- Author:
- leyla <noroozbabaee@gmail.com>
- Date:
- 2021-06-28 20:13:23+12:00
- Desc:
- Conversion of the Epithelial Modules From Python to CellML
- Permanent Source URI:
- https://models.cellml.org/workspace/6b4/rawfile/74195ac8689f1c97c4ebffbce80647281475f5a6/NHE3_Weinstein/components/NHE3.cellml
<?xml version='1.0'?>
<model cmeta:id="NHE3_model" name="NHE3_model" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink">
<!-- ======================================== Import the required units from the Units file ==================================================== -->
<import xlink:href="../general/Units_for_EpithelialCell.cellml">
<units name="millivolt" units_ref="millivolt"/>
<units name="per_second" units_ref="per_second"/>
<units name="coulomb_per_mole" units_ref="coulomb_per_mole"/>
<units name="joule_per_millimole" units_ref="joule_per_millimole"/>
<units name="molar" units_ref="molar"/>
<units name="millimole2_per_joulesecond" units_ref="millimole2_per_joulesecond"/>
<units name="millimole_per_second" units_ref="millimole_per_second"/>
<units name="millimole" units_ref="millimole"/>
<units name="joule_per_coulombmillivolt" units_ref="joule_per_coulombmillivolt"/>
<units name="millimole_per_cm2" units_ref="millimole_per_cm2"/>
</import>
<!--=================================== INPUT CONNECTIONS ============================= -->
<import xlink:href="../general/Generator.cellml">
<component component_ref="experiment" name="experiment"/>
</import>
<!-- ======================================== NHE3_TOP-LEVEL COMPONENT ============================================= -->
<connection>
<map_components component_1="experiment" component_2="Weinstein_NHE3"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="Na_I" variable_2="Na_I"/>
<map_variables variable_1="H_I" variable_2="H_I"/>
<map_variables variable_1="NH4_I" variable_2="NH4_I"/>
</connection>
<!-- ======================================== Weinstein_NHE3 Exchanger ============================================= -->
<component cmeta:id="Weinstein_NHE3" name="Weinstein_NHE3">
<!-- Inputs from other components (Generator.cellml)-->
<variable name="time" private_interface="out" public_interface="in" units="second"/>
<variable name="Na_I" private_interface="in" public_interface="out" units="molar"/>
<variable name="H_I" private_interface="in" public_interface="out" units="molar"/>
<variable name="NH4_I" private_interface="in" public_interface="out" units="molar"/>
<!-- Outputs to other components -->
<variable name="Na_NHE3_Flux" private_interface="out" public_interface="out" units="millimole_per_second"/>
<variable name="H_NHE3_Flux" private_interface="out" public_interface="out" units="millimole_per_second"/>
<variable name="NH4_NHE3_Flux" private_interface="out" public_interface="out" units="millimole_per_second"/>
<!-- Parameters from parameter_file -->
<variable name="Na_M" private_interface="out" public_interface="in" units="molar"/>
<variable name="H_M" private_interface="out" public_interface="in" units="molar"/>
<variable name="NH4_M" private_interface="out" public_interface="in" units="molar"/>
<variable name="Ami" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="k_nah_na" private_interface="out" public_interface="in" units="molar"/>
<variable name="k_nah_h" private_interface="out" public_interface="in" units="molar"/>
<variable name="k_nah_nh4" private_interface="out" public_interface="in" units="molar"/>
<variable name="p_nah_na" private_interface="out" public_interface="in" units="per_second"/>
<variable name="p_nah_h" private_interface="out" public_interface="in" units="per_second"/>
<variable name="p_nah_nh4" private_interface="out" public_interface="in" units="per_second"/>
<!-- Internal Modifier Parameters-->
<variable name="f_M" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="f_m" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="k_mod" private_interface="out" public_interface="in" units="molar"/>
<variable name="p_nah_mod_na" private_interface="out" public_interface="out" units="per_second"/>
<variable name="p_nah_mod_h" private_interface="out" public_interface="out" units="per_second"/>
<variable name="p_nah_mod_nh4" private_interface="out" public_interface="out" units="per_second"/>
<!-- Internal definitions-->
<variable name="ci_nah_na" private_interface="out" public_interface="out" units="dimensionless"/>
<variable name="ci_nah_h" private_interface="out" public_interface="out" units="dimensionless"/>
<variable name="ci_nah_nh4" private_interface="out" public_interface="out" units="dimensionless"/>
<variable name="cm_nah_na" private_interface="out" public_interface="out" units="dimensionless"/>
<variable name="cm_nah_h" private_interface="out" public_interface="out" units="dimensionless"/>
<variable name="cm_nah_nh4" private_interface="out" public_interface="out" units="dimensionless"/>
<variable name="delta_i" private_interface="out" public_interface="out" units="dimensionless"/>
<variable name="delta_m" private_interface="out" public_interface="out" units="dimensionless"/>
<variable name="epsilon_i" private_interface="out" public_interface="out" units="per_second"/>
<variable name="epsilon_m" private_interface="out" public_interface="out" units="per_second"/>
<variable name="sigma_nhe3" private_interface="out" public_interface="out" units="per_second"/>
<variable initial_value="1.0" name="ctc" public_interface="out" units="millimole"/>
