DCN_mechs2.hoc

// CN model used in Saak V Ovsepian, Volker Steuber, Marie Le 
// Berre, Liam O'Hara, Valerie B O'Leary, and J. Oliver Dolly 
// (2013). A Defined Heteromeric KV1 Channel Stabilizes the 
// Intrinsic Pacemaking and Regulates the Efferent Code of Deep 
// Cerebellar Nuclear Neurons to Thalamic Targets. Journal of 
// Physiology (epub ahead of print. 
//
// written by Johannes Luthman, modified by Volker Steuber
//
// cell mechanisms for the simulations that replicate Figure 9A-D
// in Ovsepian et al. (2013)

objref ampa[EXCTOTALSYNAPSES]
objref fnmda[EXCTOTALSYNAPSES]
objref snmda[EXCTOTALSYNAPSES]
objref gaba[INHTOTALSYNAPSES]
objref axIS_cip
objref soma_cip1
objref soma_cip2
objref ouinoise

proc DCNmechs() {
    setBiophysics()
    insertChannels()
    insertSynapses()
    insertIClamp()
    insertOUCurrentNoise()
    fixCaIons()
}

proc setBiophysics() {

    // insert biophysics common to all compartments
    forall {
        cm = CM
        Ra = RA

        insert pasDCN
        gbar_pasDCN = PASSCOND
    }

    // Change conductance and resistivity of the axon, the only compartment type with
    // "non-standard" conductance and resistivity.
    forsec axNode {
        cm = CMMYEL
        gbar_pasDCN = PASSCONDMYEL
    }
}

proc insertOUCurrentNoise() {


    soma {
	ouinoise = new Ifluct8(0.5)
	ouinoise.i0 = 0.0 //0.0 // nA
	ouinoise.tau = 2 // ms
	ouinoise.std = 0.2 //0.1 // nA
    }
}

proc insertIClamp() {

    // insert current clamp stimulus into soma and axon initial segment
    // used to replicate data from Ovsepian 

    soma {
	soma_cip1 = new IClamp(0.5)
	soma_cip1.del = SOMACIP1DEL
	soma_cip1.dur = SOMACIP1DUR
	soma_cip1.amp = SOMACIP1AMP
	soma_cip2 = new IClamp(0.5)
	soma_cip2.del = SOMACIP2DEL
	soma_cip2.dur = SOMACIP2DUR
	soma_cip2.amp = SOMACIP2AMP
    }

    axIS[9] {
	axIS_cip = new IClamp(0.5)
	axIS_cip.del = AXISCIPDEL
	axIS_cip.dur = AXISCIPDUR
	axIS_cip.amp = AXISCIPAMP
    }
}

proc insertChannels() {

    // For each type of compartment, insert NMODL mechanisms
    // (ion channels and ca-concentration).

    // The qdeltat variable is GLOBAL in the NMODLs, meaning that it only needs to be
    // specified once for each mechanism, here in the soma (which contains a copy of
    // each mechanism).
    soma {

        insert NaF
        gbar_NaF = gNaFsoma
        qdeltat_NaF = QdTchannelGating

        insert NaP
        gbar_NaP = gNaPsoma
        qdeltat_NaP = QdTchannelGating

        ena = SodiumRevPot

        insert fKdr
        gbar_fKdr = gfKdrsoma
        qdeltat_fKdr = QdTchannelGating

        insert sKdr
        gbar_sKdr = gsKdrsoma
        qdeltat_sKdr = QdTchannelGating

        insert SK
        gbar_SK = gSKsoma
        qdeltat_SK = QdTchannelGating

        ek = PotassiumRevPot


        insert h
        gbar_h = gHsoma
        qdeltat_h = QdTchannelGating
        eh_h = hRevPot


        insert TNC
        gbar_TNC = gTNCsoma
        eTNC_TNC = TNCrevPot


        // calcium channels - they use the Goldman-Hodgkin-Katz (GHK) current equation
        // and so don't have a set reversal potential.
        insert CaLVA
        perm_CaLVA = permCaLVAsoma
        qdeltat_CaLVA = QdTchannelGating

        insert CaHVA
        perm_CaHVA = permCaHVAsoma
        qdeltat_CaHVA = QdTchannelGating


        // insert a hypothetical shell below the membrane of the cell to keep track of the
        // calcium entering the cell through the CaHVA and CaLVA channels, respectively.
        // The resulting calcium concentration is used to calculate the current flow through
        // through those channels.

