<?xml version="1.0" encoding="utf-8"?>
<!--
 | @file    me.xml
 | @author  Emmet Caulfield
 | @brief   Validated SBML model for decay dimerization model.
 | @version 0.3
 |
 | This is an initial attempt at describing the reaction in 
 | H. Li and L. Petzold, "Efficient Parallelization of 
 | Stochastic Simulation Algorithm for Chemically Reacting 
 | Systems on the Graphics Processing Unit", Example 4.1. 
 |
 | $Id$
-->
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
  <annotation>
    <svn:subversion xmlns:svn="http://svnbook.red-bean.com/en/1.4/svn.advanced.props.special.keywords.html">
      <svn:Rev>$Rev$</svn:Rev>
      <svn:Id>$Id$</svn:Id>
    </svn:subversion>
    <k:provenance xmlns:k="http://polacksbacken.net/wiki/SSACBE" xmlns:s="http://www.sbml.org/sbml/level2/version3" xmlns:m="http://www.w3.org/1998/Math/MathML">
      <k:via>DecayDimerization-</k:via>
    </k:provenance>
  </annotation>
  <model name="DecayDimerization">
    <listOfCompartments>
      <compartment id="cell" size="1"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="S1" name="Species 1" initialAmount="10000" compartment="cell"/>
      <species id="S2" name="Species 2" initialAmount="0" compartment="cell"/>
      <species id="S3" name="Species 3" initialAmount="0" compartment="cell"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="c1" value="1.0"/>
      <!-- c2p = c2/2 -->
      <parameter id="c2p" value="0.001"/>
      <parameter id="c3" value="0.5"/>
      <parameter id="c4" value="0.04"/>
    </listOfParameters>
    <s:listOfReactions xmlns:s="http://www.sbml.org/sbml/level2/version3" xmlns:m="http://www.w3.org/1998/Math/MathML" xmlns:k="http://polacksbacken.net/wiki/SSACBE">
      <reaction id="R2" reversible="false">
        <listOfReactants>
          <speciesReference species="S1"/>
          <speciesReference species="S1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S2"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci>c2p</ci>
              <ci>S1</ci>
              <apply>
                <minus/>
                <ci>S1</ci>
                <cn type="integer">1</cn>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R3" reversible="false">
        <listOfReactants>
          <speciesReference species="S2"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S1"/>
          <speciesReference species="S1"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci>c3</ci>
              <ci>S2</ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R1" reversible="false">
        <listOfReactants>
          <speciesReference species="S1"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci>c1</ci>
              <ci>S1</ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="SynthS3" reversible="false">
        <listOfReactants>
          <speciesReference species="S2"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S3"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci>c4</ci>
              <ci>S2</ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </s:listOfReactions>
  </model>
</sbml>
