Location: BG_NBC @ 9663cef135e0 / BG_NBC_pH_regulation.cellml

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-07-13 15:51:00+12:00
Desc:
Moving channel initial moles to main environment from channel component
Permanent Source URI:
https://models.fieldml.org/workspace/87f/rawfile/9663cef135e064889113d2338e877c6a0f4244e0/BG_NBC_pH_regulation.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_NBC" 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="481.46" name="q_Na_i" public_interface="out" units="fmol"/>
        <variable initial_value="725.48" name="q_Na_o" public_interface="out" units="fmol"/>
        <variable initial_value="509.2" name="q_HCO3_i" public_interface="out" units="fmol"/>
        <variable initial_value="122.295" name="q_HCO3_o" public_interface="out" units="fmol"/>
        <variable initial_value="2.69019E-06" name="q_H_i" public_interface="out" units="fmol"/>
        <variable initial_value="2.06299E-07" name="q_H_o" public_interface="out" units="fmol"/>
        <!-- From submodule-->
        <variable name="v_R61_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R12_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R23_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R34_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R45_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R56_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R61_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R12_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R23_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R34_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R45_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R56_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R61_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R12_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R23_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R34_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R45_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="v_R56_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="ni" public_interface="in" units="dimensionless"/>
        <variable name="no" public_interface="in" units="dimensionless"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_Na_i</ci>
                </apply>
                <ci>v_R56_NBC</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_Na_o</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R12_NBC</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_HCO3_i</ci>
                </apply>
                <ci>v_R45_NBC</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_HCO3_o</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_R23_NBC</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_H_i</ci>
                </apply>
                <apply>
                    <times/>
                    <ci>ni</ci>
                    <apply>
                        <plus/>
                        <ci>v_R61_pHi_NBC</ci>
                        <ci>v_R12_pHi_NBC</ci>
                        <ci>v_R23_pHi_NBC</ci>
                        <ci>v_R34_pHi_NBC</ci>
                        <ci>v_R45_pHi_NBC</ci>
                        <ci>v_R56_pHi_NBC</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>time</ci>
                    </bvar>
                    <ci>q_H_o</ci>
                </apply>
                <apply>
                    <times/>
                    <apply>
                        <minus/>
                        <ci>no</ci>
                    </apply>
                    <apply>
                        <plus/>
                        <ci>v_R61_pHo_NBC</ci>
                        <ci>v_R12_pHo_NBC</ci>
                        <ci>v_R23_pHo_NBC</ci>
                        <ci>v_R34_pHo_NBC</ci>
                        <ci>v_R45_pHo_NBC</ci>
                        <ci>v_R56_pHo_NBC</ci>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
    <component name="NBC_parameters">
        <variable initial_value="0.00259289" name="kappa_R61_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="20502" name="kappa_R12_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.114834" name="kappa_R23_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.0707265" name="kappa_R34_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.000674472" name="kappa_R45_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="1392.99" name="kappa_R56_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="4.44552e+19" name="kappa_R61_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="9.24767e+19" name="kappa_R12_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="3.1453e+20" name="kappa_R23_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="4.44552e+19" name="kappa_R34_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="6.28325e+18" name="kappa_R45_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="2.13705e+19" name="kappa_R56_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="2.38256e-16" name="kappa_R61_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="4.95624e-16" name="kappa_R12_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="1.68571e-15" name="kappa_R23_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="2.38256e-16" name="kappa_R34_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="3.36747e-17" name="kappa_R45_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="1.14534e-16" name="kappa_R56_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="1.83788e-05" name="K_Na_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="1.16505e-05" name="K_Na_o" public_interface="out" units="per_fmol"/>
        <variable initial_value="11.1602" name="K_HCO3_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="7.07455" name="K_HCO3_o" public_interface="out" units="per_fmol"/>
        <variable initial_value="212.608" name="K_S1_NBC" public_interface="out" units="per_fmol"/>
        <variable initial_value="62.51" name="K_S2_NBC" public_interface="out" units="per_fmol"/>
        <variable initial_value="18.3789" name="K_S3_NBC" public_interface="out" units="per_fmol"/>
        <variable initial_value="3129.15" name="K_S4_NBC" public_interface="out" units="per_fmol"/>
        <variable initial_value="920.02" name="K_S5_NBC" public_interface="out" units="per_fmol"/>
        <variable initial_value="270.5" name="K_S6_NBC" public_interface="out" units="per_fmol"/>
        <variable initial_value="143952" name="K_H_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="2.95463e+06" name="K_H_o" public_interface="out" units="per_fmol"/>
    </component>
    <component name="NBC">
