Location: BG_HaiMurphy @ a67177c16af1 / BG_HaiMurphy.cellml

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-05-20 10:22:46+12:00
Desc:
Adding exposure files
Permanent Source URI:
https://models.cellml.org/workspace/818/rawfile/a67177c16af102ea8ec4d69929c771407a9803c7/BG_HaiMurphy.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_HaiMurphy" 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="J_per_C" units_ref="J_per_C"/>
        <units name="microm3" units_ref="microm3"/>
        <units name="fF" units_ref="fF"/>
        <units name="fC" units_ref="fC"/>
        <units name="fA" units_ref="fA"/>
        <units name="per_second" units_ref="per_second"/>
        <units name="millivolt" units_ref="millivolt"/>
        <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="fmol_per_L_per_sec" units_ref="fmol_per_L_per_sec"/>
        <units name="per_sec_per_fmol_per_L" units_ref="per_sec_per_fmol_per_L"/>
        <units name="uM" units_ref="uM"/>
        <units name="mM_per_sec" units_ref="mM_per_sec"/>
        <units name="uM_per_sec" units_ref="uM_per_sec"/>
        <units name="pL" units_ref="pL"/>
        <units name="m_to_u" units_ref="m_to_u"/>
    </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"/>
        <variable initial_value="1" name="vol" units="pL"/>
        <!-- initial values-->
        <variable initial_value="1e-6" name="q_A" public_interface="out" units="fmol"/>
        <variable initial_value="1e-6" name="q_M" public_interface="out" units="fmol"/>
        <variable initial_value="0" name="q_Mp" public_interface="out" units="fmol"/>
        <variable initial_value="0" name="q_AM" public_interface="out" units="fmol"/>
        <variable initial_value="0" name="q_AMp" public_interface="out" units="fmol"/>
        <variable initial_value="15" name="q_Pi" public_interface="out" units="fmol"/>
        <variable initial_value="1e-3" name="q_Ca_i" public_interface="out" units="fmol"/>
        <variable initial_value="1e-6" name="q_cGMP" public_interface="out" units="fmol"/>
        <!-- From submodule-->
        <variable name="v_R_12" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_34" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_56" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R_78" public_interface="in" units="fmol_per_sec"/>
        <variable initial_value="1.66" name="n_Cai_SM" public_interface="out" units="dimensionless"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_A</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <ci>v_R_34</ci>
                    </apply>
                    <ci>v_R_78</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_M</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <ci>v_R_12</ci>
                    </apply>
                    <ci>v_R_78</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_Mp</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_12</ci>
                    <ci>v_R_34</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_AM</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_56</ci>
                    <ci>v_R_78</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_AMp</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R_34</ci>
                    <ci>v_R_56</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_Pi</ci>
                </apply>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <ci>v_R_12</ci>
                    </apply>
                    <ci>v_R_56</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_Ca_i</ci>
                </apply>
                <apply>
                    <times/>
                    <ci>n_Cai_SM</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <minus/>
                            <ci>v_R_12</ci>
                        </apply>
                        <ci>v_R_56</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_cGMP</ci>
                </apply>
                <apply>
                    <plus/>
                    <ci>v_R_12</ci>
                    <ci>v_R_56</ci>
                </apply>
            </apply>
        </math>
        <!-- stress calculation: from original paper, 
 stress = AM + AMp -->
        <variable name="stress" units="dimensionless"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>stress</ci>
                <apply>
                    <divide/>
                    <apply>
                        <plus/>
                        <ci>q_AM</ci>
                        <ci>q_AMp</ci>
                    </apply>
                    <cn cellml:units="fmol">1</cn>
                </apply>
            </apply>
        </math>
    </component>
    <component name="HaiMurphy_parameters">
        <variable initial_value="0.117606" name="kappa_R_12" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="6.98167" name="kappa_R_34" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="2.11691" name="kappa_R_56" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.0270688" name="kappa_R_78" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.532601" name="K_A" public_interface="out" units="per_fmol"/>
        <variable initial_value="4.08193" name="K_M" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.0351692" name="K_Mp" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.448094" name="K_AM" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.0038607" name="K_AMp" public_interface="out" units="per_fmol"/>
        <variable initial_value="250.692" name="K_Pi" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.145785" name="K_Ca_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.0971738" name="K_cGMP" public_interface="out" units="per_fmol"/>
    </component>
    <component name="HaiMurphy">
        <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"/>
        <variable name="kappa_R_12" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R_34" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R_56" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R_78" public_interface="in" units="fmol_per_sec"/>
        <variable name="K_A" public_interface="in" units="per_fmol"/>
        <variable name="K_M" public_interface="in" units="per_fmol"/>
        <variable name="K_Mp" public_interface="in" units="per_fmol"/>
        <variable name="K_AM" public_interface="in" units="per_fmol"/>
        <variable name="K_AMp" public_interface="in" units="per_fmol"/>
        <variable name="K_Pi" public_interface="in" units="per_fmol"/>
        <variable name="K_Ca_i" public_interface="in" units="per_fmol"/>
        <variable name="K_cGMP" public_interface="in" units="per_fmol"/>
