Location: A model of intracellular pH control @ 1e42a26c1039 / model.cellml

Author:
David Nickerson <nickerso@users.sourceforge.net>
Date:
2017-07-28 12:01:05+12:00
Desc:
renaming files to try fixing an issue with the launch in OpenCOR link not working.
Permanent Source URI:
https://models.cellml.org/workspace/4a3/rawfile/1e42a26c1039ff3e94d3a9cf6bd5aaabe29207b6/model.cellml

<?xml version='1.0'?>
<model name="Boron_CO2_expts_original_eqns" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#">
    <units name="per_s">
        <unit exponent="-1" units="second"/>
    </units>
    <units name="per_m">
        <unit exponent="-1" units="metre"/>
    </units>
    <units name="m_per_s">
        <unit units="metre"/>
        <unit exponent="-1" units="second"/>
    </units>
    <units name="mol_per_m3">
        <unit units="mole"/>
        <unit exponent="-3" units="metre"/>
    </units>
    <units name="mol_per_m2_s">
        <unit exponent="1" units="mole"/>
        <unit exponent="-2" units="metre"/>
        <unit exponent="-1" units="second"/>
    </units>
    <units name="mol_per_m3_s">
        <unit exponent="1" units="mole"/>
        <unit exponent="-3" units="metre"/>
        <unit exponent="-1" units="second"/>
    </units>
    <units name="J_per_C">
        <unit units="joule"/>
        <unit exponent="-1" units="coulomb"/>
    </units>
    <units name="m3_per_mol">
        <unit exponent="3" units="metre"/>
        <unit exponent="-1" units="mole"/>
    </units>
    <component name="main">
        <variable name="t" units="second"/>
        <variable initial_value="-0.057" name="V_m" units="J_per_C"/>
        <variable initial_value="0.0256796" name="RTF" units="J_per_C"/>
        <variable name="epsilon" units="dimensionless"/>
        <variable initial_value="0.0" name="TA_i" units="mol_per_m3"/>
        <variable name="CO2_o" units="mol_per_m3"/>
        <variable name="CO2_i" units="mol_per_m3"/>
        <variable name="HCO3_i" units="mol_per_m3"/>
        <variable name="HCO3_o" units="mol_per_m3"/>
        <variable initial_value="3.981071705534970e-05" name="H_i" units="mol_per_m3"/>
        <variable initial_value="1.995262314968879e-05" name="H_o" units="mol_per_m3"/>
        <variable initial_value="3.981071705534970e-05" name="H_Lim" units="mol_per_m3"/>
        <!--Note: 5.011872336272725e-05 (7.3); 3.981071705534970e-05 (7.4)-->
        <variable name="M_CO2" units="mol_per_m2_s"/>
        <variable name="M_HCO3" units="mol_per_m2_s"/>
        <variable name="M_H" units="mol_per_m2_s"/>
        <variable name="pH_i" units="dimensionless"/>
        <variable name="pH_o" units="dimensionless"/>
        <variable name="pH_Lim" units="dimensionless"/>
        <variable initial_value="6e-5" name="P_CO2" units="m_per_s"/>
        <variable initial_value="5e-9" name="P_HCO3" units="m_per_s"/>
        <variable initial_value="0.0375" name="k" units="m_per_s"/>
        <variable initial_value="1e-3" name="K_A" units="mol_per_m3"/>
        <variable initial_value="8000" name="rho" units="per_m"/>
        <variable name="alpha_i" units="dimensionless"/>
        <variable initial_value="-26" name="beta" units="mol_per_m3"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>CO2_o</ci>
                <piecewise>
                    <piece>
                        <cn cellml:units="mol_per_m3">0</cn>
                        <apply>
                            <lt/>
                            <ci>t</ci>
                            <cn cellml:units="second">100</cn>
                        </apply>
                    </piece>
                    <piece>
                        <cn cellml:units="mol_per_m3">1.1877</cn>
                        <apply>
                            <lt/>
                            <ci>t</ci>
                            <cn cellml:units="second">2800</cn>
                        </apply>
                    </piece>
                    <otherwise>
                        <cn cellml:units="mol_per_m3">0</cn>
                    </otherwise>
                </piecewise>
            </apply>
            <apply>
                <eq/>
                <ci>HCO3_o</ci>
                <apply>
                    <divide/>
                    <apply>
                        <times/>
                        <ci>K_A</ci>
                        <ci>CO2_o</ci>
                    </apply>
                    <ci>H_o</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>epsilon</ci>
                <apply>
                    <exp/>
                    <apply>
                        <divide/>
                        <apply>
                            <minus/>
                            <ci>V_m</ci>
                        </apply>
                        <ci>RTF</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>M_CO2</ci>
                <apply>
                    <times/>
                    <ci>P_CO2</ci>
                    <apply>
                        <minus/>
                        <ci>CO2_o</ci>
                        <ci>CO2_i</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>M_HCO3</ci>
                <apply>
                    <divide/>
                    <apply>
                        <times/>
                        <apply>
                            <divide/>
                            <apply>
