Rendering of the source text

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<article>
  <articleinfo>
  <title>Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production</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 runs in both OpenCell and COR. It is the unscaled version of the model, taken from equations 16-25 in the original paper. There are no published results (figures) for the unscaled model therefore we do not know whether or not this CellML model is capable of reproducing the orignal model's results.
          </para>
  </section>
  <sect1 id="sec_structure">
<title>Model Structure</title>

<para>
ABSTRACT: Mitochondria play a central role in cellular energetic metabolism. The essential parts of this metabolism are the tricarboxylic acid (TCA) cycle, the respiratory chain and the adenosine triphosphate (ATP) synthesis machinery. Here a simplified model of these three metabolic components with a limited set of differential equations is presented. The existence of a steady state is demonstrated and results of numerical simulations are presented. The relevance of a simple model to represent actual in vivo behavior is discussed.
</para>

<para>
The original paper reference is cited below:
</para>

<para>
Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production, Nazaret C, Heiske M, Thurley K, and Mazat JP, 2009, <emphasis>Journal of Theoretical Biology</emphasis>, 258, 455-464.  <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/19007794">PubMed ID: 19007794</ulink>
</para>

<informalfigure float="0" id="fig_reaction_diagram">
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  <imageobject>
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      <title>reaction diagram</title>
    </objectinfo>
    <imagedata fileref="nazaret_2009.png"/>
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</mediaobject>
<caption>Schematic diagram of the model.</caption>
</informalfigure>

</sect1>
</article>
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        <dcterms:alternative>oxaloacetate</dcterms:alternative>  
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        <dcterms:alternative>nicotinamide adenine dinucleotide</dcterms:alternative>  
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        <dcterms:alternative>adenosine triphospahte</dcterms:alternative>  
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        <dc:title>delta_psi</dc:title>
        <dcterms:alternative>membrane potential</dcterms:alternative>  
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    <variable initial_value="0.1" name="a" units="per_millivolt"/>
    <variable initial_value="150.0" name="delta_psi_m" units="millivolt"/>
	
    <variable name="delta_psi" public_interface="in" units="millivolt"/>
	<variable name="NAD" public_interface="in" units="micromolar"/>
	<variable name="Nt" public_interface="in" units="millimolar"/>
   
    <math xmlns="http://www.w3.org/1998/Math/MathML" id="19">
      <apply id="vresp_calculation"><eq/>
        <ci> vresp </ci>
        <apply>
		  <times/>
          <ci> kresp </ci>
		  <apply>
		    <divide/>
			<apply>
		      <minus/>
			  <ci> Nt </ci>
			  <ci> NAD </ci>
		    </apply>
			<apply>
		      <minus/>
			  <apply>
		        <plus/>
				<ci> K </ci>
			    <ci> Nt </ci>
		      </apply>
			  <ci> NAD </ci>
		    </apply>
		  </apply>
		  <apply>
		    <divide/>
			<cn cellml:units="dimensionless"> 1 </cn>
			<apply>
		      <plus/>
			  <cn cellml:units="dimensionless"> 1 </cn>
			  <apply>
		        <exp/>
		        <apply>
		          <times/>
			      <ci> a </ci>
				  <apply>
		            <minus/>
				    <ci> delta_psi </ci>
			        <ci> delta_psi_m </ci>
				  </apply>
		        </apply>
			  </apply>
			</apply>
		  </apply>
		</apply>
      </apply>
    </math>
  </component>
  
  <component name="vATP">
    <variable cmeta:id="vATP_vATP" name="vATP" public_interface="out" units="micromolar_per_second"/>
    
    <variable initial_value="131.9" name="kATP" units="millimolar_per_second"/>
	<variable initial_value="4" name="b" units="per_micromolar"/>
   
    <variable name="ATP" public_interface="in" units="micromolar"/>
	<variable name="ATP_crit_delta_psi" public_interface="in" units="micromolar"/>
   