        <variable name="n_Cai_SM" public_interface="in" units="dimensionless"/>
        <!-- Input from global environment-->
        <variable name="q_A" public_interface="in" units="fmol"/>
        <variable name="q_M" public_interface="in" units="fmol"/>
        <variable name="q_Mp" public_interface="in" units="fmol"/>
        <variable name="q_AM" public_interface="in" units="fmol"/>
        <variable name="q_AMp" public_interface="in" units="fmol"/>
        <variable name="q_Pi" public_interface="in" units="fmol"/>
        <variable name="q_Ca_i" public_interface="in" units="fmol"/>
        <variable name="q_cGMP" public_interface="in" units="fmol"/>
        <!-- Constitutive parameters-->
        <variable name="mu_A" units="J_per_mol"/>
        <variable name="mu_M" units="J_per_mol"/>
        <variable name="mu_Mp" units="J_per_mol"/>
        <variable name="mu_AM" units="J_per_mol"/>
        <variable name="mu_AMp" units="J_per_mol"/>
        <variable name="mu_Pi" units="J_per_mol"/>
        <variable name="mu_Ca_i" units="J_per_mol"/>
        <variable name="mu_cGMP" units="J_per_mol"/>
        <variable name="v_R_12" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R_34" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R_56" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R_78" public_interface="out" units="fmol_per_sec"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_A</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_A</ci>
                            <ci>q_A</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_M</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_M</ci>
                            <ci>q_M</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_Mp</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Mp</ci>
                            <ci>q_Mp</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_AM</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_AM</ci>
                            <ci>q_AM</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_AMp</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_AMp</ci>
                            <ci>q_AMp</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_Pi</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Pi</ci>
                            <ci>q_Pi</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_Ca_i</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Ca_i</ci>
                            <ci>q_Ca_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_cGMP</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_cGMP</ci>
                            <ci>q_cGMP</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_R_12</ci>
                <apply>
                    <times/>
                    <ci>kappa_R_12</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_M</ci>
                                    <ci>mu_Pi</ci>
                                    <apply>
                                        <times/>
                                        <ci>n_Cai_SM</ci>
                                        <ci>mu_Ca_i</ci>
                                    </apply>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_Mp</ci>
                                    <ci>mu_cGMP</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_R_34</ci>
                <apply>
                    <times/>
                    <ci>kappa_R_34</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_A</ci>
                                    <ci>mu_Mp</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_AMp</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_R_56</ci>
                <apply>
                    <times/>
                    <ci>kappa_R_56</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_AMp</ci>
                                    <apply>
                                        <times/>
                                        <ci>n_Cai_SM</ci>
                                        <ci>mu_Ca_i</ci>
                                    </apply>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_AM</ci>
                                    <ci>mu_Pi</ci>
                                    <ci>mu_cGMP</ci>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_R_78</ci>
                <apply>
                    <times/>
                    <ci>kappa_R_78</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_AM</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_A</ci>
                                    <ci>mu_M</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="HaiMurphy"/>
        <map_variables variable_1="time" variable_2="time"/>
        <map_variables variable_1="q_A" variable_2="q_A"/>
        <map_variables variable_1="q_M" variable_2="q_M"/>
        <map_variables variable_1="q_Mp" variable_2="q_Mp"/>
        <map_variables variable_1="q_AM" variable_2="q_AM"/>
        <map_variables variable_1="q_AMp" variable_2="q_AMp"/>
        <map_variables variable_1="q_Pi" variable_2="q_Pi"/>
        <map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
        <map_variables variable_1="q_cGMP" variable_2="q_cGMP"/>
        <map_variables variable_1="v_R_12" variable_2="v_R_12"/>
        <map_variables variable_1="v_R_34" variable_2="v_R_34"/>
        <map_variables variable_1="v_R_56" variable_2="v_R_56"/>
        <map_variables variable_1="v_R_78" variable_2="v_R_78"/>
        <map_variables variable_1="n_Cai_SM" variable_2="n_Cai_SM"/>
    </connection>
    <connection>
        <map_components component_1="HaiMurphy" component_2="HaiMurphy_parameters"/>
        <map_variables variable_1="kappa_R_12" variable_2="kappa_R_12"/>
        <map_variables variable_1="kappa_R_34" variable_2="kappa_R_34"/>
        <map_variables variable_1="kappa_R_56" variable_2="kappa_R_56"/>
        <map_variables variable_1="kappa_R_78" variable_2="kappa_R_78"/>
        <map_variables variable_1="K_A" variable_2="K_A"/>
        <map_variables variable_1="K_M" variable_2="K_M"/>
        <map_variables variable_1="K_Mp" variable_2="K_Mp"/>
        <map_variables variable_1="K_AM" variable_2="K_AM"/>
        <map_variables variable_1="K_AMp" variable_2="K_AMp"/>
        <map_variables variable_1="K_Pi" variable_2="K_Pi"/>
        <map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
        <map_variables variable_1="K_cGMP" variable_2="K_cGMP"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="HaiMurphy"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
    </connection>
</model>