Location: AE1-BG @ a3e7d3ee1d1d / AE1-BG.cellml

Author:
nima <nafs080@aucklanduni.ac.nz>
Date:
2021-10-07 09:23:47+13:00
Desc:
Figure3 - Bond Graph & CellML
Permanent Source URI:
https://models.physiomeproject.org/workspace/6b9/rawfile/a3e7d3ee1d1de068eec9b205693d63ad5c4f15bf/AE1-BG.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="AE1_BG" 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="kJ_per_mol" units_ref="kJ_per_mol"/>
        <units name="mM_per_s" units_ref="mM_per_s"/>
    </import>
    <import xlink:href="Parameters.cellml">
        <component component_ref="param" name="param"/>
    </import>
    <component name="AE1">
        <variable name="t" units="second"/>
        <!-- Parameters-->
        <variable name="RT" public_interface="in" units="kJ_per_mol"/>
        <variable name="K_Cl_o" public_interface="in" units="per_mol"/>
        <variable name="K_Cl_i" public_interface="in" units="per_mol"/>
        <variable name="K_HCO3_i" public_interface="in" units="per_mol"/>
        <variable name="K_HCO3_o" public_interface="in" units="per_mol"/>
        <variable name="K_E_o" public_interface="in" units="per_mol"/>
        <variable name="K_ECl_o" public_interface="in" units="per_mol"/>
        <variable name="K_ECl_i" public_interface="in" units="per_mol"/>
        <variable name="K_E_i" public_interface="in" units="per_mol"/>
        <variable name="K_EHCO3_i" public_interface="in" units="per_mol"/>
        <variable name="K_EHCO3_o" public_interface="in" units="per_mol"/>
        <variable name="K_Re1" public_interface="in" units="mM_per_s"/>
        <variable name="K_Re2" public_interface="in" units="mM_per_s"/>
        <variable name="K_Re3" public_interface="in" units="mM_per_s"/>
        <variable name="K_Re4" public_interface="in" units="mM_per_s"/>
        <variable name="K_Re5" public_interface="in" units="mM_per_s"/>
        <variable name="K_Re6" public_interface="in" units="mM_per_s"/>
        <!-- State variables-->
        <variable initial_value="114" name="q_Cl_o" units="mole"/>
        <variable initial_value="29" name="q_Cl_i" units="mole"/>
        <variable initial_value="0.0" name="q_HCO3_i" units="mole"/>
        <variable initial_value="26" name="q_HCO3_o" units="mole"/>
        <variable initial_value="0.01738" name="q_E_o" units="mole"/>
        <variable initial_value="0.0396" name="q_ECl_o" units="mole"/>
        <variable initial_value="0.274" name="q_ECl_i" units="mole"/>
        <variable initial_value="0.473" name="q_E_i" units="mole"/>
        <variable initial_value="0.0621" name="q_EHCO3_i" units="mole"/>
        <variable initial_value="0.00228" name="q_EHCO3_o" units="mole"/>
        <variable name="v_Re1" public_interface="out" units="mM_per_s"/>
        <variable name="v_Re2" public_interface="out" units="mM_per_s"/>
        <variable name="v_Re3" public_interface="out" units="mM_per_s"/>
        <variable name="v_Re4" public_interface="out" units="mM_per_s"/>
        <variable name="v_Re5" public_interface="out" units="mM_per_s"/>
        <variable name="v_Re6" public_interface="out" units="mM_per_s"/>
        <!-- Conservation laws-->
        <!--        ode(q_Cl_o, t) = -v_Re1;
        ode(q_Cl_i, t) = v_Re3;
        ode(q_HCO3_i, t) = -v_Re4;
        ode(q_HCO3_o, t) = v_Re6;-->
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_E_o</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_Re6</ci>
                    <ci>v_Re1</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_ECl_o</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_Re1</ci>
                    <ci>v_Re2</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_ECl_i</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_Re2</ci>
                    <ci>v_Re3</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_E_i</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_Re3</ci>
                    <ci>v_Re4</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_EHCO3_i</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_Re4</ci>
                    <ci>v_Re5</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_EHCO3_o</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_Re5</ci>
                    <ci>v_Re6</ci>
                </apply>
            </apply>
            <!-- Constitutive relations-->
            <apply>
                <eq/>
                <ci>v_Re1</ci>
                <apply>
                    <times/>