    <math xmlns="http://www.w3.org/1998/Math/MathML" id="20">
      <apply id="vATP_calculation"><eq/>
        <ci> vATP </ci>
        <apply>
		  <times/>
          <ci> kATP </ci>
		  <apply>
		    <minus/>
			<apply>
		      <divide/>
			  <cn cellml:units="dimensionless"> 2 </cn>
			  <apply>
		        <plus/>
			    <cn cellml:units="dimensionless"> 1 </cn>
			    <apply>
		          <exp/>
		          <apply>
		            <times/>
			        <ci> b </ci>
				    <apply>
		              <minus/>
				      <ci> ATP </ci>
			          <ci> ATP_crit_delta_psi </ci>
					</apply>
				  </apply>
				</apply>
			  </apply>
			</apply>
			<cn cellml:units="dimensionless"> 1 </cn>
		  </apply>
		</apply>
      </apply>
    </math>
  </component>
  
  <component name="ATP_crit_delta_psi">
    <variable cmeta:id="ATP_crit_delta_psi_ATP_crit_delta_psi" name="ATP_crit_delta_psi" public_interface="out" units="micromolar"/>
    
    <variable initial_value="8.314" name="R" units="joule_per_mole_kelvin"/>
	<variable initial_value="298" name="T" units="kelvin"/>
	<variable initial_value="96485" name="F" units="coulomb_per_mole"/>
	<variable initial_value="4.4e-6" name="Kapp" units="per_millimolar"/>
	<variable name="Pi" initial_value="2.440" units="millimolar"/>
    <variable name="delta_G_transport" units="joule_per_mole"/>
   
    <variable name="At" public_interface="in" units="millimolar"/>
	<variable name="delta_psi" public_interface="in" units="millivolt"/>
	
    <math xmlns="http://www.w3.org/1998/Math/MathML" id="21">
      <apply id="ATP_crit_delta_psi_calculation"><eq/>
        <ci> ATP_crit_delta_psi </ci>
        <apply>
		  <divide/>
          <ci> At </ci>
		  <apply>
		    <plus/>
			<cn cellml:units="dimensionless"> 1 </cn>
			<apply>
		      <divide/>
			  <apply>
		        <exp/>
			    <apply>
		          <divide/>
		          <apply>
		            <times/>
			        <cn cellml:units="dimensionless"> -3 </cn>
					<ci> delta_G_transport </ci>
				  </apply>
				  <apply>
		            <times/>
				    <ci> R </ci>
			        <ci> T </ci>
				  </apply>
				</apply>
		      </apply>
			  <apply>
		        <times/>
				<ci> Kapp </ci>
			    <ci> Pi </ci>
			  </apply>
			</apply>
		  </apply>
		</apply>
      </apply>
    </math>
	
	<math xmlns="http://www.w3.org/1998/Math/MathML" id="22">
      <apply id="delta_G_transport_calculation"><eq/>
        <ci> delta_G_transport </ci>
		<apply>
          <times/>
          <cn cellml:units="dimensionless"> 0.0012 </cn>
          <ci> F </ci>
          <ci> delta_psi </ci>
        </apply>
	  </apply>
    </math>
  </component>
  
  <component name="model_parameters">
    <variable name="At" initial_value="4.160" public_interface="out" units="millimolar"/>
	<variable name="Nt" initial_value="1.070" public_interface="out" units="millimolar"/>
  </component>
  
  
  <connection>
    <map_components component_1="Pyr" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="AcCoA" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="Cit" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="KG" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="OAA" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>

  <connection>
    <map_components component_1="NAD" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="ATP" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="delta_psi" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="Pyr" component_2="v1"/>
    <map_variables variable_1="v1" variable_2="v1"/>
  </connection>
  
  <connection>
    <map_components component_1="Pyr" component_2="v2"/>
    <map_variables variable_1="Pyr" variable_2="Pyr"/>
    <map_variables variable_1="v2" variable_2="v2"/>
  </connection>
  
