- Author:
- MarionDospital <marion.dospital@gmail.com>
- Date:
- 2025-03-19 15:18:04+01:00
- Desc:
- Ajout des modeles Kapela et Parthimos OpenCor et des articles
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/cc8/rawfile/65447a1c0b5212fa84651a8d2484506c7bdddfec/Modele_PARTHIMOS.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="Parthimos" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<units name="uM">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="ms">
<unit prefix="milli" units="second"/>
</units>
<units name="uM_per_ms">
<unit units="uM"/>
<unit exponent="-1" units="ms"/>
</units>
<units name="coulomb_per_mmole">
<unit units="coulomb"/>
<unit exponent="-1" prefix="milli" units="mole"/>
</units>
<units name="per_ms">
<unit exponent="-1" units="ms"/>
</units>
<units name="millivolt">
<unit prefix="milli" units="volt"/>
</units>
<units name="millivolt_per_uM">
<unit units="millivolt"/>
<unit exponent="-1" units="uM"/>
</units>
<units name="uM_per_millivolt_per_ms">
<unit units="uM"/>
<unit exponent="-1" units="millivolt"/>
<unit exponent="-1" units="ms"/>
</units>
<units name="uM_2">
<unit exponent="2" units="uM"/>
</units>
<component name="environment">
<variable name="time" public_interface="out" units="ms"/>
</component>
<!--Membrane/////////////////////////////////////////////////////////////////////////////////////////////-->
<component name="membrane">
<variable cmeta:id="membrane_V" initial_value="-66.0" name="V" public_interface="out" units="millivolt"/>
<variable name="time" public_interface="in" units="ms"/>
<variable name="J_VOCC" public_interface="in" units="uM_per_ms"/>
<variable name="J_KCa" public_interface="in" units="uM_per_ms"/>
<variable name="J_NaCa" public_interface="in" units="uM_per_ms"/>
<variable name="J_Cl" public_interface="in" units="uM_per_ms"/>
<variable initial_value="0.00032" name="J_NaK" public_interface="out" units="uM_per_ms"/>
<variable name="J_total_membrane" public_interface="out" units="uM_per_ms"/>
<variable initial_value="1.970" name="gamma" units="millivolt_per_uM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_total_membrane</ci>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>J_Cl</ci>
<ci>J_NaK</ci>
</apply>
<ci>J_Cl</ci>
</apply>
<apply>
<times/>
<cn cellml:units="dimensionless">2</cn>
<ci>J_VOCC</ci>
</apply>
</apply>
<ci>J_NaCa</ci>
</apply>
<ci>J_KCa</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>V</ci>
</apply>
<apply>
<times/>
<ci>gamma</ci>
<ci>J_total_membrane</ci>
</apply>
</apply>
</math>
</component>
<!--Dynamique du calcium//////////////////////////////////////////////////////////////////////////////////-->
<component name="calcium_dynamics">
<variable initial_value="0.00845" name="Ca_i" public_interface="out" units="uM"/>
<variable initial_value="0.001" name="A0" units="uM_per_ms"/>
<variable name="time" public_interface="in" units="ms"/>
<variable name="J_IICR" public_interface="in" units="uM_per_ms"/>
<variable name="J_PMCA" public_interface="in" units="uM_per_ms"/>
<variable name="J_VOCC" public_interface="in" units="uM_per_ms"/>
<variable name="J_NaCa" public_interface="in" units="uM_per_ms"/>
<variable name="J_SR_total" public_interface="in" units="uM_per_ms"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca_i</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<plus/>
<ci>A0</ci>
<ci>J_IICR</ci>
</apply>
<ci>J_VOCC</ci>
</apply>
<ci>J_NaCa</ci>
</apply>
<ci>J_SR_total</ci>
</apply>
<ci>J_PMCA</ci>
</apply>
</apply>
</math>
</component>
<!--Fuite chlorique//////////////////////////////////////////////////////////////////////////////////////-->
<component name="leak_current_Cl">
<variable name="J_Cl" public_interface="out" units="uM_per_ms"/>
<variable initial_value="0.0099" name="G_Cl" units="uM_per_millivolt_per_ms"/>
<variable initial_value="-65.0" name="E_Cl" units="millivolt"/>
<variable name="V" public_interface="in" units="millivolt"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_Cl</ci>
