Location: BG_RyR @ f8155c79489c / BG_RyR.cellml

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-04-28 14:23:01+12:00
Desc:
Fixing placement of var
Permanent Source URI:
https://models.cellml.org/workspace/6e3/rawfile/f8155c79489cb9d4adae75516c0767bb53efba58/BG_RyR.cellml

<?xml version='1.0' encoding='UTF-8'?>
<!-- Ryanodine receptor: controls release of Ca from SR into cytosol of myocyte (AKA J_rel). 
 It does not sit on the sarcolemma. I am unsure of charge on the SR membrane, so neglecting this.-->
<model name="individual_RyR" 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>
    <import xlink:href="units_and_constants/ion_valency.cellml">
        <component component_ref="ion_valences" name="ion_valences"/>
    </import>
    <component name="environment">
        <variable name="t" public_interface="out" units="second"/>
        <variable initial_value="1.381e5" name="C_m" units="fF"/>
        <variable name="v_RyR" public_interface="in" units="fmol_per_sec"/>
        <variable name="F" public_interface="in" units="C_per_mol"/>
        <!-- initial values-->
        <variable initial_value="6.41e-1" name="q_Ca_SR" public_interface="out" units="fmol"/>
        <variable initial_value="3.09e-6" name="q_Ca_di" public_interface="out" units="fmol"/>
        <variable initial_value="6.82e-3" name="q_Ca_i" public_interface="out" units="fmol"/>
        <variable initial_value="2.9682830E-06" name="q_C_RyR" public_interface="out" units="fmol"/>
        <variable initial_value="2.9682830E-06" name="q_CI_RyR" public_interface="out" units="fmol"/>
        <variable initial_value="2.9682830E-06" name="q_I_RyR" public_interface="out" units="fmol"/>
        <variable initial_value="2.9682830E-06" name="q_O_RyR" public_interface="out" units="fmol"/>
        <!-- From submodule-->
        <variable name="v_RyRgate_Ca_i" public_interface="in" units="fmol_per_sec"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Ca_SR</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_RyR</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Ca_i</ci>
                </apply>
                <apply>
                    <plus/>
                    <ci>v_RyR</ci>
                    <ci>v_RyRgate_Ca_i</ci>
                </apply>
            </apply>
        </math>
    </component>
    <component name="RyR_parameters">
        <variable initial_value="34574.2" name="kappa_RyR" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="8.83262" name="kappa_OC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.12618" name="kappa_CCI" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="883.262" name="kappa_CII" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="73.6052" name="kappa_IO" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="154.436" name="K_Ca_SR" public_interface="out" units="per_fmol"/>
        <variable initial_value="100.283" name="K_Ca_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="3962.58" name="K_C_RyR" public_interface="out" units="per_fmol"/>
        <variable initial_value="39.6258" name="K_CI_RyR" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.06793" name="K_I_RyR" public_interface="out" units="per_fmol"/>
        <variable initial_value="6.793" name="K_O_RyR" public_interface="out" units="per_fmol"/>
    </component>
    <component name="RyR">
        <variable name="t" 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="F" public_interface="in" units="C_per_mol"/>
        <variable initial_value="1" name="nCa_1" public_interface="out" units="dimensionless"/>
        <variable initial_value="2" name="nCa_2" public_interface="out" units="dimensionless"/>
        <!-- parameters-->
        <variable name="kappa_RyR" public_interface="in" units="fmol_per_sec"/>
        <variable name="K_Ca_SR" public_interface="in" units="per_fmol"/>
        <variable name="K_Ca_i" public_interface="in" units="per_fmol"/>
        <variable name="kappa_OC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_CCI" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_CII" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_IO" public_interface="in" units="fmol_per_sec"/>
        <variable name="K_C_RyR" public_interface="in" units="per_fmol"/>
        <variable name="K_CI_RyR" public_interface="in" units="per_fmol"/>
        <variable name="K_I_RyR" public_interface="in" units="per_fmol"/>
        <variable name="K_O_RyR" public_interface="in" units="per_fmol"/>
        <!-- Input from global environment-->
        <variable name="q_Ca_SR" public_interface="in" units="fmol"/>
        <variable name="q_Ca_i" public_interface="in" units="fmol"/>
        <!-- Constitutive parameters-->
        <variable name="mu_Ca_SR" units="J_per_mol"/>
        <variable name="mu_Ca_i" public_interface="out" units="J_per_mol"/>
        <variable name="v_RyR" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_RyRgate_Ca_i" public_interface="out" units="fmol_per_sec"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_Ca_SR</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Ca_SR</ci>
                            <ci>q_Ca_SR</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>v_RyR</ci>
                <apply>
                    <times/>
                    <ci>kappa_RyR</ci>
                    <apply>
                        <exp/>
                        <apply>
                            <divide/>
                            <ci>mu_O_RyR</ci>
                            <apply>
                                <times/>
                                <ci>R</ci>
                                <ci>T</ci>
                            </apply>
                        </apply>
                    </apply>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_Ca_SR</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_Ca_i</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_RyRgate_Ca_i</ci>
                <apply>
                    <plus/>
                    <apply>
                        <minus/>
                        <apply>
                            <minus/>
                            <apply>
                                <times/>
                                <ci>nCa_2</ci>
                                <ci>v_OC</ci>
                            </apply>
                            <apply>
                                <times/>
                                <ci>nCa_1</ci>
                                <ci>v_CCI</ci>
                            </apply>
                        </apply>
                        <apply>
                            <times/>
                            <ci>nCa_2</ci>
                            <ci>v_CII</ci>
                        </apply>
                    </apply>
                    <apply>
                        <times/>
                        <ci>nCa_1</ci>
                        <ci>v_IO</ci>
                    </apply>
                </apply>
            </apply>
        </math>
        <!-- gate-->
        <variable name="q_C_RyR" public_interface="in" units="fmol"/>
        <variable name="q_CI_RyR" public_interface="in" units="fmol"/>
