- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2006-07-09 07:27:58+12:00
- Desc:
- committing version01 of bakker_mensonides_teusink_vanhoek_michels_westerhoff_2000
- Permanent Source URI:
- https://models.cellml.org/workspace/bakker_mensonides_teusink_vanhoek_michels_westerhoff_2000/rawfile/4d991dc02cdc4b35d885f0664bc979eba6d31cda/bakker_mensonides_teusink_vanhoek_michels_westerhoff_2000.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : bakker_model_2000.xml
CREATED : 28th August 2003
LAST MODIFIED : 20th April 2005
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 Bakker et al's 2000 mathematical model of glycolysis in the parasite Trypanosoma brucei.
CHANGES:
20/04/2005 - PJV - Changed syntax to conform with cellml1.1 specs
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:pathway_editor="http://www.physiome.com/pathway_editor/1.0#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" pathway_editor:rendering_config_file="bakker_model_2000_cellmlrender.xml" cmeta:id="bakker_mensonides_teusink_vanhoek_michels_westerhoff_2000_version01" name="bakker_mensonides_teusink_vanhoek_michels_westerhoff_2000_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Glycosomes Protect Trypanosomes from Glycolysis</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 model is consistently represented within the CellML but contains sets of algebraic equations that prevent the model from being solved in currently available software - 03/08.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
Salivarian trypanosomes are extracellular parasites of the blood and tissue fluids of mammals. When it is within the bloodstream of its host <emphasis>Homo sapiens</emphasis>, <emphasis>Trypanosoma brucei</emphasis>, (the parasite that causes African sleeping disease in humans), displays very simple metabolism. In the bloodstream form (within its host) the parasite lacks a Krebs cycle and oxidative phosphorylation, and its metabolism is restricted to the glycolytic pathway alone. As in all trypansomes, most of the glycolytic enzymes of <emphasis>Trypanosoma brucei</emphasis> are contained within a specialised organelle called a glycosome (see <xref linkend="fig_reaction_diagram"/> below). In addition to this structural difference between trypanosomes and other eukaryotic cells, trypanosomes also display differences at the biochemical level of their metabolism. Their glycolitic pathway is simpler, with few side chains and reduced allosteric enzymatic regulation. These differences between the host and parasite metabolism make the glycolytic pathway a potential target for drugs against African sleeping disease.
</para>
<para>
Most of the glycolytic enzymes of <emphasis>Trypanosoma brucei</emphasis> have been isolated and kinetically characterised. From this experimental data in 1997, Bakker <emphasis>et al</emphasis> developed a mathematical model of trypanosomal glycolysis (see <ulink url="${HTML_EXMPL_BAKKER_MODEL}">Bakker <emphasis>et al</emphasis>, 1997</ulink> for more details). Model simulations predict how the steady-state glycolytic flux and metabolite concentrations depend on the substrate and product concentrations and the enzyme-kinetic parameters. The model explains certain aspects of cell physiology, but it does have its limitations.
</para>
<para>
Bloodstream-form trypanosomes contain 65-250 glycosomes, comprising 4 percent of the total cell volume. It is unclear why glycosomes are advantageous organelles for trypanosomes. At present, it is not possible to remove a glycosome without affecting the rest of the cell. In order to study the metabolic consequences of compartmentation, in 2000, Bakker <emphasis>et al.</emphasis>, in a follow up study to their 1997 paper, developed a mathematical model which lacked a glycosomal membrane. This model has been described here in CellML and it can be downloaded in various formats as described in <xref linkend="sec_download_this_model"/>.
</para>
<para>
Although removal of the membrane did not affect steady-state flux (which argues against the idea that glycosomes increase flux by concentrating the pathway enzymes), it did cause the following:
</para>
<itemizedlist>
<listitem>
<para>The concentration of sugar phosphates rose to unphysiological levels, which was suggested to have pathological consequences; and</para>
</listitem>
<listitem>
<para>The cells failed to recover from glucose deprivation.</para>
</listitem>
</itemizedlist>
<para>
These results were explained by the biochemical organisation of the glycosome, and the authors concluded that the glycosome protects trypanosomes from the negative side effects of the <emphasis>turbo</emphasis> structure of glycolysis; that is, ATP is consumed before it is produced. The glycosome prevents a starving cell from consuming the ATP required to reinitiate glycolysis.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.pnas.org/cgi/content/abstract/97/5/2087">Compartmentation protects trypanosomes from the dangerous design of glycolysis</ulink>, Barbara M. Bakker, Femke I.C. Mensonides, Bas Teusink, Pim van Hoek, Paul A. M. Michels, and Hans V. Westerhoff, 2000, <ulink url="http://www.pnas.org/">
<emphasis>Proceedings of the National Academy of Sciences</emphasis>
</ulink>, 97, 2087-2092. (<ulink url="http://www.pnas.org/cgi/content/full/97/5/2087">Full text</ulink> and <ulink url="http://www.pnas.org/cgi/reprint/97/5/2087.pdf">PDF versions</ulink> of the article are available to subscribers of the <emphasis>pnas</emphasis> website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10681445&dopt=Abstract">PubMed ID: 10681445</ulink>
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>A reaction diagram of glycolysis</title>
</objectinfo>
<imagedata fileref="bakker_2000.png"/>
</imageobject>
</mediaobject>
<caption>A scheme of glycolysis in the bloodstream form of the parasite <emphasis>Trypanosoma brucei</emphasis>. In the model described here, the glycosome is absent.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<!--
We start the model definition with a definition of some named
sets of units for use throughout the model.
-->
<units name="minute">
<unit units="second" multiplier="60.0"/>
</units>
<units name="micromolar">
<unit units="mole" prefix="micro"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="millimolar">
<unit units="mole" prefix="milli"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="nanomolar">
<unit units="mole" prefix="nano"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="flux">
<unit units="nanomolar"/>
<unit units="minute" exponent="-1"/>
</units>
<component name="global_variables">
<variable units="second" public_interface="out" name="time"/>
</component>
<!--
The following components describe all the reactants and products involved in
reactions.
