Location: NaB protein knowledge page @ 4e6b1f1fc08f / BG_NaB.cellml

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2024-09-13 14:19:49+12:00
Desc:
Init
Permanent Source URI:
https://models.physiomeproject.org/workspace/bd4/rawfile/4e6b1f1fc08f24db7f2163799e2cf43404a692bf/BG_NaB.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="NaB_model" 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="per_mol" units_ref="per_mol"/>
        <units name="J_per_mol" units_ref="J_per_mol"/>
        <units name="J_per_C" units_ref="J_per_C"/>
        <units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
        <units name="mol_per_s" units_ref="mol_per_s"/>
        <units name="C_per_mol" units_ref="C_per_mol"/>
        <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="fmol" units_ref="fmol"/>
        <units name="fmol_per_sec" units_ref="fmol_per_sec"/>
        <units name="per_fmol" units_ref="per_fmol"/>
        <units name="pL" units_ref="pL"/>
        <units name="mA_per_mM" units_ref="mA_per_mM"/>
    </import>
    <component name="environment">
        <variable name="t" public_interface="out" units="second"/>
        <variable initial_value="1e6" name="C_m" public_interface="out" units="fF"/>
        <variable initial_value="25.8" name="w_i" public_interface="out" units="pL"/>
        <variable initial_value="3.52" name="w_o" public_interface="out" units="pL"/>
        <variable initial_value="-8.5e4" name="q_mem" public_interface="out" units="fC"/>
        <variable initial_value="8.31" name="R" public_interface="out" units="J_per_K_per_mol"/>
        <variable initial_value="310" name="T" public_interface="out" units="kelvin"/>
        <variable initial_value="96500" name="F" public_interface="out" units="C_per_mol"/>
        <variable name="v_NaB" public_interface="in" units="fmol_per_sec"/>
        <variable initial_value="9.3276" name="q_Na_o" public_interface="out" units="fmol"/>
        <variable initial_value="0.00456" name="q_Na_i" public_interface="out" units="fmol"/>
        <variable name="V_mem" public_interface="out" units="J_per_C"/>
        <variable name="I_mem_NaB" public_interface="in" units="fA"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Na_i</ci>
                </apply>
                <apply>
                    <minus/>
                    <ci>v_NaB</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_Na_o</ci>
                </apply>
                <ci>v_NaB</ci>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>q_mem</ci>
                </apply>
                <ci>I_mem_NaB</ci>
            </apply>
            <apply>
                <eq/>
                <ci>V_mem</ci>
                <apply>
                    <divide/>
                    <ci>q_mem</ci>
                    <ci>C_m</ci>
                </apply>
            </apply>
        </math>
    </component>
    <component name="NaB_parameters">
        <variable initial_value="0.217237" name="kappa_NaB" public_interface="out" units="fmol_per_sec"/>
        <variable initial_value="0.013549" name="K_Na_i" public_interface="out" units="per_fmol"/>
        <variable initial_value="0.0899434" name="K_Na_o" public_interface="out" units="per_fmol"/>
        <variable initial_value="1" name="zNa" public_interface="out" units="dimensionless"/>
    </component>
    <component name="NaB">
        <variable name="t" 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"/>
        <variable name="zNa" public_interface="in" units="dimensionless"/>
        <variable name="F" public_interface="in" units="C_per_mol"/>
        <variable name="K_Na_i" public_interface="in" units="per_fmol"/>
        <variable name="K_Na_o" public_interface="in" units="per_fmol"/>
        <variable name="kappa_NaB" public_interface="in" units="fmol_per_sec"/>
        <variable name="q_Na_i" public_interface="in" units="fmol"/>
        <variable name="q_Na_o" public_interface="in" units="fmol"/>
        <variable name="mu_Na_i" units="J_per_mol"/>
        <variable name="mu_Na_o" units="J_per_mol"/>
        <variable name="Af_NaB" units="J_per_mol"/>
        <variable name="Ar_NaB" units="J_per_mol"/>
        <variable name="Am_NaB" units="J_per_mol"/>
        <variable name="q_mem" public_interface="in" units="fC"/>
        <variable name="v_NaB" public_interface="out" units="fmol_per_sec"/>
        <variable name="I_mem_NaB" public_interface="out" units="fA"/>
        <variable name="V_mem" public_interface="in" units="J_per_C"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>mu_Na_i</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Na_i</ci>
                            <ci>q_Na_i</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>mu_Na_o</ci>
                <apply>
                    <times/>
                    <ci>R</ci>
                    <ci>T</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <times/>
                            <ci>K_Na_o</ci>
                            <ci>q_Na_o</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>Af_NaB</ci>
                <apply>
                    <plus/>
                    <ci>mu_Na_i</ci>
                    <apply>
                        <times/>
                        <apply>
                            <plus/>
                            <ci>zNa</ci>
                        </apply>
                        <ci>F</ci>
                        <ci>V_mem</ci>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>Ar_NaB</ci>
                <ci>mu_Na_o</ci>
            </apply>
            <apply>
                <eq/>
                <ci>Am_NaB</ci>
                <apply>
                    <times/>
                    <ci>zNa</ci>
                    <ci>F</ci>
                    <ci>V_mem</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>v_NaB</ci>
                <piecewise>
                    <piece>
                        <apply>
                            <times/>
                            <ci>kappa_NaB</ci>
                            <apply>
                                <minus/>
                                <apply>
                                    <exp/>
                                    <apply>
                                        <divide/>
                                        <ci>Af_NaB</ci>
                                        <apply>
                                            <times/>
