- 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>