<apply>
<times/>
<ci>G_Cl</ci>
<apply>
<minus/>
<ci>V</ci>
<ci>E_Cl</ci>
</apply>
</apply>
</apply>
</math>
</component>
<!--Canal VOCC//////////////////////////////////////////////////////////////////////////////////////////-->
<component name="VOCC_flux">
<variable name="V" public_interface="in" units="millivolt"/>
<variable initial_value="0.00957" name="G_Ca" units="uM_per_millivolt_per_ms"/>
<variable initial_value="100" name="z_Ca1" units="millivolt"/>
<variable initial_value="-24" name="z_Ca2" units="millivolt"/>
<variable initial_value="8.5" name="R_Ca" units="millivolt"/>
<variable name="J_VOCC" public_interface="out" units="uM_per_ms"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_VOCC</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>G_Ca</ci>
<apply>
<minus/>
<ci>V</ci>
<ci>z_Ca1</ci>
</apply>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<minus/>
<ci>V</ci>
<ci>z_Ca2</ci>
</apply>
</apply>
<ci>R_Ca</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<!--Echangeur Na/Ca////////////////////////////////////////////////////////////////////////////////////-->
<component name="nacax_exchanger">
<variable name="J_NaCa" public_interface="out" units="uM_per_ms"/>
<variable initial_value="0.0264" name="G_NaCa" units="uM_per_millivolt_per_ms"/>
<variable initial_value="-40.0" name="z_NaCa" units="millivolt"/>
<variable initial_value="0.5" name="x_NaCa" units="uM"/>
<variable name="Ca_i" public_interface="in" units="uM"/>
<variable name="V" public_interface="in" units="millivolt"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_NaCa</ci>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>G_NaCa</ci>
<ci>Ca_i</ci>
</apply>
<apply>
<plus/>
<ci>Ca_i</ci>
<ci>x_NaCa</ci>
</apply>
</apply>
<apply>
<minus/>
<ci>V</ci>
<ci>z_NaCa</ci>
</apply>
</apply>
</apply>
</math>
</component>
<!--porte w du canal KCa///////////////////////////////////////////////////////////////////////////////-->
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="k_flux">
<component_ref component="w_kca_gate"/>
</component_ref>
</group>
<component name="w_kca_gate">
<variable name="V" public_interface="in" units="millivolt"/>
<variable name="time" public_interface="in" units="ms"/>
<variable initial_value="0.05" name="w" public_interface="out" units="dimensionless"/>
<variable initial_value="0.045" name="lambda" units="per_ms"/>
<variable initial_value="1" name="S" units="dimensionless"/>
<variable name="Ca_i" public_interface="in" units="uM"/>
<variable initial_value="0" name="xw" units="uM"/>
<variable initial_value="0.13" name="beta" units="uM_2"/>
<variable initial_value="-27" name="zca3" units="millivolt"/>
<variable initial_value="12" name="Rk" units="millivolt"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>w</ci>
</apply>
<apply>
<times/>
<ci>lambda</ci>
<apply>
<minus/>
<apply>
<divide/>
<apply>
<times/>
<ci>S</ci>
<apply>
<power/>
<apply>
<plus/>
<ci>Ca_i</ci>
<ci>xw</ci>
</apply>
<cn cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<apply>
<plus/>
<ci>Ca_i</ci>
<ci>xw</ci>
</apply>
<cn cellml:units="dimensionless">2</cn>
</apply>
<apply>
<times/>
<ci>beta</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<minus/>
<ci>V</ci>
<ci>zca3</ci>
</apply>
</apply>
<ci>Rk</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<ci>w</ci>
</apply>
</apply>
</apply>
</math>
</component>
<!--Canal KCa//////////////////////////////////////////////////////////////////////////////////////////-->
<component name="k_flux">
<variable name="J_KCa" public_interface="out" units="uM_per_ms"/>
<variable initial_value="0.033" name="g_KCa" units="uM_per_millivolt_per_ms"/>
<variable initial_value="-94.0" name="E_K" units="millivolt"/>
<variable name="time" private_interface="out" public_interface="in" units="ms"/>
<variable name="V" private_interface="out" public_interface="in" units="millivolt"/>
<variable name="Ca_i" private_interface="out" public_interface="in" units="uM"/>