-->
<component cmeta:id="Glc_o" name="Glc_o">
<rdf:RDF>
<rdf:Description rdf:about="Glc_o">
<dc:title>Glc_o</dc:title>
<dcterms:alternative>external glucose</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="Glc_o" initial_value="0.05"/>
</component>
<component cmeta:id="Glc_i" name="Glc_i">
<rdf:RDF>
<rdf:Description rdf:about="Glc_i">
<dc:title>Glc_i</dc:title>
<dcterms:alternative>cytosolic glucose</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Glc_i"/>
<variable units="flux" public_interface="in" name="V_HK"/>
<variable units="flux" public_interface="in" name="V_glucose_transport"/>
<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>Glc_i</ci>
</apply>
<apply>
<minus/>
<ci>V_glucose_transport</ci>
<ci>V_HK</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Glc_6_P" name="Glc_6_P">
<rdf:RDF>
<rdf:Description rdf:about="Glc_6_P">
<dc:title>Glc_6_P</dc:title>
<dcterms:alternative>glucose-6-phopshate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Glc_6_P"/>
<variable units="dimensionless" name="Keq_PGI" initial_value="0.29"/>
<variable units="micromolar" public_interface="in" name="Fru_6_P"/>
<variable units="micromolar" public_interface="in" name="hexose_P"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Glc_6_P</ci>
<apply>
<divide/>
<ci>hexose_P</ci>
<ci>Keq_PGI</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Keq_PGI</ci>
<apply>
<divide/>
<ci>Fru_6_P</ci>
<ci>Glc_6_P</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Fru_6_P" name="Fru_6_P">
<rdf:RDF>
<rdf:Description rdf:about="Fru_6_P">
<dc:title>Fru_6_P</dc:title>
<dcterms:alternative>fructose 6-phopshate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Fru_6_P"/>
<variable units="micromolar" public_interface="in" name="Glc_6_P"/>
<variable units="micromolar" public_interface="in" name="hexose_P"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Fru_6_P</ci>
<apply>
<divide/>
<ci>hexose_P</ci>
<ci>Glc_6_P</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="hexose_P" name="hexose_P">
<rdf:RDF>
<rdf:Description rdf:about="hexose_P">
<dc:title>hexose_P</dc:title>
<dcterms:alternative>total concentration of six carbon phosphates</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="hexose_P"/>
<variable units="flux" public_interface="in" name="V_HK"/>
<variable units="flux" public_interface="in" name="V_PFK"/>
<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>hexose_P</ci>
</apply>
<apply>
<minus/>
<ci>V_HK</ci>
<ci>V_PFK</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Fru_1_6_BP" name="Fru_1_6_BP">
<rdf:RDF>
<rdf:Description rdf:about="Fru_1_6_BP">
<dc:title>Fru_1_6_BP</dc:title>
<dcterms:alternative>fructose 1,6-bisphopshate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Fru_1_6_BP"/>
<variable units="flux" public_interface="in" name="V_PFK"/>
<variable units="flux" public_interface="in" name="V_ALD"/>
<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>Fru_1_6_BP</ci>
</apply>
<apply>
<minus/>
<ci>V_PFK</ci>
<ci>V_ALD</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="GA_3_P" name="GA_3_P">
<rdf:RDF>
<rdf:Description rdf:about="GA_3_P">
<dc:title>GA_3_P</dc:title>
<dcterms:alternative>glyceraldehyde 3-phopshate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="GA_3_P"/>
<variable units="dimensionless" public_interface="in" name="Keq_TIM"/>
<variable units="micromolar" public_interface="in" name="DHAP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>GA_3_P</ci>
<apply>
<times/>
<ci>Keq_TIM</ci>
<ci>DHAP</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="triose_P" name="triose_P">
<rdf:RDF>
<rdf:Description rdf:about="triose_P">
<dc:title>triose_P</dc:title>
<dcterms:alternative>total concentration of three carbon phopshates</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="triose_P"/>
<variable units="flux" public_interface="in" name="V_ALD"/>
<variable units="flux" public_interface="in" name="V_GAPDH"/>
<variable units="flux" public_interface="in" name="V_GDH"/>
<variable units="flux" public_interface="in" name="V_GPO"/>
<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>triose_P</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<cn cellml:units="dimensionless"> 2.0 </cn>
<ci>V_ALD</ci>
</apply>
<ci>V_GPO</ci>
</apply>
<apply>
<plus/>
<ci>V_GAPDH</ci>
<ci>V_GDH</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="one_three_BPGA" name="one_three_BPGA">
<rdf:RDF>
<rdf:Description rdf:about="one_three_BPGA">
<dc:title>one_three_BPGA</dc:title>
<dcterms:alternative>1,3-bisphosphoglycerate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="one_three_BPGA"/>
<variable units="flux" public_interface="in" name="V_GAPDH"/>
<variable units="flux" public_interface="in" name="V_PGK"/>
<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>one_three_BPGA</ci>
</apply>
<apply>
<minus/>
<ci>V_GAPDH</ci>
<ci>V_PGK</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="three_PGA" name="three_PGA">
<rdf:RDF>
<rdf:Description rdf:about="three_PGA">
<dc:title>three_PGA</dc:title>
<dcterms:alternative>3-phosphoglycerate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="three_PGA"/>
<variable units="micromolar" public_interface="in" name="N"/>
<variable units="dimensionless" public_interface="out" name="Keq_PGM" initial_value="0.187"/>
<variable units="dimensionless" public_interface="out" name="Keq_ENO" initial_value="6.7"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>three_PGA</ci>
<apply>
<divide/>
<ci>N</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci>Keq_PGM</ci>
<apply>
<times/>
<ci>Keq_PGM</ci>
<ci>Keq_ENO</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="two_PGA" name="two_PGA">
<rdf:RDF>
<rdf:Description rdf:about="two_PGA">
<dc:title>two_PGA</dc:title>
<dcterms:alternative>2-phosphoglycerate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="two_PGA"/>
<variable units="micromolar" public_interface="in" name="three_PGA"/>
