- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2025-07-24 11:01:15+12:00
- Desc:
- Finding new param, adding V_mem argument, updating Ca conc
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d41/rawfile/38820a34c0a013adb80420c96ba30c837b9e123b/BG_SOC.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_SOC" 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.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_s"/>
<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_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.cellml">
<component component_ref="constants" name="constants"/>
</import>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<variable initial_value="-381" name="q_mem" public_interface="out" units="fC"/>
<variable initial_value="7070" name="C_m" public_interface="out" units="fF"/>
<!-- initial values-->
<variable initial_value="5.32E+01" name="q_Ca_o" public_interface="out" units="fmol"/>
<variable initial_value="1.64E-02" name="q_Ca_i" public_interface="out" units="fmol"/>
<variable initial_value="0.0242" name="q_Ca_ER" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="v_Rx_SOC" 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_Ca_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Rx_SOC</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_i</ci>
</apply>
<ci>v_Rx_SOC</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_ER</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
</math>
</component>
<component name="SOC_parameters">
<variable initial_value="0.956036" name="kappa_Rx_SOC" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.046034" name="K_Ca_o" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00693454" name="K_Ca_i" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0346475" name="K_Ca_ER" public_interface="out" units="per_fmol"/>
</component>
<component name="SOC">
<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="F" public_interface="in" units="C_per_mol"/>
<variable name="V_mem" units="J_per_C"/>
<!-- parameters-->
<variable name="kappa_Rx_SOC" public_interface="in" units="fmol_per_sec"/>
<variable name="K_Ca_o" public_interface="in" units="per_fmol"/>
<variable name="K_Ca_i" public_interface="in" units="per_fmol"/>
<variable name="K_Ca_ER" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_Ca_o" public_interface="in" units="fmol"/>
<variable name="q_Ca_i" public_interface="in" units="fmol"/>
<variable name="q_Ca_ER" public_interface="in" units="fmol"/>
<variable name="q_mem" public_interface="in" units="fC"/>
<variable name="C_m" public_interface="in" units="fF"/>
<!-- Constitutive parameters-->
<variable name="mu_Ca_o" units="J_per_mol"/>
<variable name="mu_Ca_i" units="J_per_mol"/>
<variable name="mu_Ca_ER" units="J_per_mol"/>
<variable initial_value="8" name="n" units="dimensionless"/>
<variable name="v_Rx_SOC" public_interface="out" units="fmol_per_sec"/>
<variable name="Am_Rx_SOC" units="J_per_mol"/>
<variable name="Af_Rx_SOC" units="J_per_mol"/>
<variable name="Ar_Rx_SOC" units="J_per_mol"/>
<variable initial_value="2" name="zCa" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>V_mem</ci>
<apply>
<divide/>
<ci>q_mem</ci>
<ci>C_m</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Ca_o</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_o</ci>
<ci>q_Ca_o</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_Ca_ER</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_ER</ci>
<ci>q_Ca_ER</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Am_Rx_SOC</ci>
<apply>
<times/>
<ci>zCa</ci>
<ci>F</ci>
<ci>V_mem</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Af_Rx_SOC</ci>
<apply>
<plus/>
<ci>mu_Ca_o</ci>
<ci>Am_Rx_SOC</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Ar_Rx_SOC</ci>
<ci>mu_Ca_i</ci>
</apply>
<!-- v_Rx_SOC = kappa_Rx_SOC*(exp((mu_Ca_o+n*mu_Ca_ER)/(R*T))-exp((mu_Ca_i+n*mu_Ca_ER)/(R*T)));-->
<apply>
<eq/>
<ci>v_Rx_SOC</ci>
<piecewise>
<piece>
<apply>
<times/>
<ci>kappa_Rx_SOC</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Af_Rx_SOC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>Ar_Rx_SOC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Am_Rx_SOC</ci>
<cn cellml:units="J_per_mol">0</cn>
</apply>
</piece>
<otherwise>
<apply>
<times/>
<apply>
<divide/>
<apply>
<divide/>
<apply>
<times/>
<ci>kappa_Rx_SOC</ci>
<ci>Am_Rx_SOC</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Am_Rx_SOC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<cn cellml:units="dimensionless">1</cn>
</apply>
</apply>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Af_Rx_SOC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>Ar_Rx_SOC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</otherwise>
</piecewise>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="SOC"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_mem" variable_2="q_mem"/>
<map_variables variable_1="C_m" variable_2="C_m"/>
<map_variables variable_1="q_Ca_o" variable_2="q_Ca_o"/>
<map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
<map_variables variable_1="q_Ca_ER" variable_2="q_Ca_ER"/>
<map_variables variable_1="v_Rx_SOC" variable_2="v_Rx_SOC"/>
</connection>
<connection>
<map_components component_1="SOC" component_2="SOC_parameters"/>
<map_variables variable_1="kappa_Rx_SOC" variable_2="kappa_Rx_SOC"/>
<map_variables variable_1="K_Ca_o" variable_2="K_Ca_o"/>
<map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
<map_variables variable_1="K_Ca_ER" variable_2="K_Ca_ER"/>
</connection>
<connection>
<map_components component_1="constants" component_2="SOC"/>
<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>
