Location: Models for the OpenCOR and PMR tutorial by Peter Hunter @ c702d05c6a69 / Noble62_Na_channel.cellml

Author:
David Nickerson <nickerso@users.sourceforge.net>
Date:
2016-08-31 10:38:56+12:00
Desc:
update HH IK SED-ML to match changes in OpenCOR.
Permanent Source URI:
https://models.fieldml.org/workspace/25d/rawfile/c702d05c6a698b7b97dbb5b106600a16abfbff97/Noble62_Na_channel.cellml

<?xml version='1.0'?>
<model name="sodium_ion_channel" 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="Noble62_units.cellml">
        <units name="mV" units_ref="mV"/>
        <units name="ms" units_ref="ms"/>
        <units name="mM" units_ref="mM"/>
        <units name="per_ms" units_ref="per_ms"/>
        <units name="per_mV" units_ref="per_mV"/>
        <units name="per_mV_ms" units_ref="per_mV_ms"/>
        <units name="mS" units_ref="mS"/>
        <units name="microA" units_ref="microA"/>
    </import>
    <!--    def comp environment as
        var V: mV {pub: out};
       var t: ms {pub: out};

        V = sel
            case (t > 5{ms}) and (t < 15{ms}):
                0.0{mV};
            otherwise:
                -85.0{mV};
        endsel;
    enddef;-->
    <group>
        <relationship_ref relationship="encapsulation"/>
        <component_ref component="sodium_channel">
            <component_ref component="sodium_channel_m_gate"/>
            <component_ref component="sodium_channel_h_gate"/>
        </component_ref>
    </group>
    <component name="sodium_channel">
        <variable name="V" private_interface="out" public_interface="in" units="mV"/>
        <variable name="t" private_interface="out" public_interface="in" units="ms"/>
        <variable initial_value="400" name="g_Na_max" units="mS"/>
        <variable name="g_Na" public_interface="out" units="mS"/>
        <variable name="E_Na" units="mV"/>
        <variable name="m" private_interface="in" public_interface="out" units="dimensionless"/>
        <variable name="h" private_interface="in" public_interface="out" units="dimensionless"/>
        <variable name="Nai" public_interface="in" units="mM"/>
        <variable name="Nao" public_interface="in" units="mM"/>
        <variable initial_value="25" name="RTF" units="mV"/>
        <variable name="i_Na" public_interface="out" units="microA"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>E_Na</ci>
                <apply>
                    <times/>
                    <ci>RTF</ci>
                    <apply>
                        <ln/>
                        <apply>
                            <divide/>
                            <ci>Nao</ci>
                            <ci>Nai</ci>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>g_Na</ci>
                <apply>
                    <times/>
                    <apply>
                        <power/>
                        <ci>m</ci>
                        <cn cellml:units="dimensionless">3</cn>
                    </apply>
                    <ci>h</ci>
                    <ci>g_Na_max</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>i_Na</ci>
                <apply>
                    <times/>
                    <apply>
                        <plus/>
                        <ci>g_Na</ci>
                        <cn cellml:units="mS">0.14</cn>
                    </apply>
                    <apply>
                        <minus/>
                        <ci>V</ci>
                        <ci>E_Na</ci>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
    <component name="sodium_channel_m_gate">
        <variable name="V" public_interface="in" units="mV"/>
        <variable name="t" public_interface="in" units="ms"/>
        <variable initial_value="0.01" name="m" public_interface="out" units="dimensionless"/>
        <variable name="alpha_m" units="per_ms"/>
        <variable name="beta_m" units="per_ms"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>alpha_m</ci>
                <apply>
                    <divide/>
                    <apply>
                        <times/>
                        <apply>
                            <minus/>
                            <cn cellml:units="per_mV_ms">0.10</cn>
                        </apply>
                        <apply>
                            <plus/>
                            <ci>V</ci>
                            <cn cellml:units="mV">48</cn>
                        </apply>
                    </apply>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <minus/>
                                    <apply>
                                        <plus/>
                                        <ci>V</ci>
                                        <cn cellml:units="mV">48</cn>
                                    </apply>
                                </apply>
                                <cn cellml:units="mV">15</cn>
                            </apply>
                        </apply>
                        <cn cellml:units="dimensionless">1</cn>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>beta_m</ci>
