Location: BG_RyR @ e6e50f6e49d0 / BG_RyR.cellml
- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-10-28 16:51:40+13:00
- Desc:
- Renaming kinetic_parameters.py
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6e3/rawfile/e6e50f6e49d0368dea326f0c40a41f781e8e1c09/BG_RyR.cellml
<?xml version='1.0' encoding='UTF-8'?>
<!-- Release of Calcium from ryanodine channel, from sarcolemma to diadic space (in cytosol)
Based on Stern 97
Model is of charged ion flowing through a gated channel-->
<model name="ryanodine_module" 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="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<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="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"/>
<variable name="F" public_interface="in" units="C_per_mol"/>
<variable initial_value="-0.08" name="V_m" public_interface="out" units="volt"/>
<variable initial_value="1.381e5" name="C_m" units="fF"/>
<variable name="cCa_SR" units="mM"/>
<variable name="cCa_di" units="mM"/>
<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="1.16" name="vol_SR" units="pL"/>
<variable initial_value="1.78e-2" name="vol_di" units="pL"/>
<variable name="v_RyR" public_interface="in" units="fmol_per_sec"/>
<variable name="v_gate_Ca_di" public_interface="in" units="fmol_per_sec"/>
<!-- fluxes from channel-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_SR</ci>
</apply>
<apply>
<minus/>
<ci>v_RyR</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_di</ci>
</apply>
<apply>
<plus/>
<ci>v_RyR</ci>
<ci>v_gate_Ca_di</ci>
</apply>
</apply>
<!-- membrane potential change-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>V_m</ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<apply>
<minus/>
<ci>v_RyR</ci>
</apply>
<ci>F</ci>
</apply>
<ci>C_m</ci>
</apply>
</apply>
<!-- concentrations for plotting-->
<apply>
<eq/>
<ci>cCa_SR</ci>
<apply>
<divide/>
<ci>q_Ca_SR</ci>
<ci>vol_SR</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>cCa_di</ci>
<apply>
<divide/>
<ci>q_Ca_di</ci>
<ci>vol_di</ci>
</apply>
</apply>
</math>
</component>
<component name="RyR_parameters">
<variable initial_value="10.3536" name="kappa_RyR" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2.77388" name="K_Ca_SR" public_interface="out" units="per_fmol"/>
<variable initial_value="180.769" name="K_Ca_di" public_interface="out" units="per_fmol"/>
</component>
<component name="RyR">
<variable name="t" public_interface="in" units="second"/>
<variable name="V_m" public_interface="in" units="volt"/>
<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_RyR" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2" name="z" units="dimensionless"/>
<variable initial_value="1" name="nCa_1" units="dimensionless"/>
<variable initial_value="2" name="nCa_2" units="dimensionless"/>
<!-- molecular species-->
<variable name="q_Ca_SR" public_interface="in" units="fmol"/>
<variable name="q_Ca_di" public_interface="in" units="fmol"/>
<!--BG 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_di" public_interface="in" units="per_fmol"/>
<variable name="mu_Ca_SR" units="J_per_C"/>
<variable name="mu_Ca_di" units="J_per_C"/>
<variable name="mu_SO" units="J_per_C"/>
<variable name="mu_SC" units="J_per_C"/>
<variable name="mu_SCI" units="J_per_C"/>
<variable name="mu_SI" units="J_per_C"/>
<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_di</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_di</ci>
<ci>q_Ca_di</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_RyR</ci>
<apply>
<times/>
<ci>kappa_RyR</ci>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_SO</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_Ca_SR</ci>
<apply>
<times/>
<ci>z</ci>
<ci>F</ci>
<ci>V_m</ci>
</apply>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_Ca_di</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
<!-- ------------------------------------------------------------------
gate -->
<variable initial_value="1e-11" name="q_SO" units="fmol"/>
<variable initial_value="1e-11" name="q_SC" units="fmol"/>
<variable initial_value="1e-11" name="q_SCI" units="fmol"/>
<variable initial_value="1e-11" name="q_SI" units="fmol"/>
<variable initial_value="8.83262" name="kappa_OC" units="fmol_per_sec"/>
<variable initial_value="0.12618" name="kappa_CCI" units="fmol_per_sec"/>
<variable initial_value="883.262" name="kappa_CII" units="fmol_per_sec"/>
<variable initial_value="73.6052" name="kappa_IO" units="fmol_per_sec"/>
<variable initial_value="3962.58" name="K_SC" units="per_fmol"/>
<variable initial_value="39.6258" name="K_SCI" units="per_fmol"/>
<variable initial_value="0.06793" name="K_SI" units="per_fmol"/>
<variable initial_value="6.793" name="K_SO" units="per_fmol"/>
<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"/>
<variable name="v_gate_Ca_di" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_SO</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_SO</ci>
<ci>q_SO</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_SC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_SC</ci>
<ci>q_SC</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_SCI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_SCI</ci>
<ci>q_SCI</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_SI</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_SI</ci>
<ci>q_SI</ci>
</apply>
</apply>
</apply>
</apply>
<!-- gate transitions-->
<apply>
<eq/>
<ci>v_OC</ci>
<apply>
<times/>
<ci>kappa_OC</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_SO</ci>
<apply>
<times/>
<ci>nCa_2</ci>
<ci>mu_Ca_di</ci>
</apply>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_SC</ci>
<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_SC</ci>
<apply>
<times/>
<ci>nCa_1</ci>
<ci>mu_Ca_di</ci>
</apply>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_SCI</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_SCI</ci>
<apply>
<times/>
<ci>nCa_2</ci>
<ci>mu_Ca_di</ci>
</apply>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_SI</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/>
<apply>
<plus/>
<ci>mu_SI</ci>
<apply>
<times/>
<ci>nCa_1</ci>
<ci>mu_Ca_di</ci>
</apply>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_SO</ci>
<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_SO</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_SC</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_SCI</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_SI</ci>
</apply>
<apply>
<minus/>
<ci>v_CII</ci>
<ci>v_IO</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_gate_Ca_di</ci>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<times/>
<apply>
<minus/>
<ci>nCa_2</ci>
</apply>
<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>
</component>
<connection>
<map_components component_1="environment" component_2="constants"/>
<map_variables variable_1="F" variable_2="F"/>
</connection>
<connection>
<map_components component_1="environment" component_2="RyR"/>
<map_variables variable_1="time" variable_2="t"/>
<map_variables variable_1="V_m" variable_2="V_m"/>
<map_variables variable_1="v_RyR" variable_2="v_RyR"/>
<map_variables variable_1="q_Ca_SR" variable_2="q_Ca_SR"/>
<map_variables variable_1="q_Ca_di" variable_2="q_Ca_di"/>
<map_variables variable_1="v_gate_Ca_di" variable_2="v_gate_Ca_di"/>
</connection>
<connection>
<map_components component_1="constants" component_2="RyR"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="R" variable_2="R"/>
</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_di" variable_2="K_Ca_di"/>
</connection>
</model>