Location: BG_CO2_hydration @ c7db73a7fd05 / BG_CO2_hyd.cellml

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-05-24 13:05:09+12:00
Desc:
Init
Permanent Source URI:
http://models.cellml.org/workspace/886/rawfile/c7db73a7fd0546bc1cbff02d2e7ad5d3ca4e85fa/BG_CO2_hyd.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_CO2_hyd" 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_and_constants/units_BG.cellml">
        <units name="mM" units_ref="mM"/>
        <units name="fmol" units_ref="fmol"/>
        <units name="per_fmol" units_ref="per_fmol"/>
        <units name="J_per_mol" units_ref="J_per_mol"/>
        <units name="fmol_per_sec" units_ref="fmol_per_sec"/>
        <units name="C_per_mol" units_ref="C_per_mol"/>
        <units name="fF" units_ref="fF"/>
        <units name="fC" units_ref="fC"/>
        <units name="per_second" units_ref="per_second"/>
        <units name="per_sec" units_ref="per_sec"/>
        <units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
        <units name="fmol_per_L" units_ref="fmol_per_L"/>
        <units name="pL" units_ref="pL"/>
    </import>
    <import xlink:href="units_and_constants/constants_BG.cellml">
        <component component_ref="constants" name="constants"/>
    </import>
    <component name="environment">
        <variable name="time" public_interface="out" units="second"/>
        <!-- initial values-->
        <variable initial_value="46.968" name="q_CO2_i" public_interface="out" units="fmol"/>
        <variable initial_value="509.2" name="q_HCO3_i" public_interface="out" units="fmol"/>
        <variable initial_value="2.69019E-06" name="q_H_i" public_interface="out" units="fmol"/>
        <!-- From submodule-->
        <variable name="v_Re_CO2hyd" public_interface="in" units="fmol_per_sec"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_CO2_i</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_Re_CO2hyd</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_HCO3_i</ci>
                </apply>
                <ci>v_Re_CO2hyd</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_H_i</ci>
                </apply>
                <ci>v_Re_CO2hyd</ci>
            </apply>
        </math>
        <variable name="pH_i" units="dimensionless"/>
        <variable name="cH_i" units="mM"/>
        <variable initial_value="38" name="w_i" units="pL"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>cH_i</ci>
                <apply>
                    <divide/>
                    <ci>q_H_i</ci>
                    <ci>w_i</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>pH_i</ci>
                <apply>
                    <minus/>
                    <apply>
                        <log/>
                        <ci>cH_i</ci>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
    <component name="CO2_hyd_parameters">
        <variable initial_value="153.093" name="kappa_Re_hyd" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="82.5092" name="K_CO2_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.00128495" name="K_HCO3_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.00128495" name="K_H_i" public_interface="out" units="per_fmol"/>
    </component>
    <component name="CO2_hyd">
        <variable name="time" public_interface="in" units="second"/>
        <variable name="R" public_interface="in" units="J_per_K_per_mol"/>
        <variable name="T" public_interface="in" units="kelvin"/>
        <!-- parameters-->
        <variable name="kappa_Re_hyd" public_interface="in" units="fmol_per_sec"/>
        <variable name="K_CO2_i" public_interface="in" units="per_fmol"/>
        <variable name="K_HCO3_i" public_interface="in" units="per_fmol"/>
        <variable name="K_H_i" public_interface="in" units="per_fmol"/>
        <!-- Input from global environment-->
        <variable name="q_CO2_i" public_interface="in" units="fmol"/>
        <variable name="q_HCO3_i" public_interface="in" units="fmol"/>
        <variable name="q_H_i" public_interface="in" units="fmol"/>
        <!-- Constitutive parameters-->
        <variable name="mu_CO2_i" units="J_per_mol"/>
        <variable name="mu_HCO3_i" units="J_per_mol"/>
        <variable name="mu_H_i" units="J_per_mol"/>
        <variable name="v_Re_CO2hyd" public_interface="out" units="fmol_per_sec"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_CO2_i</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_CO2_i</ci>
                            <ci>q_CO2_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_HCO3_i</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_HCO3_i</ci>
                            <ci>q_HCO3_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_H_i</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_H_i</ci>
                            <ci>q_H_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_Re_CO2hyd</ci>
                <apply>
                    <times/>
                    <ci>kappa_Re_hyd</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_CO2_i</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_HCO3_i</ci>
                                    <ci>mu_H_i</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
    <connection>
        <map_components component_1="environment" component_2="CO2_hyd"/>
        <map_variables variable_1="time" variable_2="time"/>
        <map_variables variable_1="q_CO2_i" variable_2="q_CO2_i"/>
        <map_variables variable_1="q_HCO3_i" variable_2="q_HCO3_i"/>
        <map_variables variable_1="q_H_i" variable_2="q_H_i"/>
        <map_variables variable_1="v_Re_CO2hyd" variable_2="v_Re_CO2hyd"/>
    </connection>
    <connection>
        <map_components component_1="CO2_hyd" component_2="CO2_hyd_parameters"/>
        <map_variables variable_1="kappa_Re_hyd" variable_2="kappa_Re_hyd"/>
        <map_variables variable_1="K_CO2_i" variable_2="K_CO2_i"/>
        <map_variables variable_1="K_HCO3_i" variable_2="K_HCO3_i"/>
        <map_variables variable_1="K_H_i" variable_2="K_H_i"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="CO2_hyd"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
    </connection>
</model>