  <connection>
    <map_components component_1="Pyr" component_2="v7"/>
    <map_variables variable_1="Pyr" variable_2="Pyr"/>
    <map_variables variable_1="v7" variable_2="v7"/>
  </connection>
  
  <connection>
    <map_components component_1="AcCoA" component_2="v2"/>
    <map_variables variable_1="v2" variable_2="v2"/>
  </connection>
  
  <connection>
    <map_components component_1="AcCoA" component_2="v3"/>
    <map_variables variable_1="AcCoA" variable_2="AcCoA"/>
    <map_variables variable_1="v3" variable_2="v3"/>
  </connection>
  
  <connection>
    <map_components component_1="Cit" component_2="v3"/>
    <map_variables variable_1="v3" variable_2="v3"/>
  </connection>
  
  <connection>
    <map_components component_1="Cit" component_2="v4"/>
    <map_variables variable_1="Cit" variable_2="Cit"/>
    <map_variables variable_1="v4" variable_2="v4"/>
  </connection>
  
  <connection>
    <map_components component_1="KG" component_2="v4"/>
    <map_variables variable_1="v4" variable_2="v4"/>
  </connection>
  
  <connection>
    <map_components component_1="KG" component_2="v5"/>
    <map_variables variable_1="KG" variable_2="KG"/>
    <map_variables variable_1="v5" variable_2="v5"/>
  </connection>
  
  <connection>
    <map_components component_1="KG" component_2="v6"/>
    <map_variables variable_1="KG" variable_2="KG"/>
    <map_variables variable_1="v6" variable_2="v6"/>
  </connection>
  
  <connection>
    <map_components component_1="OAA" component_2="v5"/>
    <map_variables variable_1="v5" variable_2="v5"/>
  </connection>
  
  <connection>
    <map_components component_1="OAA" component_2="v3"/>
    <map_variables variable_1="OAA" variable_2="OAA"/>
    <map_variables variable_1="v3" variable_2="v3"/>
  </connection>
  
  <connection>
    <map_components component_1="OAA" component_2="v6"/>
    <map_variables variable_1="OAA" variable_2="OAA"/>
    <map_variables variable_1="v6" variable_2="v6"/>
  </connection>
  
  <connection>
    <map_components component_1="OAA" component_2="v7"/>
    <map_variables variable_1="v7" variable_2="v7"/>
  </connection>
  
  <connection>
    <map_components component_1="OAA" component_2="v8"/>
    <map_variables variable_1="OAA" variable_2="OAA"/>
    <map_variables variable_1="v8" variable_2="v8"/>
  </connection>
  
  <connection>
    <map_components component_1="NAD" component_2="v2"/>
    <map_variables variable_1="NAD" variable_2="NAD"/>
    <map_variables variable_1="v2" variable_2="v2"/>
  </connection>
  
  <connection>
    <map_components component_1="NAD" component_2="v4"/>
    <map_variables variable_1="NAD" variable_2="NAD"/>
    <map_variables variable_1="v4" variable_2="v4"/>
  </connection>
  
  <connection>
    <map_components component_1="NAD" component_2="v5"/>
    <map_variables variable_1="NAD" variable_2="NAD"/>
	<map_variables variable_1="v5" variable_2="v5"/>
  </connection>
  
  <connection>
    <map_components component_1="NAD" component_2="vresp"/>
    <map_variables variable_1="NAD" variable_2="NAD"/>
	<map_variables variable_1="vresp" variable_2="vresp"/>
  </connection>
  
  <connection>
    <map_components component_1="ATP" component_2="vATP"/>
    <map_variables variable_1="ATP" variable_2="ATP"/>
    <map_variables variable_1="vATP" variable_2="vATP"/>
  </connection>
  
  <connection>
    <map_components component_1="ATP" component_2="vANT"/>
    <map_variables variable_1="ATP" variable_2="ATP"/>
    <map_variables variable_1="vANT" variable_2="vANT"/>
  </connection>
  
