Location: Hodgkin & Huxley (1952) model @ ab2962b87966 / BG / INa_BG_open.cellml

Author:
WeiweiAi <wai484@aucklanduni.ac.nz>
Date:
2022-03-31 10:48:40+13:00
Desc:
Add open channel IV of HH models; Add simulation and plot python scripts
Permanent Source URI:
https://models.fieldml.org/workspace/64f/rawfile/ab2962b8796666ad9938a2577611c954f006b5fd/BG/INa_BG_open.cellml

<?xml version='1.0' encoding='UTF-8'?>
<!-- The BG of open Na channel model. -->
<model name="INa_BG_open" 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="../cellLib/BG/units_BG.cellml">
        <units name="per_fmol" units_ref="per_fmol"/>
        <units name="fmol" units_ref="fmol"/>
        <units name="fmol_per_sec" units_ref="fmol_per_sec"/>
        <units name="fA" units_ref="fA"/>
        <units name="J_per_mol" units_ref="J_per_mol"/>
        <units name="C_per_mol" units_ref="C_per_mol"/>
    </import>
    <import xlink:href="../cellLib/Components/units.cellml">
        <units name="mV" units_ref="mV"/>
        <units name="mV_per_ms" units_ref="mV_per_ms"/>
    </import>
    <import xlink:href="default_values_BG.cellml">
        <component component_ref="model_para" name="model_para"/>
        <component component_ref="initials" name="initials"/>
        <component component_ref="openCH_para" name="openCH_para"/>
    </import>
    <import xlink:href="../cellLib/Protocols/Voltage_ramp_protocol.cellml">
        <component component_ref="vramp_protocol_ms" name="vramp_protocol"/>
    </import>
    <import xlink:href="../cellLib/BG/constants_BG.cellml">
        <component component_ref="constants_BG" name="constants_BG"/>
    </import>
    <import xlink:href="../cellLib/Components/time.cellml">
        <component component_ref="time_s" name="time"/>
    </import>
    <import xlink:href="../cellLib/BG/Se_BG.cellml">
        <component component_ref="Se_BG" name="Na_sa"/>
    </import>
    <import xlink:href="channelNa_BG.cellml">
        <component component_ref="channelNa_BG" name="channelNa_BG"/>
    </import>
    <!-- Connect the parameters to the protocol definition -->
    <component name="Vstim_para">
        <variable initial_value="-100" name="V_init" public_interface="out" units="mV"/>
        <variable initial_value="1" name="V_rate" public_interface="out" units="mV_per_ms"/>
    </component>
    <connection>
        <map_components component_1="Vstim_para" component_2="vramp_protocol"/>
        <map_variables variable_1="V_init" variable_2="V_init"/>
        <map_variables variable_1="V_rate" variable_2="V_rate"/>
    </connection>
    <connection>
        <map_components component_1="vramp_protocol" component_2="boundary_conditions"/>
        <map_variables variable_1="V" variable_2="V_m"/>
    </connection>
    <connection>
        <map_components component_1="time" component_2="vramp_protocol"/>
        <map_variables variable_1="time" variable_2="time"/>
    </connection>
    <component name="boundary_conditions">
        <variable name="F" public_interface="in" units="C_per_mol"/>
        <variable name="V_m" public_interface="in" units="volt"/>
        <variable name="mu_p" public_interface="out" units="J_per_mol"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_p</ci>
                <apply>
                    <times/>
                    <ci>F</ci>
                    <ci>V_m</ci>
                </apply>
            </apply>
        </math>
    </component>
    <component name="outputs">
        <variable name="F" public_interface="in" units="C_per_mol"/>
        <variable name="time" public_interface="in" units="second"/>
        <variable name="v_p_Na" public_interface="in" units="fmol_per_sec"/>
        <variable name="I_Na" public_interface="out" units="fA"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>I_Na</ci>
                <apply>
                    <times/>
                    <ci>F</ci>
                    <ci>v_p_Na</ci>
                </apply>
            </apply>
        </math>
    </component>
    <component name="INa_BG_open">
        <!--Parameters-->
        <variable name="T" private_interface="out" public_interface="in" units="kelvin"/>
        <variable name="kappa_Na" private_interface="out" public_interface="in" units="fmol_per_sec"/>
        <variable name="z_Na" private_interface="out" public_interface="in" units="dimensionless"/>
        <variable name="K_i_Na" private_interface="out" public_interface="in" units="per_fmol"/>