<variable units="dimensionless" public_interface="in" name="Keq_PGM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>two_PGA</ci>
<apply>
<times/>
<ci>Keq_PGM</ci>
<ci>three_PGA</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="N" name="N">
<rdf:RDF>
<rdf:Description rdf:about="N">
<dc:title>N</dc:title>
<dcterms:alternative>the sum of 3-phosphoglycerate, 2-phosphoglycerate, and phosphoenolpyruvate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="N"/>
<variable units="flux" public_interface="in" name="V_PGK"/>
<variable units="flux" public_interface="in" name="V_PYK"/>
<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>N</ci>
</apply>
<apply>
<minus/>
<ci>V_PGK</ci>
<ci>V_PYK</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="PEP" name="PEP">
<rdf:RDF>
<rdf:Description rdf:about="PEP">
<dc:title>PEP</dc:title>
<dcterms:alternative>phosphoenolpyruvate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="PEP"/>
<variable units="micromolar" public_interface="in" name="two_PGA"/>
<variable units="dimensionless" public_interface="in" name="Keq_ENO"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>PEP</ci>
<apply>
<times/>
<ci>Keq_ENO</ci>
<ci>two_PGA</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="pyruvate_i" name="pyruvate_i">
<rdf:RDF>
<rdf:Description rdf:about="pyruvate_i">
<dc:title>pyruvate_i</dc:title>
<dcterms:alternative>cytosolic pyruvate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="pyruvate_i"/>
<variable units="flux" public_interface="in" name="V_PYK"/>
<variable units="flux" public_interface="in" name="V_pyruvate_transport"/>
<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>pyruvate_i</ci>
</apply>
<apply>
<minus/>
<ci>V_PYK</ci>
<ci>V_pyruvate_transport</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="pyruvate_o" name="pyruvate_o">
<rdf:RDF>
<rdf:Description rdf:about="pyruvate_o">
<dc:title>pyruvate_o</dc:title>
<dcterms:alternative>extracellular pyruvate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="pyruvate_o"/>
</component>
<component name="glycerol">
<variable units="micromolar" public_interface="out" name="glycerol"/>
</component>
<component cmeta:id="DHAP" name="DHAP">
<rdf:RDF>
<rdf:Description rdf:about="DHAP">
<dc:title>DHAP</dc:title>
<dcterms:alternative>dihydroxyacetone phosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="DHAP"/>
<variable units="micromolar" public_interface="in" name="triose_P"/>
<variable units="dimensionless" public_interface="out" name="Keq_TIM" initial_value="0.045"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>DHAP</ci>
<apply>
<divide/>
<ci>triose_P</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<ci>Keq_TIM</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="Gly_3_P" name="Gly_3_P">
<rdf:RDF>
<rdf:Description rdf:about="Gly_3_P">
<dc:title>Gly_3_P</dc:title>
<dcterms:alternative>glyceraldehyde 3-phopshate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Gly_3_P"/>
<variable units="flux" public_interface="in" name="V_GDH"/>
<variable units="flux" public_interface="in" name="V_GK"/>
<variable units="flux" public_interface="in" name="V_GPO"/>
<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>Gly_3_P</ci>
</apply>
<apply>
<minus/>
<ci>V_GDH</ci>
<apply>
<plus/>
<ci>V_GK</ci>
<ci>V_GPO</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="H2O" name="H2O">
<rdf:RDF>
<rdf:Description rdf:about="H2O">
<dc:title>H2O</dc:title>
<dcterms:alternative>water</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="H2O"/>
</component>
<component cmeta:id="O2" name="O2">
<rdf:RDF>
<rdf:Description rdf:about="O2">
<dc:title>O2</dc:title>
<dcterms:alternative>oxygen</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="O2"/>
</component>
<component cmeta:id="NAD" name="NAD">
<rdf:RDF>
<rdf:Description rdf:about="NAD">
<dc:title>NAD</dc:title>
<dcterms:alternative>nicotinamide adenine dinucleotide positive</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="NAD"/>
<variable units="micromolar" public_interface="in" name="NADH"/>
<variable units="micromolar" public_interface="in" name="C7"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>NAD</ci>
<apply>
<minus/>
<ci>C7</ci>
<ci>NADH</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="NADH" name="NADH">
<rdf:RDF>
<rdf:Description rdf:about="NADH">
<dc:title>NADH</dc:title>
<dcterms:alternative>nicotinamide adenine dinucleotide</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="NADH"/>
<variable units="flux" public_interface="in" name="V_GAPDH"/>
<variable units="flux" public_interface="in" name="V_GDH"/>
<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>NADH</ci>
</apply>
<apply>
<minus/>
<ci>V_GAPDH</ci>
<ci>V_GDH</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="P" name="P">
<rdf:RDF>
<rdf:Description rdf:about="P">
<dc:title>P</dc:title>
<dcterms:alternative>total concentration of adenosine phosphates</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="P"/>
<variable units="flux" public_interface="in" name="V_HK"/>
<variable units="flux" public_interface="in" name="V_PGK"/>
<variable units="flux" public_interface="in" name="V_PFK"/>
<variable units="flux" public_interface="in" name="V_GK"/>
<variable units="flux" public_interface="in" name="V_PYK"/>
<variable units="flux" public_interface="in" name="V_ATP_utilisation"/>
<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>P</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>V_PGK</ci>
<ci>V_GK</ci>
<ci>V_PYK</ci>
</apply>
<apply>
<plus/>
<ci>V_HK</ci>
<ci>V_PFK</ci>
<ci>V_ATP_utilisation</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="ATP" name="ATP">
<rdf:RDF>
<rdf:Description rdf:about="ATP">
<dc:title>ATP</dc:title>
<dcterms:alternative>adenosine triphosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="ATP"/>
<variable units="micromolar" public_interface="out" name="P"/>
<variable units="dimensionless" name="Keq_AK" initial_value="0.442"/>
