- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-07-13 15:26:37+12:00
- Desc:
- Moving channel initial moles to main environment from channel component
- Permanent Source URI:
- http://models.cellml.org/workspace/882/rawfile/e479536490c5930360f79e4e2d44a90ed4a2cf38/BG_AE.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_AE" 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="5.902" name="q_HCO3_i" public_interface="out" units="fmol"/>
<variable initial_value="112.2952" name="q_HCO3_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"/>
<variable initial_value="1.666e-7" name="q_S1_AE" public_interface="out" units="fmol"/>
<variable initial_value="1.666e-7" name="q_S2_AE" public_interface="out" units="fmol"/>
<variable initial_value="1.666e-7" name="q_S3_AE" public_interface="out" units="fmol"/>
<variable initial_value="1.666e-7" name="q_S4_AE" public_interface="out" units="fmol"/>
<variable initial_value="1.666e-7" name="q_S5_AE" public_interface="out" units="fmol"/>
<variable initial_value="1.666e-7" name="q_S6_AE" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="v_R61_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R12_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R23_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R34_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R45_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R56_AE" 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_HCO3_i</ci>
</apply>
<apply>
<minus/>
<ci>v_R56_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_HCO3_o</ci>
</apply>
<ci>v_R12_AE</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Cl_i</ci>
</apply>
<ci>v_R45_AE</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Cl_o</ci>
</apply>
<apply>
<minus/>
<ci>v_R23_AE</ci>
</apply>
</apply>
</math>
</component>
<component name="AE_parameters">
<variable initial_value="0.0390374" name="kappa_R61_AE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="124875" name="kappa_R12_AE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="317575" name="kappa_R23_AE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0114249" name="kappa_R34_AE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="312282" name="kappa_R45_AE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="123101" name="kappa_R56_AE" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.072148" name="K_HCO3_i" public_interface="out" units="per_fmol"/>
<variable initial_value="0.526989" name="K_HCO3_o" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0284406" name="K_Cl_i" public_interface="out" units="per_fmol"/>
<variable initial_value="0.207219" name="K_Cl_o" public_interface="out" units="per_fmol"/>
<variable initial_value="8888.91" name="K_S1_AE" public_interface="out" units="per_fmol"/>
<variable initial_value="2.93242" name="K_S2_AE" public_interface="out" units="per_fmol"/>
<variable initial_value="30984.8" name="K_S3_AE" public_interface="out" units="per_fmol"/>
<variable initial_value="31510" name="K_S4_AE" public_interface="out" units="per_fmol"/>
<variable initial_value="2.96299" name="K_S5_AE" public_interface="out" units="per_fmol"/>
<variable initial_value="9016.99" name="K_S6_AE" public_interface="out" units="per_fmol"/>
</component>
<component name="AE">
<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_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R12_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R23_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R34_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R45_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R56_AE" public_interface="in" units="fmol_per_sec"/>
<variable name="K_HCO3_i" public_interface="in" units="per_fmol"/>
<variable name="K_HCO3_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_AE" public_interface="in" units="per_fmol"/>
<variable name="K_S2_AE" public_interface="in" units="per_fmol"/>
<variable name="K_S3_AE" public_interface="in" units="per_fmol"/>
<variable name="K_S4_AE" public_interface="in" units="per_fmol"/>
<variable name="K_S5_AE" public_interface="in" units="per_fmol"/>
<variable name="K_S6_AE" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_HCO3_i" public_interface="in" units="fmol"/>
<variable name="q_HCO3_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 name="q_S1_AE" public_interface="in" units="fmol"/>
<variable name="q_S2_AE" public_interface="in" units="fmol"/>
<variable name="q_S3_AE" public_interface="in" units="fmol"/>
<variable name="q_S4_AE" public_interface="in" units="fmol"/>
<variable name="q_S5_AE" public_interface="in" units="fmol"/>
<variable name="q_S6_AE" public_interface="in" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_HCO3_i" units="J_per_mol"/>
<variable name="mu_HCO3_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_AE" units="J_per_mol"/>
<variable name="mu_S2_AE" units="J_per_mol"/>
<variable name="mu_S3_AE" units="J_per_mol"/>
<variable name="mu_S4_AE" units="J_per_mol"/>
<variable name="mu_S5_AE" units="J_per_mol"/>
<variable name="mu_S6_AE" units="J_per_mol"/>
<variable name="v_R61_AE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R12_AE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R23_AE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R34_AE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R45_AE" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R56_AE" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_HCO3_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_HCO3_i</ci>
<ci>q_HCO3_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_HCO3_o</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_HCO3_o</ci>
