Location: Strain channel - The Physics of Physiology @ 917d47ae334d / BG_strainchannel.cellml
- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2025-06-06 14:18:47+12:00
- Desc:
- Adding stoich file
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d29/rawfile/917d47ae334dcdb04d320d5288f5baeea626aeea/BG_strainchannel.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="strain_channel" 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="per_mol" units_ref="per_mol"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_mol"/>
<units name="mol_per_s" units_ref="mol_per_s"/>
<units name="C_per_mol" units_ref="C_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="fmol" units_ref="fmol"/>
<units name="fmol_per_sec" units_ref="fmol_per_s"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="pL" units_ref="pL"/>
<units name="mA_per_mM" units_ref="mA_per_mM"/>
</import>
<component name="environment">
<variable name="t" public_interface="out" units="second"/>
<variable initial_value="153400" name="C_m" public_interface="out" units="fF"/>
<variable initial_value="9.3276" name="q_Na_o" public_interface="out" units="fmol"/>
<variable initial_value="0.00456" name="q_Na_i" public_interface="out" units="fmol"/>
<variable initial_value="-13039" name="q_mem" public_interface="out" units="fC"/>
<variable initial_value="8.31" name="R" public_interface="out" units="J_per_K_per_mol"/>
<variable initial_value="310" name="T" public_interface="out" units="kelvin"/>
<variable initial_value="96500" name="F" public_interface="out" units="C_per_mol"/>
<variable name="v_NaChannel" public_interface="in" units="fmol_per_sec"/>
<variable name="V_mem" public_interface="out" units="J_per_C"/>
<variable name="I_mem_NaChannel" public_interface="in" units="fA"/>
<variable name="u_strain" public_interface="out" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_Na_i</ci>
</apply>
<ci>v_NaChannel</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_Na_o</ci>
</apply>
<apply>
<minus/>
<ci>v_NaChannel</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_mem</ci>
</apply>
<ci>I_mem_NaChannel</ci>
</apply>
<apply>
<eq/>
<ci>V_mem</ci>
<apply>
<divide/>
<ci>q_mem</ci>
<ci>C_m</ci>
</apply>
</apply>
<!-- strain is dimensionless-->
<apply>
<eq/>
<ci>u_strain</ci>
<cn cellml:units="dimensionless">0.05</cn>
</apply>
</math>
</component>
<component name="NaChannel_parameters">
<variable initial_value="0.0722023" name="kappa_NaChannel" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.00781119" name="K_Na_i" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0518535" name="K_Na_o" public_interface="out" units="per_fmol"/>
<variable initial_value="2" name="zNa" public_interface="out" units="dimensionless"/>
<variable initial_value="5e-88" name="Gamma" public_interface="out" units="J_per_mol"/>
</component>
<component name="NaChannel">
<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="zNa" public_interface="in" units="dimensionless"/>
<variable name="F" public_interface="in" units="C_per_mol"/>
<variable name="K_Na_i" public_interface="in" units="per_fmol"/>
<variable name="K_Na_o" public_interface="in" units="per_fmol"/>
<variable name="kappa_NaChannel" public_interface="in" units="fmol_per_sec"/>
<variable name="q_Na_i" public_interface="in" units="fmol"/>
<variable name="q_Na_o" public_interface="in" units="fmol"/>
<variable name="mu_Na_i" units="J_per_mol"/>
<variable name="mu_Na_o" units="J_per_mol"/>
<variable name="mu_membrane" units="J_per_mol"/>
<variable name="mu_strain" units="J_per_mol"/>
<variable name="Af_NaChannel" units="J_per_mol"/>
<variable name="Ar_NaChannel" units="J_per_mol"/>
<variable name="Am_NaChannel" units="J_per_mol"/>
<variable name="q_mem" public_interface="in" units="fC"/>
<variable name="v_NaChannel" public_interface="out" units="fmol_per_sec"/>
<variable name="I_mem_NaChannel" public_interface="out" units="fA"/>
<variable name="V_mem" public_interface="in" units="J_per_C"/>
<variable name="Gamma" public_interface="in" units="J_per_mol"/>
<variable name="u_strain" public_interface="in" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_Na_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Na_i</ci>
