter"/>
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      <variable initial_value="40" name="k_1" public_interface="out" units="per_second"/>
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      <variable cmeta:id="id_00004" initial_value="1" name="Total_CB" public_interface="out" units="dimensionless"/>
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      <variable cmeta:id="TnCa_TnCa" initial_value="0" name="TnCa" public_interface="out" units="dimensionless"/>
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      <variable cmeta:id="id_00010" name="Ca_t" public_interface="in" units="dimensionless"/>
      <variable cmeta:id="id_00009" name="Total_Tn" public_interface="in" units="dimensionless"/>
      <variable name="k_1" public_interface="in" units="per_second"/>
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                  <ci>Ca_t</ci>
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                     <ci>TnCa</ci>
                  </apply>
               </apply>
               <apply>
                  <times/>
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                  <ci>TnCa</ci>
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            </apply>
         </apply>
      </math>
   </component>
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      <variable name="t" public_interface="in" units="second"/>
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      </math>
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      <variable cmeta:id="CumCB_CumCB_off" initial_value="0" name="CumCB_off" public_interface="out" units="dimensionless"/>
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      <variable name="Total_CB" public_interface="in" units="dimensionless"/>
      <variable cmeta:id="id_00017" name="TnCa" public_interface="in" units="dimensionless"/>
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      <variable name="FLA" public_interface="out" units="energy"/>
      <variable name="t" public_interface="in" units="second"/>
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      <variable initial_value="0" name="L_0" units="meter"/>
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      </math>
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   </component>
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      <variable name="Economy" units="second_per_meter"/>
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      <map_variables variable_1="t" variable_2="t"/>
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      <map_variables variable_1="TnCa" variable_2="TnCa"/>
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      <map_variables variable_1="Ca_max" variable_2="Ca_max"/>
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      <map_variables variable_1="Total_Tn" variable_2="Total_Tn"/>
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      <map_variables variable_1="f" variable_2="f"/>
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      <map_variables variable_1="Total_CB" variable_2="Total_CB"/>
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   <connection>
      <map_components component_1="parameters" component_2="CumCB"/>
      <map_variables variable_1="f" variable_2="f"/>
      <map_variables variable_1="g" variable_2="g"/>
      <map_variables variable_1="Total_CB" variable_2="Total_CB"/>
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   <connection>
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      <map_variables variable_1="CB_on" variable_2="CB_on"/>
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      <map_variables variable_1="TnCa" variable_2="TnCa"/>
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      <map_variables variable_1="CB_on" variable_2="CB_on"/>
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      <map_variables variable_1="phi" variable_2="phi"/>
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   <connection>
      <map_components component_1="equations_main" component_2="ATP"/>
      <map_variables variable_1="ATP_energy" variable_2="ATP_energy"/>
      <map_variables variable_1="epsilon" variable_2="epsilon"/>
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   <connection>
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      <map_variables variable_1="g" variable_2="g"/>
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