<variable units="micromolar" public_interface="in" name="C6"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>ATP</ci>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<minus/>
<ci>C6</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>P</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<ci>Keq_AK</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<power/>
<apply>
<minus/>
<apply>
<power/>
<apply>
<minus/>
<ci>C6</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>P</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<ci>Keq_AK</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
<apply>
<times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<apply>
<minus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<ci>Keq_AK</ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<minus/>
<ci>Keq_AK</ci>
</apply>
<apply>
<power/>
<ci>P</ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
</apply>
</apply>
</apply>
<cn cellml:units="dimensionless"> 0.5 </cn>
</apply>
</apply>
<apply>
<times/>
<cn cellml:units="dimensionless"> 2.0 </cn>
<apply>
<minus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<times/>
<cn cellml:units="dimensionless"> 4.0 </cn>
<ci>Keq_AK</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="ADP" name="ADP">
<rdf:RDF>
<rdf:Description rdf:about="ADP">
<dc:title>ADP</dc:title>
<dcterms:alternative>adenosine diphosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="ADP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" public_interface="in" name="P"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>ADP</ci>
<apply>
<minus/>
<ci>P</ci>
<apply>
<times/>
<cn cellml:units="dimensionless"> 2.0 </cn>
<ci>ATP</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="AMP" name="AMP">
<rdf:RDF>
<rdf:Description rdf:about="AMP">
<dc:title>AMP</dc:title>
<dcterms:alternative>adenosine monophosphate</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="millimolar" public_interface="out" name="AMP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="C6"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>AMP</ci>
<apply>
<minus/>
<ci>C6</ci>
<apply>
<plus/>
<ci>ATP</ci>
<ci>ADP</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="C6">
<variable units="millimolar" public_interface="out" name="C6" initial_value="4.0"/>
<variable units="millimolar" public_interface="in" name="AMP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>C6</ci>
<apply>
<plus/>
<ci>ATP</ci>
<ci>ADP</ci>
<ci>AMP</ci>
</apply>
</apply>
</math>
</component>
<component name="C7">
<variable units="millimolar" public_interface="out" name="C7" initial_value="4.0"/>
<variable units="millimolar" public_interface="in" name="NAD"/>
<variable units="millimolar" public_interface="in" name="NADH"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>C7</ci>
<apply>
<plus/>
<ci>NADH</ci>
<ci>NAD</ci>
</apply>
</apply>
</math>
</component>
<!--
The following components describe the reactions of the model.
-->
<component name="V_glucose_transport">
<variable units="flux" public_interface="out" name="V_glucose_transport"/>
<variable units="millimolar" public_interface="in" name="Glc_o"/>
<variable units="millimolar" public_interface="in" name="Glc_i"/>
<variable units="millimolar" name="K_Glc" initial_value="2.0"/>
<variable units="dimensionless" name="alpha" initial_value="0.75"/>
<variable units="flux" name="V_glucose_transport_max" initial_value="106.2"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_glucose_transport_calculation">
<eq/>
<ci> V_glucose_transport </ci>
<apply>
<times/>
<ci> V_glucose_transport_max </ci>
<apply>
<divide/>
<apply>
<minus/>
<ci> Glc_o </ci>
<ci> Glc_i </ci>
</apply>
<apply>
<plus/>
<ci> K_Glc </ci>
<ci> Glc_o </ci>
<ci> Glc_i </ci>
<apply>
<times/>
<ci> alpha </ci>
<ci> Glc_o </ci>
<apply>
<divide/>
<ci> Glc_i </ci>
<ci> K_Glc </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_pyruvate_transport">
<variable units="flux" public_interface="out" name="V_pyruvate_transport"/>
<variable units="millimolar" public_interface="in" name="pyruvate_i"/>
<variable units="millimolar" name="K_pyruvate" initial_value="1.96"/>
<variable units="flux" name="V_pyruvate_transport_max" initial_value="200.0"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_pyruvate_transport_calculation">
<eq/>
<ci> V_pyruvate_transport </ci>
<apply>
<times/>
<ci> V_pyruvate_transport_max </ci>
<apply>
<divide/>
<ci> pyruvate_i </ci>
<ci> K_pyruvate </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> pyruvate_i </ci>
<ci> K_pyruvate </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_GPO">
<variable units="flux" public_interface="out" name="V_GPO"/>
<variable units="millimolar" public_interface="in" name="Gly_3_P"/>
<variable units="millimolar" name="K_Gly_3_P" initial_value="1.7"/>
<variable units="flux" name="V_GPO_max" initial_value="200.0"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_GPO_calculation">
<eq/>
<ci> V_GPO </ci>
<apply>
<times/>
<ci> V_GPO_max </ci>
<apply>
<divide/>
<ci> Gly_3_P </ci>
<ci> K_Gly_3_P </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> Gly_3_P </ci>
<ci> K_Gly_3_P </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_HK">
<variable units="flux" public_interface="out" name="V_HK"/>
<variable units="millimolar" public_interface="in" name="Glc_i"/>
<variable units="millimolar" public_interface="in" name="Glc_6_P"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" name="K_Glc_i" initial_value="0.1"/>
<variable units="millimolar" name="K_Glc_6_P" initial_value="12.0"/>
<variable units="millimolar" name="K_ATP" initial_value="0.116"/>
<variable units="millimolar" name="K_ADP" initial_value="0.126"/>
<variable units="flux" name="V_HK_max" initial_value="625.0"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_HK_calculation">
<eq/>
<ci> V_HK </ci>
<apply>
<times/>
<ci> V_HK_max </ci>
<apply>
<divide/>
<apply>
<divide/>
<ci> Glc_i </ci>
<ci> K_Glc_i </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> Glc_i </ci>
