- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2025-09-05 14:27:21+12:00
- Desc:
- Adding Cellml with params
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d56/rawfile/daf905e976c1e5bb1b29f8c1035040da8f7fe659/BG_NMDA.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_NMDA" 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="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_s"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="J_per_C" units_ref="J_per_C"/>
<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="millivolt" units_ref="millivolt"/>
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_mol"/>
<units name="fmol_per_L" units_ref="fmol_per_L"/>
<units name="fmol_per_L_per_sec" units_ref="fmol_per_L_per_sec"/>
<units name="per_sec_per_fmol_per_L" units_ref="per_sec_per_fmol_per_L"/>
<units name="uM" units_ref="uM"/>
<units name="mM_per_sec" units_ref="mM_per_sec"/>
<units name="uM_per_sec" units_ref="uM_per_sec"/>
<units name="pL" units_ref="pL"/>
<units name="m_to_u" units_ref="m_to_u"/>
</import>
<import xlink:href="units_and_constants/constants.cellml">
<component component_ref="constants" name="constants"/>
</import>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<!-- initial values-->
<variable initial_value="1e-18" name="q_Ca_o" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_Ca_i" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_R_Mg" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_R_Mg_open" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_R_open" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_Gly" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_Glu" public_interface="out" units="fmol"/>
<variable initial_value="1e-18" name="q_Mg_o" public_interface="out" units="fmol"/>
<variable name="nGly" public_interface="in" units="dimensionless"/>
<variable name="nGlu" public_interface="in" units="dimensionless"/>
<!-- From submodule-->
<variable name="v_Re_bind" public_interface="in" units="fmol_per_sec"/>
<variable name="v_Re_depol" public_interface="in" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_depol</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_i</ci>
</apply>
<ci>v_Re_depol</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_Mg</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_bind</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_Mg_open</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_bind</ci>
<ci>v_Re_depol</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_open</ci>
</apply>
<ci>v_Re_depol</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Gly</ci>
</apply>
<apply>
<times/>
<apply>
<minus/>
<ci>v_Re_bind</ci>
</apply>
<ci>nGly</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Glu</ci>
</apply>
<apply>
<times/>
<apply>
<minus/>
<ci>v_Re_bind</ci>
</apply>
<ci>nGlu</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Mg_o</ci>
</apply>
<ci>v_Re_depol</ci>
</apply>
</math>
</component>
<component name="NMDA_parameters">
<variable initial_value="0.000158922" name="kappa_Re_bind" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="3.27185" name="kappa_Re_depol" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="6.39112e+08" name="K_Ca_o" public_interface="out" units="per_fmol"/>
<variable initial_value="0.000549429" name="K_Ca_i" public_interface="out" units="per_fmol"/>
<variable initial_value="1.00061" name="K_R_Mg" public_interface="out" units="per_fmol"/>
<variable initial_value="0.000513247" name="K_R_Mg_open" public_interface="out" units="per_fmol"/>
<variable initial_value="0.000549429" name="K_R_open" public_interface="out" units="per_fmol"/>
<variable initial_value="1.98016e+08" name="K_Gly" public_interface="out" units="per_fmol"/>
<variable initial_value="1.98016e+08" name="K_Glu" public_interface="out" units="per_fmol"/>
<variable initial_value="8863.16" name="K_Mg_o" public_interface="out" units="per_fmol"/>
<variable initial_value="2" name="nGly" public_interface="out" units="dimensionless"/>
<variable initial_value="2" name="nGlu" public_interface="out" units="dimensionless"/>
</component>
<component name="NMDA">
<variable name="time" 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"/>
<!-- parameters-->
<variable name="kappa_Re_bind" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_Re_depol" public_interface="in" units="fmol_per_sec"/>
<variable name="K_Ca_o" public_interface="in" units="per_fmol"/>
<variable name="K_Ca_i" public_interface="in" units="per_fmol"/>
<variable name="K_R_Mg" public_interface="in" units="per_fmol"/>
<variable name="K_R_Mg_open" public_interface="in" units="per_fmol"/>
<variable name="K_R_open" public_interface="in" units="per_fmol"/>
<variable name="K_Gly" public_interface="in" units="per_fmol"/>
