Human-L2-3-Cortical-Microcircuit/NeuroML2/CaDynamics_E2_NML2.nml

<?xml version="1.0" encoding="ISO-8859-1"?>
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta3.xsd"
         id="CaDynamics_E2_NML2">

    <notes>NeuroML 2 implementation of the Ca Pool mechanism</notes>

    <!--<decayingPoolConcentrationModel id="CaDynamics_E2_NML2" restingConc="1e-10mol_per_cm3" decayConstant="80ms" ion="ca" shellThickness="2.787e-4cm"/>-->

    <concentrationModel id="CaDynamics_E2_NML2_PV_somatic" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="531.0255920416845 ms" depth="0.1 um" gamma="5e-4" ion="ca"/>
    <concentrationModel id="CaDynamics_E2_NML2_PV_axonal" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="163.03538024059918 ms" depth="0.1 um" gamma="5e-4" ion="ca"/>
    <concentrationModel id="CaDynamics_E2_NML2_PYR_somatic" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="20 ms" depth="0.1 um" gamma="5e-4" ion="ca"/>
    <concentrationModel id="CaDynamics_E2_NML2_PYR_axonal" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="226 ms" depth="0.1 um" gamma="5e-4" ion="ca"/>
    <concentrationModel id="CaDynamics_E2_NML2_SST_somatic" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="465 ms" depth="0.1 um" gamma="5e-4" ion="ca"/>
    <concentrationModel id="CaDynamics_E2_NML2_SST_axonal" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="469 ms" depth="0.1 um" gamma="5e-4" ion="ca"/>
    <concentrationModel id="CaDynamics_E2_NML2_VIP_somatic" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="25.159166441555044 ms" depth="0.1 um" gamma="5e-4" ion="ca"/>
    <concentrationModel id="CaDynamics_E2_NML2_VIP_axonal" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="75.78875619470153 ms" depth="0.1 um" gamma="5e-4" ion="ca"/>

    <!--
    This is a new, custom ComponentType to handle the calcium mechanism with parameters

    PARAMETER	{
        gamma = 0.05 : percent of free calcium (not buffered)
        decay = 80 (ms) : rate of removal of calcium
        depth = 0.1 (um) : depth of shell
        minCai = 1e-4 (mM)
    }

    and derivative mechanism:

    DERIVATIVE states	{
        cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay
    }

    See https://github.com/OpenSourceBrain/L5bPyrCellHayEtAl2011/blob/master/neuroConstruct/cellMechanisms/CaDynamics_E2_init_mod/CaDynamics_E2.mod

    -->


    <ComponentType name="concentrationModelHayEtAl" extends="concentrationModel" description="Model of buffering of concentration of specific to Hay Et Al 2011">

        <Parameter name="gamma" dimension="none"/>
        <Parameter name="minCai" dimension="concentration"/>
        <Parameter name="decay" dimension="time"/>
        <Parameter name="depth" dimension="length"/>


        <Constant name="Faraday" dimension="charge_per_mole" value="96485.3C_per_mol"/>

        <Requirement name="iCa" dimension="current"/>

        <Text name="species"/>

        <Dynamics>

            <StateVariable name="concentration" exposure="concentration" dimension="concentration"/>
            <StateVariable name="extConcentration" exposure="extConcentration" dimension="concentration"/>

            <DerivedVariable name="currDensCa" dimension="currentDensity" value="iCa / surfaceArea"/>

            <TimeDerivative variable="concentration" value="(currDensCa * gamma/(2 * Faraday * depth)) - ((concentration - minCai) / decay)"/>

            <OnStart>
                <StateAssignment variable="concentration" value="initialConcentration"/>
                <StateAssignment variable="extConcentration" value="initialExtConcentration"/>
            </OnStart>

        </Dynamics>

    </ComponentType>


</neuroml>