<ci>q_Na_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Na_o</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Na_o</ci>
<ci>q_Na_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_membrane</ci>
<apply>
<times/>
<ci>zNa</ci>
<ci>F</ci>
<ci>V_mem</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_strain</ci>
<apply>
<times/>
<ci>Gamma</ci>
<ci>u_strain</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Af_NaChannel</ci>
<apply>
<plus/>
<ci>mu_Na_o</ci>
<ci>mu_membrane</ci>
<ci>mu_strain</ci>
<ci>mu_O_gate</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Ar_NaChannel</ci>
<apply>
<plus/>
<ci>mu_Na_i</ci>
<ci>mu_O_gate</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Am_NaChannel</ci>
<apply>
<times/>
<ci>zNa</ci>
<ci>F</ci>
<ci>V_mem</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_NaChannel</ci>
<piecewise>
<piece>
<apply>
<times/>
<ci>kappa_NaChannel</ci>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_O_gate</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Af_NaChannel</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>Ar_NaChannel</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Am_NaChannel</ci>
<cn cellml:units="J_per_mol">0</cn>
</apply>
</piece>
<otherwise>
<apply>
<times/>
<apply>
<divide/>
<apply>
<divide/>
<apply>
<times/>
<ci>kappa_NaChannel</ci>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_O_gate</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<ci>Am_NaChannel</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>Am_NaChannel</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_NaChannel</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>Ar_NaChannel</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>I_mem_NaChannel</ci>
<apply>
<times/>
<apply>
<minus/>
<ci>zNa</ci>
</apply>
<ci>F</ci>
<ci>v_NaChannel</ci>
</apply>
</apply>
</math>
<!--
gate
-->
<variable name="mu_O_gate" public_interface="out" units="J_per_mol"/>
<variable name="mu_C_gate" public_interface="out" units="J_per_mol"/>
<variable initial_value="1e-88" name="kappa_gate" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1e-88" name="K_O_gate" public_interface="out" units="per_fmol"/>
<variable initial_value="1e-88" name="K_C_gate" public_interface="out" units="per_fmol"/>
<variable initial_value="1e-88" name="q_O_gate" units="fmol"/>
<variable initial_value="1e-88" name="q_C_gate" units="fmol"/>
<variable name="v_gate" units="fmol_per_sec"/>
<!-- gate: only Open and Closed states-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_O_gate</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_O_gate</ci>
<ci>q_O_gate</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_C_gate</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_C_gate</ci>
<ci>q_C_gate</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_gate</ci>
<apply>
<times/>
<ci>kappa_gate</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_C_gate</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_O_gate</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_O_gate</ci>
</apply>
<ci>v_gate</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_C_gate</ci>
</apply>
<apply>
<minus/>
<ci>v_gate</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="NaChannel"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="v_NaChannel" variable_2="v_NaChannel"/>
<map_variables variable_1="I_mem_NaChannel" variable_2="I_mem_NaChannel"/>
<map_variables variable_1="q_Na_i" variable_2="q_Na_i"/>
<map_variables variable_1="q_Na_o" variable_2="q_Na_o"/>
<map_variables variable_1="q_mem" variable_2="q_mem"/>
<map_variables variable_1="V_mem" variable_2="V_mem"/>
<map_variables variable_1="u_strain" variable_2="u_strain"/>
</connection>
<connection>
<map_components component_1="NaChannel" component_2="NaChannel_parameters"/>
<map_variables variable_1="K_Na_i" variable_2="K_Na_i"/>
<map_variables variable_1="K_Na_o" variable_2="K_Na_o"/>
<map_variables variable_1="kappa_NaChannel" variable_2="kappa_NaChannel"/>
<map_variables variable_1="zNa" variable_2="zNa"/>
<map_variables variable_1="Gamma" variable_2="Gamma"/>
</connection>
</model>