<variable name="w" private_interface="in" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_KCa</ci>
<apply>
<times/>
<ci>g_KCa</ci>
<ci>w</ci>
<apply>
<minus/>
<ci>V</ci>
<ci>E_K</ci>
</apply>
</apply>
</apply>
</math>
</component>
<!--Reticulum Sarcoplasmique///////////////////////////////////////////////////////////////////////////////-->
<component name="SR">
<variable name="time" public_interface="in" units="ms"/>
<variable name="J_SR_total" public_interface="out" units="uM_per_ms"/>
<variable name="J_fuite" public_interface="in" units="uM_per_ms"/>
<variable name="J_SERCA" public_interface="in" units="uM_per_ms"/>
<variable name="J_CICR" public_interface="in" units="uM_per_ms"/>
<variable initial_value="0.0326" name="Ca_SR" public_interface="out" units="uM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_SR_total</ci>
<apply>
<minus/>
<apply>
<minus/>
<ci>J_SERCA</ci>
<ci>J_CICR</ci>
</apply>
<ci>J_fuite</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Ca_SR</ci>
</apply>
<ci>J_SR_total</ci>
</apply>
</math>
</component>
<!--InsP3R////////////////////////////////////////////////////////////////////////////////////////////////-->
<component name="InsP3R">
<variable name="J_IICR" public_interface="out" units="uM_per_ms"/>
<variable initial_value="0.00005" name="J_IICR_constante" units="uM_per_ms"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_IICR</ci>
<ci>J_IICR_constante</ci>
</apply>
</math>
</component>
<!--Fuite passive/////////////////////////////////////////////////////////////////////////////////////////-->
<component name="fuite_passive">
<variable name="J_fuite" public_interface="out" units="uM_per_ms"/>
<variable name="Ca_SR" public_interface="in" units="uM"/>
<variable name="Ca_i" public_interface="in" units="uM"/>
<variable initial_value="0.000025" name="g_fuite" units="per_ms"/>
<!-- J_fuite = g_fuite*(Ca_SR-Ca_i);-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_fuite</ci>
<apply>
<times/>
<ci>g_fuite</ci>
<ci>Ca_SR</ci>
</apply>
</apply>
</math>
</component>
<!--PMCA//////////////////////////////////////////////////////////////////////////////////////////////////-->
<component name="PMCA">
<variable name="J_PMCA" public_interface="out" units="uM_per_ms"/>
<variable name="Ca_i" public_interface="in" units="uM"/>
<variable name="V" public_interface="in" units="millivolt"/>
<variable initial_value="1" name="q" units="dimensionless"/>
<variable initial_value="0.003" name="D" units="per_ms"/>
<variable initial_value="-100" name="zd" units="millivolt"/>
<variable initial_value="250" name="Rd" units="millivolt"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_PMCA</ci>
<apply>
<times/>
<ci>D</ci>
<apply>
<power/>
<ci>Ca_i</ci>
<ci>q</ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<divide/>
<apply>
<minus/>
<ci>V</ci>
<ci>zd</ci>
</apply>
<ci>Rd</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<!--SERCA////////////////////////////////////////////////////////////////////////////////////////////////-->
<component name="SERCA">
<variable name="J_SERCA" public_interface="out" units="uM_per_ms"/>
<variable initial_value="0.0125" name="B" units="uM_per_ms"/>
<variable name="Ca_i" public_interface="in" units="uM"/>
<variable initial_value="2" name="n" units="dimensionless"/>
<variable initial_value="1" name="x_b" units="uM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_SERCA</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="dimensionless">1</cn>
<ci>B</ci>
<apply>
<power/>
<ci>Ca_i</ci>
<ci>n</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>Ca_i</ci>
<ci>n</ci>
</apply>
<apply>
<power/>
<ci>x_b</ci>
<ci>n</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<!--CICR//////////////////////////////////////////////////////////////////////////////////////////////////-->
<component name="CICR">
<variable name="J_CICR" public_interface="out" units="uM_per_ms"/>
<variable initial_value="0.1625" name="C" units="uM_per_ms"/>