<ci> K_Glc_i </ci>
</apply>
<apply>
<divide/>
<ci> Glc_6_P </ci>
<ci> K_Glc_6_P </ci>
</apply>
</apply>
</apply>
<apply>
<divide/>
<apply>
<divide/>
<ci> ATP </ci>
<ci> K_ATP </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> ATP </ci>
<ci> K_ATP </ci>
</apply>
<apply>
<divide/>
<ci> ADP </ci>
<ci> K_ADP </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_GAPDH">
<variable units="flux" public_interface="out" name="V_GAPDH"/>
<variable units="millimolar" public_interface="in" name="NAD"/>
<variable units="millimolar" public_interface="in" name="GA_3_P"/>
<variable units="millimolar" public_interface="in" name="one_three_BPGA"/>
<variable units="millimolar" public_interface="in" name="NADH"/>
<variable units="millimolar" name="K_NAD" initial_value="0.45"/>
<variable units="millimolar" name="K_GA_3_P" initial_value="0.15"/>
<variable units="millimolar" name="K_one_three_BPGA" initial_value="0.1"/>
<variable units="millimolar" name="K_NADH" initial_value="0.02"/>
<variable units="flux" name="V_GAPDH_max_plus" initial_value="1470.0"/>
<variable units="dimensionless" name="V_GAPDH_max_ratio" initial_value="0.67"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_GAPDH_calculation">
<eq/>
<ci> V_GAPDH </ci>
<apply>
<times/>
<ci> V_GAPDH_max_plus </ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<ci> GA_3_P </ci>
<ci> K_GA_3_P </ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<ci> NAD </ci>
<ci> K_NAD </ci>
</apply>
<ci> V_GAPDH_max_ratio </ci>
</apply>
<apply>
<divide/>
<ci> one_three_BPGA </ci>
<ci> K_one_three_BPGA </ci>
</apply>
<apply>
<divide/>
<ci> NADH </ci>
<ci> K_NADH </ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> GA_3_P </ci>
<ci> K_GA_3_P </ci>
</apply>
<apply>
<divide/>
<ci> one_three_BPGA </ci>
<ci> K_one_three_BPGA </ci>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> NAD </ci>
<ci> K_NAD </ci>
</apply>
<apply>
<divide/>
<ci> NADH </ci>
<ci> K_NADH </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_PGK">
<variable units="flux" public_interface="out" name="V_PGK"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="one_three_BPGA"/>
<variable units="millimolar" public_interface="in" name="three_PGA"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" name="K_ADP" initial_value="0.1"/>
<variable units="millimolar" name="K_one_three_BPGA" initial_value="0.05"/>
<variable units="millimolar" name="K_3_PGA" initial_value="1.62"/>
<variable units="millimolar" name="K_ATP" initial_value="0.29"/>
<variable units="flux" name="V_PGK_max_plus" initial_value="640.0"/>
<variable units="dimensionless" name="V_PGK_max_ratio" initial_value="0.029"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_PGK_calculation">
<eq/>
<ci> V_PGK </ci>
<apply>
<times/>
<ci> V_PGK_max_plus </ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<ci> one_three_BPGA </ci>
<ci> K_one_three_BPGA </ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<ci> ADP </ci>
<ci> K_ADP </ci>
</apply>
<ci> V_PGK_max_ratio </ci>
</apply>
<apply>
<divide/>
<ci> three_PGA </ci>
<ci> K_3_PGA </ci>
</apply>
<apply>
<divide/>
<ci> ATP </ci>
<ci> K_ATP </ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> one_three_BPGA </ci>
<ci> K_one_three_BPGA </ci>
</apply>
<apply>
<divide/>
<ci> three_PGA </ci>
<ci> K_3_PGA </ci>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> ADP </ci>
<ci> K_ADP </ci>
</apply>
<apply>
<divide/>
<ci> ATP </ci>
<ci> K_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_GK">
<variable units="flux" public_interface="out" name="V_GK"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="Gly_3_P"/>
<variable units="millimolar" public_interface="in" name="glycerol"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" name="K_ADP" initial_value="0.12"/>
<variable units="millimolar" name="K_Gly_3_P" initial_value="5.1"/>
<variable units="millimolar" name="K_glycerol" initial_value="0.12"/>
<variable units="millimolar" name="K_ATP" initial_value="0.19"/>
<variable units="flux" name="V_GK_max_plus" initial_value="0.0"/>
<variable units="dimensionless" name="V_GK_max_ratio" initial_value="167.0"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_GK_calculation">
<eq/>
<ci> V_GK </ci>
<apply>
<times/>
<ci> V_GK_max_plus </ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<ci> Gly_3_P </ci>
<ci> K_Gly_3_P </ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<ci> ADP </ci>
<ci> K_ADP </ci>
</apply>
<ci> V_GK_max_ratio </ci>
</apply>
<apply>
<divide/>
<ci> glycerol </ci>
<ci> K_glycerol </ci>
</apply>
<apply>
<divide/>
<ci> ATP </ci>
<ci> K_ATP </ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> Gly_3_P </ci>
<ci> K_Gly_3_P </ci>
</apply>
<apply>
<divide/>
<ci> glycerol </ci>
<ci> K_glycerol </ci>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> ADP </ci>
<ci> K_ADP </ci>
</apply>
<apply>
<divide/>
<ci> ATP </ci>
<ci> K_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_GDH">
<variable units="flux" public_interface="out" name="V_GDH"/>
<variable units="millimolar" public_interface="in" name="NADH"/>
<variable units="millimolar" public_interface="in" name="Gly_3_P"/>
<variable units="millimolar" public_interface="in" name="DHAP"/>
<variable units="millimolar" public_interface="in" name="NAD"/>
<variable units="millimolar" name="K_NADH" initial_value="0.01"/>
<variable units="millimolar" name="K_Gly_3_P" initial_value="2.0"/>
<variable units="millimolar" name="K_DHAP" initial_value="0.1"/>
<variable units="millimolar" name="K_NAD" initial_value="0.4"/>
<variable units="flux" name="V_GDH_max_plus" initial_value="533.0"/>
<variable units="dimensionless" name="V_GDH_max_ratio" initial_value="0.28"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_GDH_calculation">
<eq/>
<ci> V_GDH </ci>
<apply>
<times/>
<ci> V_GDH_max_plus </ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<ci> DHAP </ci>
<ci> K_DHAP </ci>
</apply>
<apply>
<minus/>
<apply>
<divide/>
<ci> NADH </ci>
<ci> K_NADH </ci>
</apply>