        <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_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R12_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R23_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R34_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R45_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R56_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R61_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R12_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R23_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R34_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R45_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R56_pHi_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R61_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R12_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R23_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R34_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R45_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="kappa_R56_pHo_NBC" public_interface="in" units="fmol_per_sec"/>
        <variable name="K_Na_i" public_interface="in" units="per_fmol"/>
        <variable name="K_Na_o" public_interface="in" units="per_fmol"/>
        <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_S1_NBC" public_interface="in" units="per_fmol"/>
        <variable name="K_S2_NBC" public_interface="in" units="per_fmol"/>
        <variable name="K_S3_NBC" public_interface="in" units="per_fmol"/>
        <variable name="K_S4_NBC" public_interface="in" units="per_fmol"/>
        <variable name="K_S5_NBC" public_interface="in" units="per_fmol"/>
        <variable name="K_S6_NBC" public_interface="in" units="per_fmol"/>
        <variable name="K_H_i" public_interface="in" units="per_fmol"/>
        <variable name="K_H_o" public_interface="in" units="per_fmol"/>
        <variable initial_value="2.91" name="ni" public_interface="out" units="dimensionless"/>
        <variable initial_value="2.18" name="no" public_interface="out" units="dimensionless"/>
        <!-- Input from global environment-->
        <variable name="q_Na_i" public_interface="in" units="fmol"/>
        <variable name="q_Na_o" public_interface="in" units="fmol"/>
        <variable name="q_HCO3_i" public_interface="in" units="fmol"/>
        <variable name="q_HCO3_o" public_interface="in" units="fmol"/>
        <variable initial_value="1.666e-7" name="q_S1_NBC" units="fmol"/>
        <variable initial_value="1.666e-7" name="q_S2_NBC" units="fmol"/>
        <variable initial_value="1.666e-7" name="q_S3_NBC" units="fmol"/>
        <variable initial_value="1.666e-7" name="q_S4_NBC" units="fmol"/>
        <variable initial_value="1.666e-7" name="q_S5_NBC" units="fmol"/>
        <variable initial_value="1.666e-7" name="q_S6_NBC" units="fmol"/>
        <variable name="q_H_i" public_interface="in" units="fmol"/>
        <variable name="q_H_o" public_interface="in" units="fmol"/>
        <!-- Constitutive parameters-->
        <variable name="mu_Na_i" units="J_per_mol"/>
        <variable name="mu_Na_o" units="J_per_mol"/>
        <variable name="mu_HCO3_i" units="J_per_mol"/>
        <variable name="mu_HCO3_o" units="J_per_mol"/>
        <variable name="mu_S1_NBC" units="J_per_mol"/>
        <variable name="mu_S2_NBC" units="J_per_mol"/>
        <variable name="mu_S3_NBC" units="J_per_mol"/>
        <variable name="mu_S4_NBC" units="J_per_mol"/>
        <variable name="mu_S5_NBC" units="J_per_mol"/>
        <variable name="mu_S6_NBC" units="J_per_mol"/>
        <variable name="mu_H_i" units="J_per_mol"/>
        <variable name="mu_H_o" units="J_per_mol"/>
        <variable name="v_R61_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R12_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R23_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R34_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R45_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R56_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R61_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
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        <variable name="v_R23_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R34_pHi_NBC" public_interface="out" units="fmol_per_sec"/>
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        <variable name="v_R61_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
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        <variable name="v_R23_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
        <variable name="v_R34_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
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        <variable name="v_R56_pHo_NBC" public_interface="out" units="fmol_per_sec"/>
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                <eq/>
                <ci>mu_Na_i</ci>
                <apply>
                    <times/>
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                        <ln/>
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                            <times/>
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                <eq/>
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                    <times/>
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                        <ln/>
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                            <times/>
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                <ci>mu_H_i</ci>
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                        <ln/>
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                                <divide/>
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        <map_variables variable_1="kappa_R12_pHi_NBC" variable_2="kappa_R12_pHi_NBC"/>
        <map_variables variable_1="kappa_R23_pHi_NBC" variable_2="kappa_R23_pHi_NBC"/>
        <map_variables variable_1="kappa_R34_pHi_NBC" variable_2="kappa_R34_pHi_NBC"/>
        <map_variables variable_1="kappa_R45_pHi_NBC" variable_2="kappa_R45_pHi_NBC"/>
        <map_variables variable_1="kappa_R56_pHi_NBC" variable_2="kappa_R56_pHi_NBC"/>
        <map_variables variable_1="kappa_R61_pHo_NBC" variable_2="kappa_R61_pHo_NBC"/>
        <map_variables variable_1="kappa_R12_pHo_NBC" variable_2="kappa_R12_pHo_NBC"/>
        <map_variables variable_1="kappa_R23_pHo_NBC" variable_2="kappa_R23_pHo_NBC"/>
        <map_variables variable_1="kappa_R34_pHo_NBC" variable_2="kappa_R34_pHo_NBC"/>
        <map_variables variable_1="kappa_R45_pHo_NBC" variable_2="kappa_R45_pHo_NBC"/>
        <map_variables variable_1="kappa_R56_pHo_NBC" variable_2="kappa_R56_pHo_NBC"/>
        <map_variables variable_1="K_Na_i" variable_2="K_Na_i"/>
        <map_variables variable_1="K_Na_o" variable_2="K_Na_o"/>
        <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_S1_NBC" variable_2="K_S1_NBC"/>
        <map_variables variable_1="K_S2_NBC" variable_2="K_S2_NBC"/>
        <map_variables variable_1="K_S3_NBC" variable_2="K_S3_NBC"/>
        <map_variables variable_1="K_S4_NBC" variable_2="K_S4_NBC"/>
        <map_variables variable_1="K_S5_NBC" variable_2="K_S5_NBC"/>
        <map_variables variable_1="K_S6_NBC" variable_2="K_S6_NBC"/>
        <map_variables variable_1="K_H_i" variable_2="K_H_i"/>
        <map_variables variable_1="K_H_o" variable_2="K_H_o"/>
    </connection>
    <connection>
        <map_components component_1="constants" component_2="NBC"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
    </connection>
</model>