Location: BondGraph Basic @ 72c47d6a1652 / BG Tutorial Biochemical Systems / Biochemical 2.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 2.cellml

<?xml version='1.0'?>
<model name="Biochemical2" 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="0.01" name="K_Re1" units="mol_per_s"/>
        <!-- State variables-->
        <variable initial_value="10" name="q1" units="mole"/>
        <variable initial_value="1e-6" name="q2" units="mole"/>
        <variable initial_value="1e-6" name="q3" 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"/>
        <!-- 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>
                <ci>v1</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q3</ci>
                </apply>
                <ci>v1</ci>
            </apply>
            <apply>
                <eq/>
                <ci>u4</ci>
                <apply>
                    <plus/>
                    <ci>u2</ci>
                    <ci>u3</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>v1</ci>
                <apply>
                    <times/>
                    <ci>K_Re1</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>u1</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>u4</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
</model>