<ci> V_GDH_max_ratio </ci>
</apply>
<apply>
<divide/>
<ci> Gly_3_P </ci>
<ci> K_Gly_3_P </ci>
</apply>
<apply>
<divide/>
<ci> NAD </ci>
<ci> K_NAD </ci>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> DHAP </ci>
<ci> K_DHAP </ci>
</apply>
<apply>
<divide/>
<ci> Gly_3_P </ci>
<ci> K_Gly_3_P </ci>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> NADH </ci>
<ci> K_NADH </ci>
</apply>
<apply>
<divide/>
<ci> NAD </ci>
<ci> K_NAD </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_PFK">
<variable units="flux" public_interface="out" name="V_PFK"/>
<variable units="millimolar" public_interface="in" name="Fru_6_P"/>
<variable units="millimolar" public_interface="in" name="Fru_1_6_BP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" name="Ki_1" initial_value="15.8"/>
<variable units="millimolar" name="Ki_2" initial_value="10.7"/>
<variable units="millimolar" name="KM_Fru_6_P" initial_value="0.82"/>
<variable units="millimolar" name="KM_ATP" initial_value="2.6E-2"/>
<variable units="flux" name="V_PFK_max" initial_value="780.0"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_PFK_calculation">
<eq/>
<ci> V_PFK </ci>
<apply>
<times/>
<ci> V_PFK_max </ci>
<apply>
<divide/>
<ci> Ki_1 </ci>
<apply>
<plus/>
<ci> Fru_1_6_BP </ci>
<ci> Ki_1 </ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<divide/>
<ci> Fru_6_P </ci>
<ci> KM_Fru_6_P </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> Fru_6_P </ci>
<ci> KM_Fru_6_P </ci>
</apply>
<apply>
<divide/>
<ci> Fru_1_6_BP </ci>
<ci> Ki_2 </ci>
</apply>
</apply>
</apply>
<apply>
<divide/>
<apply>
<divide/>
<ci> ATP </ci>
<ci> KM_ATP </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> ATP </ci>
<ci> KM_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_PYK">
<variable units="flux" public_interface="out" name="V_PYK"/>
<variable units="millimolar" public_interface="in" name="PEP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" name="KM_PEP"/>
<variable units="millimolar" name="KM_ADP" initial_value="0.114"/>
<variable units="dimensionless" name="n" initial_value="2.5"/>
<variable units="flux" name="V_PYK_max" initial_value="2.6E3"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_PYK_calculation">
<eq/>
<ci> V_PYK </ci>
<apply>
<times/>
<ci> V_PYK_max </ci>
<apply>
<divide/>
<apply>
<power/>
<apply>
<divide/>
<ci> PEP </ci>
<ci> KM_PEP </ci>
</apply>
<ci> n </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> PEP </ci>
<ci> KM_PEP </ci>
</apply>
<ci> n </ci>
</apply>
</apply>
</apply>
<apply>
<divide/>
<apply>
<divide/>
<ci> ADP </ci>
<ci> KM_ADP </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> ADP </ci>
<ci> KM_ADP </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply id="KM_PEP_calculation">
<eq/>
<ci> KM_PEP </ci>
<apply>
<times/>
<cn cellml:units="millimolar"> 0.34 </cn>
<apply>
<plus/>
<cn cellml:units="millimolar"> 1.0 </cn>
<apply>
<divide/>
<ci> ATP </ci>
<cn cellml:units="millimolar"> 0.57 </cn>
</apply>
<apply>
<divide/>
<ci> ADP </ci>
<cn cellml:units="millimolar"> 0.64 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_ALD">
<variable units="flux" public_interface="out" name="V_ALD"/>
<variable units="millimolar" public_interface="in" name="Fru_1_6_BP"/>
<variable units="millimolar" public_interface="in" name="GA_3_P"/>
<variable units="millimolar" public_interface="in" name="DHAP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="AMP"/>
<variable units="millimolar" name="KM_Fru_1_6_BP"/>
<variable units="millimolar" name="KM_GA_3_P" initial_value="6.7E-2"/>
<variable units="millimolar" name="Ki_GA_3_P" initial_value="9.8E-2"/>
<variable units="millimolar" name="KM_DHAP" initial_value="1.5E-2"/>
<variable units="flux" name="V_ALD_max_plus" initial_value="780.0"/>
<variable units="dimensionless" name="V_ALD_max_ratio" initial_value="1.19"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_ALD_calculation">
<eq/>
<ci> V_ALD </ci>
<apply>
<times/>
<ci> V_ALD_max_plus </ci>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<divide/>
<ci> Fru_1_6_BP </ci>
<ci> KM_Fru_1_6_BP </ci>
</apply>
<apply>
<times/>
<ci> V_ALD_max_ratio </ci>
<apply>
<divide/>
<ci> GA_3_P </ci>
<ci> DHAP </ci>
</apply>
<apply>
<times/>
<ci> KM_GA_3_P </ci>
<ci> KM_DHAP </ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> Fru_1_6_BP </ci>
<ci> KM_Fru_1_6_BP </ci>
</apply>
<apply>
<divide/>
<ci> GA_3_P </ci>
<ci> KM_GA_3_P </ci>
</apply>
<apply>
<divide/>
<ci> DHAP </ci>
<ci> KM_DHAP </ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci> Fru_1_6_BP </ci>
<ci> GA_3_P </ci>
</apply>
<apply>
<times/>
<ci> KM_Fru_1_6_BP </ci>
<ci> Ki_GA_3_P </ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci> DHAP </ci>
<ci> GA_3_P </ci>
</apply>
<apply>
<times/>
<ci> KM_DHAP </ci>
<ci> KM_GA_3_P </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply id="KM_Fru_1_6_BP_calculation">
<eq/>
<ci> KM_Fru_1_6_BP </ci>
<apply>
<times/>
<cn cellml:units="millimolar"> 9.0E-3 </cn>
<apply>
<plus/>
<cn cellml:units="millimolar"> 1.0 </cn>
<apply>
<divide/>
<ci> ATP </ci>
<cn cellml:units="millimolar"> 0.68 </cn>
</apply>
<apply>
<divide/>
<ci> ADP </ci>
<cn cellml:units="millimolar"> 1.51 </cn>
</apply>
<apply>
<divide/>
<ci> AMP </ci>
<cn cellml:units="millimolar"> 3.65 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_ATP_utilisation">
<variable units="flux" public_interface="out" name="V_ATP_utilisation"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="flux" name="k" initial_value="50"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_ATP_utilisation_calculation">
<eq/>
<ci> V_ATP_utilisation </ci>
<apply>
<times/>
<ci> k </ci>
<apply>
<divide/>
<ci> ATP </ci>
<ci> ADP </ci>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_2="V_glucose_transport" component_1="Glc_o"/>
<map_variables variable_2="Glc_o" variable_1="Glc_o"/>
</connection>
<connection>
<map_components component_2="V_glucose_transport" component_1="Glc_i"/>
<map_variables variable_2="Glc_i" variable_1="Glc_i"/>
