- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-23 13:19:19+12:00
- Desc:
- Move channel state calculations to channel component
- Permanent Source URI:
- https://models.fieldml.org/workspace/881/rawfile/611538ed9fe9c2672c6d8f932d27b2f7612686e6/BG_CHE.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_CHE" 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_BG.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_sec"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="fF" units_ref="fF"/>
<units name="fC" units_ref="fC"/>
<units name="per_second" units_ref="per_second"/>
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="fmol_per_L" units_ref="fmol_per_L"/>
<units name="pL" units_ref="pL"/>
</import>
<import xlink:href="units_and_constants/constants_BG.cellml">
<component component_ref="constants" name="constants"/>
</import>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<!-- initial values-->
<variable initial_value="5.36764E-06" name="q_OH_i" public_interface="out" units="fmol"/>
<variable initial_value="1.30166E-06" name="q_OH_o" public_interface="out" units="fmol"/>
<variable initial_value="824.6" name="q_Cl_i" public_interface="out" units="fmol"/>
<variable initial_value="725.48" name="q_Cl_o" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="v_R61_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R12_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R23_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R34_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R45_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R56_CHE" 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_OH_i</ci>
</apply>
<apply>
<minus/>
<ci>v_R56_CHE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_OH_o</ci>
</apply>
<ci>v_R12_CHE</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Cl_i</ci>
</apply>
<ci>v_R45_CHE</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Cl_o</ci>
</apply>
<apply>
<minus/>
<ci>v_R23_CHE</ci>
</apply>
</apply>
</math>
<variable name="pH_i" units="dimensionless"/>
<variable name="pH_o" units="dimensionless"/>
<variable name="cOH_i" units="mM"/>
<variable name="cOH_o" units="mM"/>
<variable initial_value="38" name="w_i" units="pL"/>
<variable initial_value="5.182" name="w_o" units="pL"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>cOH_i</ci>
<apply>
<divide/>
<ci>q_OH_i</ci>
<ci>w_i</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>cOH_o</ci>
<apply>
<divide/>
<ci>q_OH_o</ci>
<ci>w_o</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>pH_i</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless">14</cn>
<apply>
<log/>
<ci>cOH_i</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>pH_o</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless">14</cn>
<apply>
<log/>
<ci>cOH_o</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="CHE_parameters">
<variable initial_value="8.77838" name="kappa_R61_CHE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.031295" name="kappa_R12_CHE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="50940.7" name="kappa_R23_CHE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.000192726" name="kappa_R34_CHE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2.96501e+06" name="kappa_R45_CHE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.82153e+06" name="kappa_R56_CHE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0253475" name="K_OH_i" public_interface="out" units="per_fmol"/>
<variable initial_value="7203.46" name="K_OH_o" public_interface="out" units="per_fmol"/>
<variable initial_value="0.015572" name="K_Cl_i" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00442538" name="K_Cl_o" public_interface="out" units="per_fmol"/>
<variable initial_value="0.749449" name="K_S1_CHE" public_interface="out" units="per_fmol"/>
<variable initial_value="22.527" name="K_S2_CHE" public_interface="out" units="per_fmol"/>
<variable initial_value="9298.74" name="K_S3_CHE" public_interface="out" units="per_fmol"/>
<variable initial_value="159.758" name="K_S4_CHE" public_interface="out" units="per_fmol"/>
<variable initial_value="0.014999" name="K_S5_CHE" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0128605" name="K_S6_CHE" public_interface="out" units="per_fmol"/>
</component>
<component name="CHE">
<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_R61_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R12_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R23_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R34_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R45_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R56_CHE" public_interface="in" units="fmol_per_sec"/>
<variable name="K_OH_i" public_interface="in" units="per_fmol"/>
<variable name="K_OH_o" public_interface="in" units="per_fmol"/>
<variable name="K_Cl_i" public_interface="in" units="per_fmol"/>
<variable name="K_Cl_o" public_interface="in" units="per_fmol"/>
<variable name="K_S1_CHE" public_interface="in" units="per_fmol"/>
<variable name="K_S2_CHE" public_interface="in" units="per_fmol"/>
<variable name="K_S3_CHE" public_interface="in" units="per_fmol"/>
<variable name="K_S4_CHE" public_interface="in" units="per_fmol"/>
<variable name="K_S5_CHE" public_interface="in" units="per_fmol"/>
<variable name="K_S6_CHE" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_OH_i" public_interface="in" units="fmol"/>
<variable name="q_OH_o" public_interface="in" units="fmol"/>
<variable name="q_Cl_i" public_interface="in" units="fmol"/>
<variable name="q_Cl_o" public_interface="in" units="fmol"/>
<variable initial_value="1.666e-4" name="q_S1_CHE" units="fmol"/>
<variable initial_value="1.666e-4" name="q_S2_CHE" units="fmol"/>
<variable initial_value="1.666e-4" name="q_S3_CHE" units="fmol"/>
<variable initial_value="1.666e-4" name="q_S4_CHE" units="fmol"/>
<variable initial_value="1.666e-4" name="q_S5_CHE" units="fmol"/>
<variable initial_value="1.666e-4" name="q_S6_CHE" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_OH_i" units="J_per_mol"/>
<variable name="mu_OH_o" units="J_per_mol"/>