  <connection>
    <map_components component_1="ATP" component_2="v5"/>
    <map_variables variable_1="ATP" variable_2="ATP"/>
	<map_variables variable_1="v5" variable_2="v5"/>
  </connection>
  
  <connection>
    <map_components component_1="ATP" component_2="v7"/>
    <map_variables variable_1="ATP" variable_2="ATP"/>
	<map_variables variable_1="v7" variable_2="v7"/>
  </connection>
  
  <connection>
    <map_components component_1="delta_psi" component_2="vresp"/>
    <map_variables variable_1="delta_psi" variable_2="delta_psi"/>
	<map_variables variable_1="vresp" variable_2="vresp"/>
  </connection>
  
  <connection>
    <map_components component_1="delta_psi" component_2="vATP"/>
    <map_variables variable_1="vATP" variable_2="vATP"/>
  </connection>
  
  <connection>
    <map_components component_1="delta_psi" component_2="vleak"/>
    <map_variables variable_1="delta_psi" variable_2="delta_psi"/>
	<map_variables variable_1="vleak" variable_2="vleak"/>
  </connection>
  
  <connection>
    <map_components component_1="delta_psi" component_2="vANT"/>
    <map_variables variable_1="vANT" variable_2="vANT"/>
  </connection>
  
  <connection>
    <map_components component_1="vresp" component_2="model_parameters"/>
    <map_variables variable_1="Nt" variable_2="Nt"/>
  </connection>
  
  <connection>
    <map_components component_1="v5" component_2="model_parameters"/>
    <map_variables variable_1="At" variable_2="At"/>
  </connection>
  
  <connection>
    <map_components component_1="ATP_crit_delta_psi" component_2="model_parameters"/>
    <map_variables variable_1="At" variable_2="At"/>
  </connection>
  
  <connection>
    <map_components component_1="ATP_crit_delta_psi" component_2="vATP"/>
    <map_variables variable_1="ATP_crit_delta_psi" variable_2="ATP_crit_delta_psi"/>
  </connection>
  
  <connection>
    <map_components component_1="ATP_crit_delta_psi" component_2="delta_psi"/>
    <map_variables variable_1="delta_psi" variable_2="delta_psi"/>
  </connection>
  
  <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" 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#">
    
	<rdf:Description rdf:about="">
      <dc:title>Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production (unscaled version)</dc:title>
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          <rdf:value>c.lloyd@auckland.ac.nz</rdf:value>
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        </vCard:EMAIL>
        <vCard:ORG rdf:parseType="Resource">
          <vCard:Orgname>The University of Auckland</vCard:Orgname>
          <vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
        </vCard:ORG>
      </dc:creator>
    </rdf:Description>
    
    <rdf:Description rdf:about="#nazarat_2009">
      <bqs:reference rdf:parseType="Resource">
        <dc:subject rdf:parseType="Resource">
          <bqs:subject_type>keyword</bqs:subject_type>
          <rdf:value>
            <rdf:Bag>
              <rdf:li>metabolism</rdf:li>
			  <rdf:li>TCA cycle</rdf:li>
            </rdf:Bag>
          </rdf:value>
        </dc:subject>
      </bqs:reference>

      <bqs:reference rdf:parseType="Resource">
        <bqs:Pubmed_id>19007794</bqs:Pubmed_id>
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			  <rdf:li rdf:parseType="Resource">
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				  </vCard:N>
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                    <vCard:Given>K</vCard:Given>
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			  <rdf:li rdf:parseType="Resource">
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              </rdf:li>
            </rdf:Seq>
          </dc:creator>
          <dc:title>
            Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production
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          <dcterms:issued rdf:parseType="Resource">
            <dcterms:W3CDTF>2009-06-07</dcterms:W3CDTF>
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            <dc:title>Journal of Theoretical Biology</dc:title>
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