        <variable name="q_I_RyR" public_interface="in" units="fmol"/>
        <variable name="q_O_RyR" public_interface="in" units="fmol"/>
        <variable name="q_Ca_gate_complexes" public_interface="out" units="fmol"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>q_Ca_gate_complexes</ci>
                <apply>
                    <plus/>
                    <apply>
                        <times/>
                        <ci>nCa_2</ci>
                        <ci>q_O_RyR</ci>
                    </apply>
                    <apply>
                        <times/>
                        <ci>nCa_1</ci>
                        <ci>q_CI_RyR</ci>
                    </apply>
                    <apply>
                        <times/>
                        <apply>
                            <plus/>
                            <ci>nCa_1</ci>
                            <ci>nCa_2</ci>
                        </apply>
                        <ci>q_I_RyR</ci>
                    </apply>
                </apply>
            </apply>
        </math>
        <variable name="mu_C_RyR" units="J_per_mol"/>
        <variable name="mu_CI_RyR" units="J_per_mol"/>
        <variable name="mu_I_RyR" units="J_per_mol"/>
        <variable name="mu_O_RyR" units="J_per_mol"/>
        <variable name="v_OC" units="fmol_per_sec"/>
        <variable name="v_CCI" units="fmol_per_sec"/>
        <variable name="v_CII" units="fmol_per_sec"/>
        <variable name="v_IO" units="fmol_per_sec"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_C_RyR</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_C_RyR</ci>
                            <ci>q_C_RyR</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_CI_RyR</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_CI_RyR</ci>
                            <ci>q_CI_RyR</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_I_RyR</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_I_RyR</ci>
                            <ci>q_I_RyR</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_O_RyR</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_O_RyR</ci>
                            <ci>q_O_RyR</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_OC</ci>
                <apply>
                    <times/>
                    <ci>kappa_OC</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_O_RyR</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_C_RyR</ci>
                                    <apply>
                                        <times/>
                                        <ci>nCa_2</ci>
                                        <ci>mu_Ca_i</ci>
                                    </apply>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_CCI</ci>
                <apply>
                    <times/>
                    <ci>kappa_CCI</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_C_RyR</ci>
                                    <apply>
                                        <times/>
                                        <ci>nCa_1</ci>
                                        <ci>mu_Ca_i</ci>
                                    </apply>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_CI_RyR</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_CII</ci>
                <apply>
                    <times/>
                    <ci>kappa_CII</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_CI_RyR</ci>
                                    <apply>
                                        <times/>
                                        <ci>nCa_2</ci>
                                        <ci>mu_Ca_i</ci>
                                    </apply>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_I_RyR</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_IO</ci>
                <apply>
                    <times/>
                    <ci>kappa_IO</ci>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <ci>mu_I_RyR</ci>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>mu_O_RyR</ci>
                                    <apply>
                                        <times/>
                                        <ci>nCa_1</ci>
                                        <ci>mu_Ca_i</ci>
                                    </apply>
                                </apply>
                                <apply>
                                    <times/>
                                    <ci>R</ci>
                                    <ci>T</ci>
                                </apply>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_O_RyR</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_IO</ci>
                    <ci>v_OC</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_C_RyR</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_OC</ci>
                    <ci>v_CCI</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_CI_RyR</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_CCI</ci>
                    <ci>v_CII</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_I_RyR</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_CII</ci>
                    <ci>v_IO</ci>
                </apply>
            </apply>
        </math>
    </component>
    <connection>
        <map_components component_1="environment" component_2="RyR"/>
        <map_variables variable_1="t" variable_2="t"/>
        <map_variables variable_1="v_RyR" variable_2="v_RyR"/>
        <map_variables variable_1="v_RyRgate_Ca_i" variable_2="v_RyRgate_Ca_i"/>
        <map_variables variable_1="q_Ca_SR" variable_2="q_Ca_SR"/>
        <map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
        <map_variables variable_1="q_C_RyR" variable_2="q_C_RyR"/>
        <map_variables variable_1="q_O_RyR" variable_2="q_O_RyR"/>
        <map_variables variable_1="q_CI_RyR" variable_2="q_CI_RyR"/>
        <map_variables variable_1="q_I_RyR" variable_2="q_I_RyR"/>
    </connection>
    <connection>
        <map_components component_1="RyR" component_2="RyR_parameters"/>
        <map_variables variable_1="kappa_RyR" variable_2="kappa_RyR"/>
        <map_variables variable_1="K_Ca_SR" variable_2="K_Ca_SR"/>
        <map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
        <map_variables variable_1="kappa_OC" variable_2="kappa_OC"/>
        <map_variables variable_1="kappa_CCI" variable_2="kappa_CCI"/>
        <map_variables variable_1="kappa_CII" variable_2="kappa_CII"/>
        <map_variables variable_1="kappa_IO" variable_2="kappa_IO"/>
        <map_variables variable_1="K_C_RyR" variable_2="K_C_RyR"/>
        <map_variables variable_1="K_CI_RyR" variable_2="K_CI_RyR"/>
        <map_variables variable_1="K_I_RyR" variable_2="K_I_RyR"/>
        <map_variables variable_1="K_O_RyR" variable_2="K_O_RyR"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="environment"/>
        <map_variables variable_1="F" variable_2="F"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="RyR"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
        <map_variables variable_1="F" variable_2="F"/>
    </connection>
</model>