<variable name="K_Glu" public_interface="in" units="per_fmol"/>
<variable name="K_Mg_o" public_interface="in" units="per_fmol"/>
<variable name="nGly" public_interface="in" units="dimensionless"/>
<variable name="nGlu" public_interface="in" units="dimensionless"/>
<!-- Input from global environment-->
<variable name="q_Ca_o" public_interface="in" units="fmol"/>
<variable name="q_Ca_i" public_interface="in" units="fmol"/>
<variable name="q_R_Mg" public_interface="in" units="fmol"/>
<variable name="q_R_Mg_open" public_interface="in" units="fmol"/>
<variable name="q_R_open" public_interface="in" units="fmol"/>
<variable name="q_Gly" public_interface="in" units="fmol"/>
<variable name="q_Glu" public_interface="in" units="fmol"/>
<variable name="q_Mg_o" public_interface="in" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_Ca_o" units="J_per_mol"/>
<variable name="mu_Ca_i" units="J_per_mol"/>
<variable name="mu_R_Mg" units="J_per_mol"/>
<variable name="mu_R_Mg_open" units="J_per_mol"/>
<variable name="mu_R_open" units="J_per_mol"/>
<variable name="mu_Gly" units="J_per_mol"/>
<variable name="mu_Glu" units="J_per_mol"/>
<variable name="mu_Mg_o" units="J_per_mol"/>
<variable name="v_Re_bind" public_interface="out" units="fmol_per_sec"/>
<variable name="v_Re_depol" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_Ca_o</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_o</ci>
<ci>q_Ca_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Ca_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_i</ci>
<ci>q_Ca_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_Mg</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_Mg</ci>
<ci>q_R_Mg</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_Mg_open</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_Mg_open</ci>
<ci>q_R_Mg_open</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_open</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_open</ci>
<ci>q_R_open</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Gly</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Gly</ci>
<ci>q_Gly</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Glu</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Glu</ci>
<ci>q_Glu</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Mg_o</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Mg_o</ci>
<ci>q_Mg_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_bind</ci>
<apply>
<times/>
<ci>kappa_Re_bind</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_R_Mg</ci>
<apply>
<times/>
<ci>nGly</ci>
<ci>mu_Gly</ci>
</apply>
<apply>
<times/>
<ci>nGlu</ci>
<ci>mu_Glu</ci>
</apply>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_R_Mg_open</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_depol</ci>
<apply>
<times/>
<ci>kappa_Re_depol</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_Ca_o</ci>
<ci>mu_R_Mg_open</ci>
<ci>mu_Glu</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_R_open</ci>
<ci>mu_Mg_o</ci>
<ci>mu_Ca_i</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="NMDA"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_Ca_o" variable_2="q_Ca_o"/>
<map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
<map_variables variable_1="q_R_Mg" variable_2="q_R_Mg"/>
<map_variables variable_1="q_R_Mg_open" variable_2="q_R_Mg_open"/>
<map_variables variable_1="q_R_open" variable_2="q_R_open"/>
<map_variables variable_1="q_Gly" variable_2="q_Gly"/>
<map_variables variable_1="q_Glu" variable_2="q_Glu"/>
<map_variables variable_1="q_Mg_o" variable_2="q_Mg_o"/>
<map_variables variable_1="v_Re_bind" variable_2="v_Re_bind"/>
<map_variables variable_1="v_Re_depol" variable_2="v_Re_depol"/>
<map_variables variable_1="nGlu" variable_2="nGlu"/>
<map_variables variable_1="nGly" variable_2="nGly"/>
</connection>
<connection>
<map_components component_1="NMDA" component_2="NMDA_parameters"/>
<map_variables variable_1="kappa_Re_bind" variable_2="kappa_Re_bind"/>
<map_variables variable_1="kappa_Re_depol" variable_2="kappa_Re_depol"/>
<map_variables variable_1="K_Ca_o" variable_2="K_Ca_o"/>
<map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
<map_variables variable_1="K_R_Mg" variable_2="K_R_Mg"/>
<map_variables variable_1="K_R_Mg_open" variable_2="K_R_Mg_open"/>
<map_variables variable_1="K_R_open" variable_2="K_R_open"/>
<map_variables variable_1="K_Gly" variable_2="K_Gly"/>
<map_variables variable_1="K_Glu" variable_2="K_Glu"/>
<map_variables variable_1="K_Mg_o" variable_2="K_Mg_o"/>
<map_variables variable_1="nGlu" variable_2="nGlu"/>
<map_variables variable_1="nGly" variable_2="nGly"/>
</connection>
<connection>
<map_components component_1="constants" component_2="NMDA"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