                                <times/>
                                <ci>P_HCO3</ci>
                                <ci>V_m</ci>
                            </apply>
                            <ci>RTF</ci>
                        </apply>
                        <apply>
                            <minus/>
                            <ci>HCO3_o</ci>
                            <apply>
                                <times/>
                                <ci>HCO3_i</ci>
                                <ci>epsilon</ci>
                            </apply>
                        </apply>
                    </apply>
                    <apply>
                        <minus/>
                        <cn cellml:units="dimensionless">1</cn>
                        <ci>epsilon</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>pH_Lim</ci>
                <apply>
                    <minus/>
                    <apply>
                        <log/>
                        <apply>
                            <times/>
                            <cn cellml:units="m3_per_mol" type="e-notation">1<sep/>-3</cn>
                            <ci>H_Lim</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>M_H</ci>
                <piecewise>
                    <piece>
                        <apply>
                            <times/>
                            <ci>k</ci>
                            <apply>
                                <minus/>
                                <ci>H_i</ci>
                                <ci>H_Lim</ci>
                            </apply>
                        </apply>
                        <apply>
                            <lt/>
                            <ci>pH_i</ci>
                            <ci>pH_Lim</ci>
                        </apply>
                    </piece>
                    <otherwise>
                        <cn cellml:units="mol_per_m2_s">0</cn>
                    </otherwise>
                </piecewise>
            </apply>
            <apply>
                <eq/>
                <ci>pH_i</ci>
                <apply>
                    <minus/>
                    <apply>
                        <log/>
                        <apply>
                            <times/>
                            <cn cellml:units="m3_per_mol" type="e-notation">1<sep/>-3</cn>
                            <ci>H_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>pH_o</ci>
                <apply>
                    <minus/>
                    <apply>
                        <log/>
                        <apply>
                            <times/>
                            <cn cellml:units="m3_per_mol" type="e-notation">1<sep/>-3</cn>
                            <ci>H_o</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>alpha_i</ci>
                <apply>
                    <divide/>
                    <ci>H_i</ci>
                    <apply>
                        <plus/>
                        <ci>H_i</ci>
                        <ci>K_A</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>CO2_i</ci>
                <apply>
                    <times/>
                    <ci>alpha_i</ci>
                    <ci>TA_i</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>HCO3_i</ci>
                <apply>
                    <times/>
                    <apply>
                        <minus/>
                        <cn cellml:units="dimensionless">1</cn>
                        <ci>alpha_i</ci>
                    </apply>
                    <ci>TA_i</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>TA_i</ci>
                </apply>
                <apply>
                    <times/>
                    <ci>rho</ci>
                    <apply>
                        <plus/>
                        <ci>M_CO2</ci>
                        <ci>M_HCO3</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>H_i</ci>
                </apply>
                <apply>
                    <times/>
                    <apply>
                        <divide/>
                        <apply>
                            <times/>
                            <apply>
                                <minus/>
                                <cn cellml:units="dimensionless">2.303</cn>
                            </apply>
                            <ci>H_i</ci>
                        </apply>
                        <ci>beta</ci>
                    </apply>
                    <ci>rho</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <minus/>
                            <apply>
                                <times/>
                                <apply>
                                    <minus/>
                                    <cn cellml:units="dimensionless">1</cn>
                                    <ci>alpha_i</ci>
                                </apply>
                                <ci>M_CO2</ci>
                            </apply>
                            <apply>
                                <times/>
                                <ci>alpha_i</ci>
                                <ci>M_HCO3</ci>
                            </apply>
                        </apply>
                        <ci>M_H</ci>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
</model>