                <apply>
                    <divide/>
                    <apply>
                        <times/>
                        <cn cellml:units="per_mV_ms">0.12</cn>
                        <apply>
                            <plus/>
                            <ci>V</ci>
                            <cn cellml:units="mV">8</cn>
                        </apply>
                    </apply>
                    <apply>
                        <minus/>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <plus/>
                                    <ci>V</ci>
                                    <cn cellml:units="mV">8</cn>
                                </apply>
                                <cn cellml:units="mV">5</cn>
                            </apply>
                        </apply>
                        <cn cellml:units="dimensionless">1</cn>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>m</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <times/>
                        <ci>alpha_m</ci>
                        <apply>
                            <minus/>
                            <cn cellml:units="dimensionless">1</cn>
                            <ci>m</ci>
                        </apply>
                    </apply>
                    <apply>
                        <times/>
                        <ci>beta_m</ci>
                        <ci>m</ci>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
    <component name="sodium_channel_h_gate">
        <variable name="V" public_interface="in" units="mV"/>
        <variable name="t" public_interface="in" units="ms"/>
        <variable initial_value="0.8" name="h" public_interface="out" units="dimensionless"/>
        <variable name="alpha_h" units="per_ms"/>
        <variable name="beta_h" units="per_ms"/>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>alpha_h</ci>
                <apply>
                    <times/>
                    <cn cellml:units="per_ms">0.17</cn>
                    <apply>
                        <exp/>
                        <apply>
                            <divide/>
                            <apply>
                                <minus/>
                                <apply>
                                    <plus/>
                                    <ci>V</ci>
                                    <cn cellml:units="mV">90</cn>
                                </apply>
                            </apply>
                            <cn cellml:units="mV">20</cn>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>beta_h</ci>
                <apply>
                    <divide/>
                    <cn cellml:units="per_ms">1.00</cn>
                    <apply>
                        <plus/>
                        <cn cellml:units="dimensionless">1</cn>
                        <apply>
                            <exp/>
                            <apply>
                                <divide/>
                                <apply>
                                    <minus/>
                                    <apply>
                                        <plus/>
                                        <ci>V</ci>
                                        <cn cellml:units="mV">42</cn>
                                    </apply>
                                </apply>
                                <cn cellml:units="mV">10</cn>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply>
                <eq/>
                <apply>
                    <diff/>
                    <bvar>
                        <ci>t</ci>
                    </bvar>
                    <ci>h</ci>
                </apply>
                <apply>
                    <minus/>
                    <apply>
                        <times/>
                        <ci>alpha_h</ci>
                        <apply>
                            <minus/>
                            <cn cellml:units="dimensionless">1</cn>
                            <ci>h</ci>
                        </apply>
                    </apply>
                    <apply>
                        <times/>
                        <ci>beta_h</ci>
                        <ci>h</ci>
                    </apply>
                </apply>
            </apply>
        </math>
    </component>
    <!--    def map between environment and sodium_channel for
        vars V and V;
        vars t and t;
    enddef;-->
    <connection>
        <map_components component_1="sodium_channel" component_2="sodium_channel_m_gate"/>
        <map_variables variable_1="V" variable_2="V"/>
        <map_variables variable_1="t" variable_2="t"/>
        <map_variables variable_1="m" variable_2="m"/>
    </connection>
    <connection>
        <map_components component_1="sodium_channel" component_2="sodium_channel_h_gate"/>
        <map_variables variable_1="V" variable_2="V"/>
        <map_variables variable_1="t" variable_2="t"/>
        <map_variables variable_1="h" variable_2="h"/>
    </connection>
</model>