<variable initial_value="2" name="m" units="dimensionless"/>
<variable name="Ca_SR" public_interface="in" units="uM"/>
<variable initial_value="0.1" name="y_c" units="uM"/>
<variable name="Ca_i" public_interface="in" units="uM"/>
<variable initial_value="4" name="p" units="dimensionless"/>
<variable initial_value="0.9" name="x_c" units="uM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>J_CICR</ci>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>C</ci>
<apply>
<power/>
<ci>Ca_SR</ci>
<ci>m</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>Ca_SR</ci>
<ci>m</ci>
</apply>
<apply>
<power/>
<ci>y_c</ci>
<ci>m</ci>
</apply>
</apply>
</apply>
<apply>
<power/>
<ci>Ca_i</ci>
<ci>p</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>Ca_i</ci>
<ci>p</ci>
</apply>
<apply>
<power/>
<ci>x_c</ci>
<ci>p</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<!--Mapping/////////////////////////////////////////////////////////////////////////////////////////////// -->
<!--Mapping SR - autres composants////////////////////////////////////////////////////////////////////-->
<connection>
<map_components component_1="SR" component_2="fuite_passive"/>
<map_variables variable_1="J_fuite" variable_2="J_fuite"/>
<map_variables variable_1="Ca_SR" variable_2="Ca_SR"/>
</connection>
<connection>
<map_components component_1="SR" component_2="SERCA"/>
<map_variables variable_1="J_SERCA" variable_2="J_SERCA"/>
</connection>
<connection>
<map_components component_1="SR" component_2="CICR"/>
<map_variables variable_1="J_CICR" variable_2="J_CICR"/>
<map_variables variable_1="Ca_SR" variable_2="Ca_SR"/>
</connection>
<!--Mapping Membrane - autres composants//////////////////////////////////////////////////////////////-->
<connection>
<map_components component_1="membrane" component_2="PMCA"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<connection>
<map_components component_1="membrane" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="k_flux" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="k_flux" component_2="w_kca_gate"/>
<map_variables variable_1="w" variable_2="w"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="k_flux"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="nacax_exchanger"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
<map_variables variable_1="J_NaCa" variable_2="J_NaCa"/>
</connection>
<connection>
<map_components component_1="VOCC_flux" component_2="calcium_dynamics"/>
<map_variables variable_1="J_VOCC" variable_2="J_VOCC"/>
</connection>
<connection>
<map_components component_1="k_flux" component_2="membrane"/>
<map_variables variable_1="J_KCa" variable_2="J_KCa"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<connection>
<map_components component_1="VOCC_flux" component_2="membrane"/>
<map_variables variable_1="J_VOCC" variable_2="J_VOCC"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<connection>
<map_components component_1="nacax_exchanger" component_2="membrane"/>
<map_variables variable_1="J_NaCa" variable_2="J_NaCa"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<connection>
<map_components component_1="leak_current_Cl" component_2="membrane"/>
<map_variables variable_1="J_Cl" variable_2="J_Cl"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="SERCA"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="InsP3R"/>
<map_variables variable_1="J_IICR" variable_2="J_IICR"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="PMCA"/>
<map_variables variable_1="J_PMCA" variable_2="J_PMCA"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="fuite_passive"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="CICR"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<connection>
<map_components component_1="calcium_dynamics" component_2="SR"/>
<map_variables variable_1="J_SR_total" variable_2="J_SR_total"/>
</connection>
<connection>
<map_components component_1="SR" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
</model>