<variable name="NNHE3" private_interface="out" public_interface="in" units="dimensionless"/>
<variable initial_value="0.0" name="m" public_interface="out" units="second"/>
<!-- Internal Modifier Equations-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>p_nah_mod_na</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>p_nah_na</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>f_M</ci>
<ci>H_I</ci>
</apply>
<apply>
<times/>
<ci>f_m</ci>
<ci>k_mod</ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<ci>H_I</ci>
<ci>k_mod</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>p_nah_mod_h</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>p_nah_h</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>f_M</ci>
<ci>H_I</ci>
</apply>
<apply>
<times/>
<ci>f_m</ci>
<ci>k_mod</ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<ci>H_I</ci>
<ci>k_mod</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>p_nah_mod_nh4</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>p_nah_nh4</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>f_M</ci>
<ci>H_I</ci>
</apply>
<apply>
<times/>
<ci>f_m</ci>
<ci>k_mod</ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<ci>H_I</ci>
<ci>k_mod</ci>
</apply>
</apply>
</apply>
<!-- Normalized Concentrations For Internal and External Solutes-->
<apply>
<eq/>
<ci>ci_nah_na</ci>
<apply>
<divide/>
<ci>Na_I</ci>
<ci>k_nah_na</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>ci_nah_h</ci>
<apply>
<divide/>
<ci>H_I</ci>
<ci>k_nah_h</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>ci_nah_nh4</ci>
<apply>
<divide/>
<ci>NH4_I</ci>
<ci>k_nah_nh4</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>cm_nah_na</ci>
<apply>
<divide/>
<ci>Na_M</ci>
<ci>k_nah_na</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>cm_nah_h</ci>
<apply>
<divide/>
<ci>H_M</ci>
<ci>k_nah_h</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>cm_nah_nh4</ci>
<apply>
<divide/>
<ci>NH4_M</ci>
<ci>k_nah_nh4</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>delta_i</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<ci>ci_nah_na</ci>
<ci>ci_nah_h</ci>
<ci>ci_nah_nh4</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>delta_m</ci>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<ci>cm_nah_na</ci>
<ci>cm_nah_h</ci>
<ci>cm_nah_nh4</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>epsilon_i</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>p_nah_mod_na</ci>
<ci>ci_nah_na</ci>
</apply>
<apply>
<times/>
<ci>p_nah_mod_h</ci>
<ci>ci_nah_h</ci>
</apply>
<apply>
<times/>
<ci>p_nah_mod_nh4</ci>
<ci>ci_nah_nh4</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>epsilon_m</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>p_nah_mod_na</ci>
<ci>cm_nah_na</ci>
</apply>
<apply>
<times/>
<ci>p_nah_mod_h</ci>
<ci>cm_nah_h</ci>
</apply>
<apply>
<times/>
<ci>p_nah_mod_nh4</ci>
<ci>cm_nah_nh4</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>sigma_nhe3</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>delta_i</ci>
<ci>epsilon_m</ci>
</apply>
<apply>
<times/>
<ci>delta_m</ci>
<ci>epsilon_i</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Na_NHE3_Flux</ci>
<apply>
<plus/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>NNHE3</ci>
<ci>Ami</ci>
<ci>p_nah_mod_na</ci>
<ci>p_nah_mod_h</ci>
<ci>ctc</ci>
</apply>
<ci>sigma_nhe3</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>cm_nah_na</ci>
<ci>ci_nah_h</ci>
</apply>
<apply>
<times/>
<ci>ci_nah_na</ci>
<ci>cm_nah_h</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>p_nah_mod_na</ci>
<ci>p_nah_mod_nh4</ci>
<ci>ctc</ci>
</apply>
<ci>sigma_nhe3</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>cm_nah_na</ci>
<ci>ci_nah_nh4</ci>
</apply>
<apply>
<times/>
<ci>ci_nah_na</ci>
<ci>cm_nah_nh4</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>H_NHE3_Flux</ci>
<apply>
<plus/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>NNHE3</ci>
<ci>Ami</ci>
<ci>p_nah_mod_h</ci>
<ci>p_nah_mod_na</ci>
<ci>ctc</ci>
</apply>
<ci>sigma_nhe3</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>cm_nah_h</ci>
<ci>ci_nah_na</ci>
</apply>
<apply>
<times/>
<ci>ci_nah_h</ci>
<ci>cm_nah_na</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>p_nah_mod_h</ci>
<ci>p_nah_mod_nh4</ci>
<ci>ctc</ci>
</apply>
<ci>sigma_nhe3</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>cm_nah_h</ci>
<ci>ci_nah_nh4</ci>
</apply>
<apply>
<times/>
<ci>ci_nah_h</ci>
<ci>cm_nah_nh4</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>NH4_NHE3_Flux</ci>
<apply>
<plus/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>NNHE3</ci>
<ci>Ami</ci>
<ci>p_nah_mod_nh4</ci>
<ci>p_nah_mod_na</ci>
<ci>ctc</ci>
</apply>
<ci>sigma_nhe3</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>cm_nah_nh4</ci>
<ci>ci_nah_na</ci>
</apply>
<apply>
<times/>
<ci>ci_nah_nh4</ci>
<ci>cm_nah_na</ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>p_nah_mod_nh4</ci>
<ci>p_nah_mod_h</ci>
<ci>ctc</ci>
</apply>
<ci>sigma_nhe3</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>cm_nah_nh4</ci>
<ci>ci_nah_h</ci>
</apply>
<apply>
<times/>
<ci>cm_nah_h</ci>
<ci>ci_nah_nh4</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>m</ci>
</apply>
<cn cellml:units="dimensionless">1</cn>
</apply>
</math>
</component>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="Weinstein_NHE3">
<component_ref component="experiment"/>
</component_ref>
</group>
</model>