        <variable name="q_i_Na_init" private_interface="out" public_interface="in" units="fmol"/>
        <variable name="K_e_Na" private_interface="out" public_interface="in" units="per_fmol"/>
        <variable name="q_e_Na_init" private_interface="out" public_interface="in" units="fmol"/>
        <variable name="K_sa_Na" private_interface="out" public_interface="in" units="per_fmol"/>
        <variable name="q_sa_Na" private_interface="out" public_interface="in" units="fmol"/>
        <variable initial_value="0" name="v_sa_Na" private_interface="out" units="fmol_per_sec"/>
        <!--Inputs-->
        <variable name="t" private_interface="out" public_interface="in" units="second"/>
        <variable name="mu_p" private_interface="out" public_interface="in" units="J_per_mol"/>
        <!--Outputs-->
        <variable name="v_p_Na" private_interface="in" public_interface="out" units="fmol_per_sec"/>
    </component>
    <group>
        <relationship_ref relationship="encapsulation"/>
        <component_ref component="INa_BG_open">
            <component_ref component="channelNa_BG"/>
            <component_ref component="Na_sa"/>
        </component_ref>
    </group>
    <connection>
        <map_components component_1="outputs" component_2="time"/>
        <map_variables variable_1="time" variable_2="time"/>
    </connection>
    <connection>
        <map_components component_1="outputs" component_2="INa_BG_open"/>
        <map_variables variable_1="v_p_Na" variable_2="v_p_Na"/>
    </connection>
    <connection>
        <map_components component_1="INa_BG_open" component_2="time"/>
        <map_variables variable_1="t" variable_2="time"/>
    </connection>
    <connection>
        <map_components component_1="boundary_conditions" component_2="INa_BG_open"/>
        <map_variables variable_1="mu_p" variable_2="mu_p"/>
    </connection>
    <connection>
        <map_components component_1="boundary_conditions" component_2="constants_BG"/>
        <map_variables variable_1="F" variable_2="F"/>
    </connection>
    <connection>
        <map_components component_1="outputs" component_2="constants_BG"/>
        <map_variables variable_1="F" variable_2="F"/>
    </connection>
    <connection>
        <map_components component_1="INa_BG_open" component_2="Na_sa"/>
        <map_variables variable_1="T" variable_2="T"/>
        <map_variables variable_1="t" variable_2="t"/>
        <map_variables variable_1="K_sa_Na" variable_2="K"/>
        <map_variables variable_1="q_sa_Na" variable_2="q_init"/>
        <map_variables variable_1="v_sa_Na" variable_2="v"/>
    </connection>
    <connection>
        <map_components component_1="channelNa_BG" component_2="Na_sa"/>
        <map_variables variable_1="A_g_Na" variable_2="mu"/>
    </connection>
    <connection>
        <map_components component_1="INa_BG_open" component_2="channelNa_BG"/>
        <map_variables variable_1="T" variable_2="T"/>
        <map_variables variable_1="t" variable_2="t"/>
        <map_variables variable_1="kappa_Na" variable_2="kappa_Na"/>
        <map_variables variable_1="z_Na" variable_2="z_Na"/>
        <map_variables variable_1="K_i_Na" variable_2="K_i_Na"/>
        <map_variables variable_1="q_i_Na_init" variable_2="q_i_Na_init"/>
        <map_variables variable_1="K_e_Na" variable_2="K_e_Na"/>
        <map_variables variable_1="q_e_Na_init" variable_2="q_e_Na_init"/>
        <map_variables variable_1="mu_p" variable_2="mu_p"/>
        <map_variables variable_1="v_p_Na" variable_2="v_p_Na"/>
    </connection>
    <connection>
        <map_components component_1="model_para" component_2="INa_BG_open"/>
        <map_variables variable_1="T" variable_2="T"/>
        <map_variables variable_1="z_Na" variable_2="z_Na"/>
    </connection>
    <connection>
        <map_components component_1="openCH_para" component_2="INa_BG_open"/>
        <map_variables variable_1="kappa_Na" variable_2="kappa_Na"/>
        <map_variables variable_1="K_i_Na" variable_2="K_i_Na"/>
        <map_variables variable_1="K_e_Na" variable_2="K_e_Na"/>
        <map_variables variable_1="K_sa_Na" variable_2="K_sa_Na"/>
        <map_variables variable_1="q_sa_Na" variable_2="q_sa_Na"/>
    </connection>
    <connection>
        <map_components component_1="initials" component_2="INa_BG_open"/>
        <map_variables variable_1="q_i_Na_init" variable_2="q_i_Na_init"/>
        <map_variables variable_1="q_e_Na_init" variable_2="q_e_Na_init"/>
    </connection>
</model>