Location: BondGraph Basic @ 72c47d6a1652 / BG Tutorial Biochemical Systems / Biochemical 1.cellml
- Author:
- Soroush Safaei <ssaf006@aucklanduni.ac.nz>
- Date:
- 2017-10-24 21:23:07+13:00
- Desc:
- Merge remote-tracking branch 'origin/master'
- Permanent Source URI:
- https://models.fieldml.org/workspace/43b/rawfile/72c47d6a1652b471e8099a43052408d2a962c783/BG Tutorial Biochemical Systems/Biochemical 1.cellml
<?xml version='1.0'?>
<model name="Biochemical1" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="Units.cellml">
<units name="per_mol" units_ref="per_mol"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="J_per_mol_K" units_ref="J_per_mol_K"/>
<units name="mol_per_s" units_ref="mol_per_s"/>
</import>
<component name="state">
<variable initial_value="0.0" name="t" units="second"/>
<!-- Parameters-->
<variable initial_value="8.324" name="R" units="J_per_mol_K"/>
<variable initial_value="300" name="T" units="kelvin"/>
<variable initial_value="50.0" name="K_q1" units="per_mol"/>
<variable initial_value="35.0" name="K_q2" units="per_mol"/>
<variable initial_value="20.0" name="K_q3" units="per_mol"/>
<variable initial_value="20.0" name="K_q4" units="per_mol"/>
<variable initial_value="0.0001" name="K_Re1" units="mol_per_s"/>
<!-- State variables-->
<variable initial_value="10" name="q1" units="mole"/>
<variable initial_value="10" name="q2" units="mole"/>
<variable initial_value="1e-6" name="q3" units="mole"/>
<variable initial_value="1e-6" name="q4" units="mole"/>
<variable name="v1" units="mol_per_s"/>
<variable name="u1" units="J_per_mol"/>
<variable name="u2" units="J_per_mol"/>
<variable name="u3" units="J_per_mol"/>
<variable name="u4" units="J_per_mol"/>
<variable name="u5" units="J_per_mol"/>
<variable name="u6" units="J_per_mol"/>
<!-- Conservation laws-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q1</ci>
</apply>
<apply>
<minus/>
<ci>v1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q2</ci>
</apply>
<apply>
<minus/>
<ci>v1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q3</ci>
</apply>
<ci>v1</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q4</ci>
</apply>
<ci>v1</ci>
</apply>
<apply>
<eq/>
<ci>u5</ci>
<apply>
<plus/>
<ci>u1</ci>
<ci>u2</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>u6</ci>
<apply>
<plus/>
<ci>u3</ci>
<ci>u4</ci>
</apply>
</apply>
<!-- Constitutive relations-->
<apply>
<eq/>
<ci>u1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_q1</ci>
<ci>q1</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>u2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_q2</ci>
<ci>q2</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>u3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_q3</ci>
<ci>q3</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>u4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_q4</ci>
<ci>q4</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v1</ci>
<apply>
<times/>
<ci>K_Re1</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>u5</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>u6</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
</model>