<ci>q_HCO3_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_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S1_AE</ci>
<ci>q_S1_AE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S2_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S2_AE</ci>
<ci>q_S2_AE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S3_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S3_AE</ci>
<ci>q_S3_AE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S4_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S4_AE</ci>
<ci>q_S4_AE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S5_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S5_AE</ci>
<ci>q_S5_AE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_S6_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_S6_AE</ci>
<ci>q_S6_AE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R61_AE</ci>
<apply>
<times/>
<ci>kappa_R61_AE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S6_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S1_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R12_AE</ci>
<apply>
<times/>
<ci>kappa_R12_AE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S1_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S2_AE</ci>
<ci>mu_HCO3_o</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R23_AE</ci>
<apply>
<times/>
<ci>kappa_R23_AE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S2_AE</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_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R34_AE</ci>
<apply>
<times/>
<ci>kappa_R34_AE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S3_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S4_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R45_AE</ci>
<apply>
<times/>
<ci>kappa_R45_AE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S4_AE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S5_AE</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_AE</ci>
<apply>
<times/>
<ci>kappa_R56_AE</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_S5_AE</ci>
<ci>mu_HCO3_i</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_S6_AE</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_AE</ci>
</apply>
<apply>
<minus/>
<ci>v_R61_AE</ci>
<ci>v_R12_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S2_AE</ci>
</apply>
<apply>
<minus/>
<ci>v_R12_AE</ci>
<ci>v_R23_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S3_AE</ci>
</apply>
<apply>
<minus/>
<ci>v_R23_AE</ci>
<ci>v_R34_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S4_AE</ci>
</apply>
<apply>
<minus/>
<ci>v_R34_AE</ci>
<ci>v_R45_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S5_AE</ci>
</apply>
<apply>
<minus/>
<ci>v_R45_AE</ci>
<ci>v_R56_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_S6_AE</ci>
</apply>
<apply>
<minus/>
<ci>v_R56_AE</ci>
<ci>v_R61_AE</ci>
</apply>
</apply>
</math>
<!-- check conservation -->
<variable name="B_tot" units="fmol"/>
<variable name="S_tot" units="fmol"/>
<variable name="S1S6_tot" units="fmol"/>
<variable name="Cl_tot" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>B_tot</ci>
<apply>
<plus/>
<ci>q_HCO3_i</ci>
<ci>q_HCO3_o</ci>
<ci>q_S1_AE</ci>
<ci>q_S6_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>S1S6_tot</ci>
<apply>
<plus/>
<ci>q_S1_AE</ci>
<ci>q_S6_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>S_tot</ci>
<apply>
<plus/>
<ci>q_S1_AE</ci>
<ci>q_S2_AE</ci>
<ci>q_S3_AE</ci>
<ci>q_S4_AE</ci>
<ci>q_S5_AE</ci>
<ci>q_S6_AE</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Cl_tot</ci>
<apply>
<plus/>
<ci>q_Cl_i</ci>
<ci>q_Cl_o</ci>
<ci>q_S3_AE</ci>
<ci>q_S4_AE</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="AE"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_HCO3_i" variable_2="q_HCO3_i"/>
<map_variables variable_1="q_HCO3_o" variable_2="q_HCO3_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_AE" variable_2="v_R61_AE"/>
<map_variables variable_1="v_R12_AE" variable_2="v_R12_AE"/>
<map_variables variable_1="v_R23_AE" variable_2="v_R23_AE"/>
<map_variables variable_1="v_R34_AE" variable_2="v_R34_AE"/>
<map_variables variable_1="v_R45_AE" variable_2="v_R45_AE"/>
<map_variables variable_1="v_R56_AE" variable_2="v_R56_AE"/>
<map_variables variable_1="q_S1_AE" variable_2="q_S1_AE"/>
<map_variables variable_1="q_S2_AE" variable_2="q_S2_AE"/>
<map_variables variable_1="q_S3_AE" variable_2="q_S3_AE"/>
<map_variables variable_1="q_S4_AE" variable_2="q_S4_AE"/>
<map_variables variable_1="q_S5_AE" variable_2="q_S5_AE"/>
<map_variables variable_1="q_S6_AE" variable_2="q_S6_AE"/>
</connection>
<connection>
<map_components component_1="AE" component_2="AE_parameters"/>
<map_variables variable_1="kappa_R61_AE" variable_2="kappa_R61_AE"/>
<map_variables variable_1="kappa_R12_AE" variable_2="kappa_R12_AE"/>
<map_variables variable_1="kappa_R23_AE" variable_2="kappa_R23_AE"/>
<map_variables variable_1="kappa_R34_AE" variable_2="kappa_R34_AE"/>
<map_variables variable_1="kappa_R45_AE" variable_2="kappa_R45_AE"/>
<map_variables variable_1="kappa_R56_AE" variable_2="kappa_R56_AE"/>
<map_variables variable_1="K_HCO3_i" variable_2="K_HCO3_i"/>
<map_variables variable_1="K_HCO3_o" variable_2="K_HCO3_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_AE" variable_2="K_S1_AE"/>
<map_variables variable_1="K_S2_AE" variable_2="K_S2_AE"/>
<map_variables variable_1="K_S3_AE" variable_2="K_S3_AE"/>
<map_variables variable_1="K_S4_AE" variable_2="K_S4_AE"/>
<map_variables variable_1="K_S5_AE" variable_2="K_S5_AE"/>
<map_variables variable_1="K_S6_AE" variable_2="K_S6_AE"/>
</connection>
<connection>
<map_components component_1="constants" component_2="AE"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