<map_variables variable_2="V_glucose_transport" variable_1="V_glucose_transport"/>
</connection>
<connection>
<map_components component_2="V_HK" component_1="Glc_i"/>
<map_variables variable_2="Glc_i" variable_1="Glc_i"/>
<map_variables variable_2="V_HK" variable_1="V_HK"/>
</connection>
<connection>
<map_components component_2="V_HK" component_1="Glc_6_P"/>
<map_variables variable_2="Glc_6_P" variable_1="Glc_6_P"/>
</connection>
<connection>
<map_components component_2="V_HK" component_1="hexose_P"/>
<map_variables variable_2="V_HK" variable_1="V_HK"/>
</connection>
<connection>
<map_components component_2="V_PFK" component_1="Fru_6_P"/>
<map_variables variable_2="Fru_6_P" variable_1="Fru_6_P"/>
</connection>
<connection>
<map_components component_2="V_PFK" component_1="hexose_P"/>
<map_variables variable_2="V_PFK" variable_1="V_PFK"/>
</connection>
<connection>
<map_components component_2="V_PFK" component_1="Fru_1_6_BP"/>
<map_variables variable_2="Fru_1_6_BP" variable_1="Fru_1_6_BP"/>
<map_variables variable_2="V_PFK" variable_1="V_PFK"/>
</connection>
<connection>
<map_components component_2="V_ALD" component_1="Fru_1_6_BP"/>
<map_variables variable_2="Fru_1_6_BP" variable_1="Fru_1_6_BP"/>
<map_variables variable_2="V_ALD" variable_1="V_ALD"/>
</connection>
<connection>
<map_components component_2="V_ALD" component_1="DHAP"/>
<map_variables variable_2="DHAP" variable_1="DHAP"/>
</connection>
<connection>
<map_components component_2="V_GDH" component_1="DHAP"/>
<map_variables variable_2="DHAP" variable_1="DHAP"/>
</connection>
<connection>
<map_components component_2="V_ALD" component_1="triose_P"/>
<map_variables variable_2="V_ALD" variable_1="V_ALD"/>
</connection>
<connection>
<map_components component_2="V_GAPDH" component_1="triose_P"/>
<map_variables variable_2="V_GAPDH" variable_1="V_GAPDH"/>
</connection>
<connection>
<map_components component_2="V_GDH" component_1="triose_P"/>
<map_variables variable_2="V_GDH" variable_1="V_GDH"/>
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<connection>
<map_components component_2="V_GPO" component_1="triose_P"/>
<map_variables variable_2="V_GPO" variable_1="V_GPO"/>
</connection>
<connection>
<map_components component_2="V_ALD" component_1="GA_3_P"/>
<map_variables variable_2="GA_3_P" variable_1="GA_3_P"/>
</connection>
<connection>
<map_components component_2="V_GAPDH" component_1="GA_3_P"/>
<map_variables variable_2="GA_3_P" variable_1="GA_3_P"/>
</connection>
<connection>
<map_components component_2="V_GDH" component_1="Gly_3_P"/>
<map_variables variable_2="Gly_3_P" variable_1="Gly_3_P"/>
<map_variables variable_2="V_GDH" variable_1="V_GDH"/>
</connection>
<connection>
<map_components component_2="V_GK" component_1="Gly_3_P"/>
<map_variables variable_2="Gly_3_P" variable_1="Gly_3_P"/>
<map_variables variable_2="V_GK" variable_1="V_GK"/>
</connection>
<connection>
<map_components component_2="V_GAPDH" component_1="one_three_BPGA"/>
<map_variables variable_2="one_three_BPGA" variable_1="one_three_BPGA"/>
<map_variables variable_2="V_GAPDH" variable_1="V_GAPDH"/>
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<connection>
<map_components component_2="V_PGK" component_1="one_three_BPGA"/>
<map_variables variable_2="one_three_BPGA" variable_1="one_three_BPGA"/>
<map_variables variable_2="V_PGK" variable_1="V_PGK"/>
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<connection>
<map_components component_2="V_PYK" component_1="PEP"/>
<map_variables variable_2="PEP" variable_1="PEP"/>
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<connection>
<map_components component_2="V_PGK" component_1="N"/>
<map_variables variable_2="V_PGK" variable_1="V_PGK"/>
</connection>
<connection>
<map_components component_2="V_PYK" component_1="N"/>
<map_variables variable_2="V_PYK" variable_1="V_PYK"/>
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<connection>
<map_components component_2="V_PYK" component_1="pyruvate_i"/>
<map_variables variable_2="V_PYK" variable_1="V_PYK"/>
</connection>
<connection>
<map_components component_2="V_pyruvate_transport" component_1="pyruvate_i"/>
<map_variables variable_2="pyruvate_i" variable_1="pyruvate_i"/>
<map_variables variable_2="V_pyruvate_transport" variable_1="V_pyruvate_transport"/>
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<connection>
<map_components component_2="V_HK" component_1="P"/>
<map_variables variable_2="V_HK" variable_1="V_HK"/>
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<connection>
<map_components component_2="V_PFK" component_1="P"/>
<map_variables variable_2="V_PFK" variable_1="V_PFK"/>
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<connection>
<map_components component_2="V_PGK" component_1="P"/>
<map_variables variable_2="V_PGK" variable_1="V_PGK"/>
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<connection>
<map_components component_2="V_GK" component_1="P"/>
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<connection>
<map_components component_2="V_PYK" component_1="P"/>
<map_variables variable_2="V_PYK" variable_1="V_PYK"/>
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<connection>
<map_components component_2="V_ATP_utilisation" component_1="P"/>
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<connection>
<map_components component_2="global_variables" component_1="Glc_i"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="Glc_6_P"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="Fru_6_P"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="Fru_1_6_BP"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="DHAP"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="Gly_3_P"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="one_three_BPGA"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="pyruvate_i"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="NADH"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="hexose_P"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="triose_P"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="N"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="global_variables" component_1="P"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="Glc_6_P" component_1="Fru_6_P"/>