                                            <ci>R</ci>
                                            <ci>T</ci>
                                        </apply>
                                    </apply>
                                </apply>
                                <apply>
                                    <exp/>
                                    <apply>
                                        <divide/>
                                        <ci>Ar_NaB</ci>
                                        <apply>
                                            <times/>
                                            <ci>R</ci>
                                            <ci>T</ci>
                                        </apply>
                                    </apply>
                                </apply>
                            </apply>
                        </apply>
                        <apply>
                            <eq/>
                            <ci>Am_NaB</ci>
                            <cn cellml:units="J_per_mol">0</cn>
                        </apply>
                    </piece>
                    <otherwise>
                        <apply>
                            <times/>
                            <apply>
                                <divide/>
                                <apply>
                                    <divide/>
                                    <apply>
                                        <times/>
                                        <ci>kappa_NaB</ci>
                                        <ci>Am_NaB</ci>
                                    </apply>
                                    <apply>
                                        <times/>
                                        <ci>R</ci>
                                        <ci>T</ci>
                                    </apply>
                                </apply>
                                <apply>
                                    <minus/>
                                    <apply>
                                        <exp/>
                                        <apply>
                                            <divide/>
                                            <ci>Am_NaB</ci>
                                            <apply>
                                                <times/>
                                                <ci>R</ci>
                                                <ci>T</ci>
                                            </apply>
                                        </apply>
                                    </apply>
                                    <cn cellml:units="dimensionless">1</cn>
                                </apply>
                            </apply>
                            <apply>
                                <minus/>
                                <apply>
                                    <exp/>
                                    <apply>
                                        <divide/>
                                        <ci>Af_NaB</ci>
                                        <apply>
                                            <times/>
                                            <ci>R</ci>
                                            <ci>T</ci>
                                        </apply>
                                    </apply>
                                </apply>
                                <apply>
                                    <exp/>
                                    <apply>
                                        <divide/>
                                        <ci>Ar_NaB</ci>
                                        <apply>
                                            <times/>
                                            <ci>R</ci>
                                            <ci>T</ci>
                                        </apply>
                                    </apply>
                                </apply>
                            </apply>
                        </apply>
                    </otherwise>
                </piecewise>
            </apply>
            <apply>
                <eq/>
                <ci>I_mem_NaB</ci>
                <apply>
                    <times/>
                    <apply>
                        <minus/>
                        <ci>zNa</ci>
                    </apply>
                    <ci>F</ci>
                    <ci>v_NaB</ci>
                </apply>
            </apply>
        </math>
    </component>
    <connection>
        <map_components component_1="environment" component_2="NaB"/>
        <map_variables variable_1="t" variable_2="t"/>
        <map_variables variable_1="R" variable_2="R"/>
        <map_variables variable_1="T" variable_2="T"/>
        <map_variables variable_1="F" variable_2="F"/>
        <map_variables variable_1="v_NaB" variable_2="v_NaB"/>
        <map_variables variable_1="I_mem_NaB" variable_2="I_mem_NaB"/>
        <map_variables variable_1="q_Na_i" variable_2="q_Na_i"/>
        <map_variables variable_1="q_Na_o" variable_2="q_Na_o"/>
        <map_variables variable_1="q_mem" variable_2="q_mem"/>
        <map_variables variable_1="V_mem" variable_2="V_mem"/>
    </connection>
    <connection>
        <map_components component_1="NaB" component_2="NaB_parameters"/>
        <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="kappa_NaB" variable_2="kappa_NaB"/>
        <map_variables variable_1="zNa" variable_2="zNa"/>
    </connection>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#model">
            <bqs:reference xmlns:bqs="http://www.cellml.org/bqs/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <dc:subject xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                    <bqs:subject_type xmlns:bqs="http://www.cellml.org/bqs/1.0#">keyword</bqs:subject_type>
                    <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                        <rdf:Bag xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                            <rdf:li xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">protein-modules</rdf:li>
                        </rdf:Bag>
                    </rdf:value>
                </dc:subject>
            </bqs:reference>
        </rdf:Description>
    </rdf:RDF>
</model>