                    <ci>K_Re1</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <times/>
                            <ci>K_Cl_o</ci>
                            <ci>q_Cl_o</ci>
                            <ci>K_E_o</ci>
                            <ci>q_E_o</ci>
                        </apply>
                        <apply>
                            <times/>
                            <ci>K_ECl_o</ci>
                            <ci>q_ECl_o</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_Re2</ci>
                <apply>
                    <times/>
                    <ci>K_Re2</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <times/>
                            <ci>K_ECl_o</ci>
                            <ci>q_ECl_o</ci>
                        </apply>
                        <apply>
                            <times/>
                            <ci>K_ECl_i</ci>
                            <ci>q_ECl_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_Re3</ci>
                <apply>
                    <times/>
                    <ci>K_Re3</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <times/>
                            <ci>K_ECl_i</ci>
                            <ci>q_ECl_i</ci>
                        </apply>
                        <apply>
                            <times/>
                            <ci>K_Cl_i</ci>
                            <ci>q_Cl_i</ci>
                            <ci>K_E_i</ci>
                            <ci>q_E_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_Re4</ci>
                <apply>
                    <times/>
                    <ci>K_Re4</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <times/>
                            <ci>K_HCO3_i</ci>
                            <ci>q_HCO3_i</ci>
                            <ci>K_E_i</ci>
                            <ci>q_E_i</ci>
                        </apply>
                        <apply>
                            <times/>
                            <ci>K_EHCO3_i</ci>
                            <ci>q_EHCO3_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_Re5</ci>
                <apply>
                    <times/>
                    <ci>K_Re5</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <times/>
                            <ci>K_EHCO3_i</ci>
                            <ci>q_EHCO3_i</ci>
                        </apply>
                        <apply>
                            <times/>
                            <ci>K_EHCO3_o</ci>
                            <ci>q_EHCO3_o</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_Re6</ci>
                <apply>
                    <times/>
                    <ci>K_Re6</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <times/>
                            <ci>K_EHCO3_o</ci>
                            <ci>q_EHCO3_o</ci>
                        </apply>
                        <apply>
                            <times/>
                            <ci>K_HCO3_o</ci>
                            <ci>q_HCO3_o</ci>
                            <ci>K_E_o</ci>
                            <ci>q_E_o</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
    <!-- Mapping to the Parameters module-->
    <connection>
        <map_components component_1="param" component_2="AE1"/>
        <map_variables variable_1="RT" variable_2="RT"/>
        <map_variables variable_1="K_Cl_o" variable_2="K_Cl_o"/>
        <map_variables variable_1="K_Cl_i" variable_2="K_Cl_i"/>
        <map_variables variable_1="K_HCO3_i" variable_2="K_HCO3_i"/>
        <map_variables variable_1="K_HCO3_o" variable_2="K_HCO3_o"/>
        <map_variables variable_1="K_E_o" variable_2="K_E_o"/>
        <map_variables variable_1="K_ECl_o" variable_2="K_ECl_o"/>
        <map_variables variable_1="K_ECl_i" variable_2="K_ECl_i"/>
        <map_variables variable_1="K_E_i" variable_2="K_E_i"/>
        <map_variables variable_1="K_EHCO3_i" variable_2="K_EHCO3_i"/>
        <map_variables variable_1="K_EHCO3_o" variable_2="K_EHCO3_o"/>
        <map_variables variable_1="K_Re1" variable_2="K_Re1"/>
        <map_variables variable_1="K_Re2" variable_2="K_Re2"/>
        <map_variables variable_1="K_Re3" variable_2="K_Re3"/>
        <map_variables variable_1="K_Re4" variable_2="K_Re4"/>
        <map_variables variable_1="K_Re5" variable_2="K_Re5"/>
        <map_variables variable_1="K_Re6" variable_2="K_Re6"/>
    </connection>
</model>