<map_variables variable_2="Fru_6_P" variable_1="Fru_6_P"/>
<map_variables variable_2="Glc_6_P" variable_1="Glc_6_P"/>
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<connection>
<map_components component_2="Glc_6_P" component_1="hexose_P"/>
<map_variables variable_2="hexose_P" variable_1="hexose_P"/>
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<connection>
<map_components component_2="Fru_6_P" component_1="hexose_P"/>
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<connection>
<map_components component_2="DHAP" component_1="GA_3_P"/>
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<map_variables variable_2="DHAP" variable_1="DHAP"/>
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<connection>
<map_components component_2="three_PGA" component_1="N"/>
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<connection>
<map_components component_2="two_PGA" component_1="three_PGA"/>
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<map_variables variable_2="Keq_PGM" variable_1="Keq_PGM"/>
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<connection>
<map_components component_2="PEP" component_1="two_PGA"/>
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<connection>
<map_components component_2="PEP" component_1="three_PGA"/>
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<connection>
<map_components component_2="DHAP" component_1="triose_P"/>
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<map_components component_2="V_GPO" component_1="Gly_3_P"/>
<map_variables variable_2="V_GPO" variable_1="V_GPO"/>
<map_variables variable_2="Gly_3_P" variable_1="Gly_3_P"/>
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<connection>
<map_components component_2="NADH" component_1="NAD"/>
<map_variables variable_2="NADH" variable_1="NADH"/>
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<connection>
<map_components component_2="C7" component_1="NAD"/>
<map_variables variable_2="C7" variable_1="C7"/>
<map_variables variable_2="NAD" variable_1="NAD"/>
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<connection>
<map_components component_2="C7" component_1="NADH"/>
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<connection>
<map_components component_2="V_GAPDH" component_1="NADH"/>
<map_variables variable_2="V_GAPDH" variable_1="V_GAPDH"/>
<map_variables variable_2="NADH" variable_1="NADH"/>
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<connection>
<map_components component_2="V_GDH" component_1="NADH"/>
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<map_variables variable_2="NADH" variable_1="NADH"/>
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<connection>
<map_components component_2="C6" component_1="ATP"/>
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<map_variables variable_2="ATP" variable_1="ATP"/>
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<connection>
<map_components component_2="ADP" component_1="ATP"/>
<map_variables variable_2="ATP" variable_1="ATP"/>
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<connection>
<map_components component_2="ADP" component_1="P"/>
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<connection>
<map_components component_2="AMP" component_1="ATP"/>
<map_variables variable_2="ATP" variable_1="ATP"/>
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<connection>
<map_components component_2="AMP" component_1="ADP"/>
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<connection>
<map_components component_2="C6" component_1="AMP"/>
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<map_components component_2="V_HK" component_1="ATP"/>
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<connection>
<map_components component_2="V_GK" component_1="ATP"/>
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<connection>
<map_components component_2="V_PYK" component_1="ATP"/>
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<connection>
<map_components component_2="V_ALD" component_1="ATP"/>
<map_variables variable_2="ATP" variable_1="ATP"/>
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<map_components component_2="V_ATP_utilisation" component_1="ATP"/>
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<map_components component_2="V_ATP_utilisation" component_1="ADP"/>
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<map_components component_2="V_HK" component_1="ADP"/>
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<map_components component_2="V_ALD" component_1="AMP"/>
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<map_components component_2="V_GK" component_1="ADP"/>
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<connection>
<map_components component_2="V_PYK" component_1="ADP"/>
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<map_components component_2="V_PGK" component_1="ATP"/>
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<connection>
<map_components component_2="V_PFK" component_1="ATP"/>
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<map_components component_2="V_GAPDH" component_1="NAD"/>
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<map_components component_2="V_PGK" component_1="three_PGA"/>
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<connection>
<map_components component_2="V_GDH" component_1="NAD"/>
<map_variables variable_2="NAD" variable_1="NAD"/>
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Compartmentation protects trypanosomes from the dangerous design of
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Bakker et al's 2000 mathematical model of glycolysis in the parasite
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