<variable name="mu_Cl_i" units="J_per_mol"/>
<variable name="mu_Cl_o" units="J_per_mol"/>
<variable name="mu_S1_CHE" units="J_per_mol"/>
<variable name="mu_S2_CHE" units="J_per_mol"/>
<variable name="mu_S3_CHE" units="J_per_mol"/>
<variable name="mu_S4_CHE" units="J_per_mol"/>
<variable name="mu_S5_CHE" units="J_per_mol"/>
<variable name="mu_S6_CHE" units="J_per_mol"/>
<variable name="v_R61_CHE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R12_CHE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R23_CHE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R34_CHE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R45_CHE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R56_CHE" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_OH_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_OH_i</ci>
<ci>q_OH_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_OH_o</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_OH_o</ci>
<ci>q_OH_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Cl_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Cl_i</ci>
<ci>q_Cl_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Cl_o</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Cl_o</ci>
<ci>q_Cl_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S1_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S1_CHE</ci>
<ci>q_S1_CHE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S2_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S2_CHE</ci>
<ci>q_S2_CHE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S3_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S3_CHE</ci>
<ci>q_S3_CHE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S4_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S4_CHE</ci>
<ci>q_S4_CHE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S5_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S5_CHE</ci>
<ci>q_S5_CHE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S6_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S6_CHE</ci>
<ci>q_S6_CHE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R61_CHE</ci>
<apply>
<times/>
<ci>kappa_R61_CHE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S6_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S1_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R12_CHE</ci>
<apply>
<times/>
<ci>kappa_R12_CHE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S1_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S2_CHE</ci>
<ci>mu_OH_o</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R23_CHE</ci>
<apply>
<times/>
<ci>kappa_R23_CHE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S2_CHE</ci>
<ci>mu_Cl_o</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S3_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R34_CHE</ci>
<apply>
<times/>
<ci>kappa_R34_CHE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S3_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S4_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R45_CHE</ci>
<apply>
<times/>
<ci>kappa_R45_CHE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S4_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S5_CHE</ci>
<ci>mu_Cl_i</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R56_CHE</ci>
<apply>
<times/>
<ci>kappa_R56_CHE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S5_CHE</ci>
<ci>mu_OH_i</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S6_CHE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S1_CHE</ci>
</apply>
<apply>
<minus/>
<ci>v_R61_CHE</ci>
<ci>v_R12_CHE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S2_CHE</ci>
</apply>
<apply>
<minus/>
<ci>v_R12_CHE</ci>
<ci>v_R23_CHE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S3_CHE</ci>
</apply>
<apply>
<minus/>
<ci>v_R23_CHE</ci>
<ci>v_R34_CHE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S4_CHE</ci>
</apply>
<apply>
<minus/>
<ci>v_R34_CHE</ci>
<ci>v_R45_CHE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S5_CHE</ci>
</apply>
<apply>
<minus/>
<ci>v_R45_CHE</ci>
<ci>v_R56_CHE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S6_CHE</ci>
</apply>
<apply>
<minus/>
<ci>v_R56_CHE</ci>
<ci>v_R61_CHE</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="CHE"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_OH_i" variable_2="q_OH_i"/>
<map_variables variable_1="q_OH_o" variable_2="q_OH_o"/>
<map_variables variable_1="q_Cl_i" variable_2="q_Cl_i"/>
<map_variables variable_1="q_Cl_o" variable_2="q_Cl_o"/>
<map_variables variable_1="v_R61_CHE" variable_2="v_R61_CHE"/>
<map_variables variable_1="v_R12_CHE" variable_2="v_R12_CHE"/>
<map_variables variable_1="v_R23_CHE" variable_2="v_R23_CHE"/>
<map_variables variable_1="v_R34_CHE" variable_2="v_R34_CHE"/>
<map_variables variable_1="v_R45_CHE" variable_2="v_R45_CHE"/>
<map_variables variable_1="v_R56_CHE" variable_2="v_R56_CHE"/>
</connection>
<connection>
<map_components component_1="CHE" component_2="CHE_parameters"/>
<map_variables variable_1="kappa_R61_CHE" variable_2="kappa_R61_CHE"/>
<map_variables variable_1="kappa_R12_CHE" variable_2="kappa_R12_CHE"/>
<map_variables variable_1="kappa_R23_CHE" variable_2="kappa_R23_CHE"/>
<map_variables variable_1="kappa_R34_CHE" variable_2="kappa_R34_CHE"/>
<map_variables variable_1="kappa_R45_CHE" variable_2="kappa_R45_CHE"/>
<map_variables variable_1="kappa_R56_CHE" variable_2="kappa_R56_CHE"/>
<map_variables variable_1="K_OH_i" variable_2="K_OH_i"/>
<map_variables variable_1="K_OH_o" variable_2="K_OH_o"/>
<map_variables variable_1="K_Cl_i" variable_2="K_Cl_i"/>
<map_variables variable_1="K_Cl_o" variable_2="K_Cl_o"/>
<map_variables variable_1="K_S1_CHE" variable_2="K_S1_CHE"/>
<map_variables variable_1="K_S2_CHE" variable_2="K_S2_CHE"/>
<map_variables variable_1="K_S3_CHE" variable_2="K_S3_CHE"/>
<map_variables variable_1="K_S4_CHE" variable_2="K_S4_CHE"/>
<map_variables variable_1="K_S5_CHE" variable_2="K_S5_CHE"/>
<map_variables variable_1="K_S6_CHE" variable_2="K_S6_CHE"/>
</connection>
<connection>
<map_components component_1="constants" component_2="CHE"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