        // For the CaHVA channel:

        insert CaConc
        tauCa_CaConc = tauCaConcSoma
        kCa_CaConc = kCaCaConcSoma

        // For the soma, the calculation of shell thickness is different from
        // the dendrites since it is a sphere in GENESIS and a cylinder
        // in NEURON. See how it's done in GENESIS file cn_comp_dj10.g and
        // divide that expression by the surface area of the NEURON soma to get
        // the following expression:
        depth_CaConc = SHELLTHICK - 2*SHELLTHICK^2/diam + \
                4*SHELLTHICK^3/(3*diam^2) // =0.196215


        // For the CaLVA channel:

        insert CalConc
        tauCal_CalConc = tauCaConcSoma
        kCal_CalConc = kCaCaConcSoma
        depth_CalConc = SHELLTHICK - 2*SHELLTHICK^2/diam + \
                4*SHELLTHICK^3/(3*diam^2) // =0.196215
    }

    forsec axHillock {
        insert NaF
        gbar_NaF = gNaFaxHill
        ena = SodiumRevPot

        insert fKdr
        gbar_fKdr = gfKdraxHill
        insert sKdr
        gbar_sKdr = gsKdraxHill
        ek = PotassiumRevPot

        insert TNC
        gbar_TNC = gTNCaxHill
        eTNC_TNC = TNCrevPot
    }

    forsec axIniSeg {
        insert NaF
        gbar_NaF = gNaFaxIniSeg
        ena = SodiumRevPot

        insert fKdr
        gbar_fKdr = gfKdraxIniSeg
        insert sKdr
        gbar_sKdr = gsKdraxIniSeg
        ek = PotassiumRevPot

        insert TNC
        gbar_TNC = gTNCaxIniSeg
        eTNC_TNC = TNCrevPot
    }

    // No channels in the axon.
    // forsec axNode {
    // }

    forsec proxDend {
        insert NaF
        gbar_NaF = gNaFpDend
        ena = SodiumRevPot

        insert fKdr
        gbar_fKdr = gfKdrpDend
        insert sKdr
        gbar_sKdr = gsKdrpDend
        insert SK
        gbar_SK = gSKpDend
        ek = PotassiumRevPot

        insert h
        gbar_h = gHpDend
        eh_h = hRevPot

        insert TNC
        gbar_TNC = gTNCpDend
        eTNC_TNC = TNCrevPot

        insert CaLVA
        perm_CaLVA = permCaLVAdend

        insert CaHVA
        perm_CaHVA = permCaHVAdend

        insert CaConc
        kCa_CaConc = kCaCaConcDend
        depth_CaConc = SHELLTHICK - (SHELLTHICK*SHELLTHICK/diam)

        insert CalConc
        kCal_CalConc = kCaCaConcDend
        depth_CalConc = SHELLTHICK - (SHELLTHICK*SHELLTHICK/diam)
    }

    forsec distDend {
        insert SK
        gbar_SK = gSKdDend
        ek = PotassiumRevPot

        insert h
        gbar_h = gHdDend
        eh_h = hRevPot

        insert CaLVA
        perm_CaLVA = permCaLVAdend

        insert CaHVA
        perm_CaHVA = permCaHVAdend

        insert CaConc
        kCa_CaConc = kCaCaConcDend
        depth_CaConc = SHELLTHICK - (SHELLTHICK*SHELLTHICK/diam)

        insert CalConc
        kCal_CalConc = kCaCaConcDend
        depth_CalConc = SHELLTHICK - (SHELLTHICK*SHELLTHICK/diam)
    }
} // end proc insertChannels()

proc insertSynapses() {

    // GABAergic synapses
    // If the short term depression variant of the GABA synapse is used, then calculate
    // the depression level to start out with. Set the level to that reached at steady state
    // with the present input frequency, using the equation from DCNsynGABA.mod giving "relProbSS".
    if (useGABAsyndep == 1) {
        initDeprLevel = 0.08 + 0.60*exp(-2.84*inhibitoryHz) + 0.32*exp(-0.02*inhibitoryHz)
    }
    
    c = 0
    forsec inhSynapseComps {
        if (useGABAsyndep == 1) {
            gaba[c] = new DCNsynGABA(0.5)
            gaba[c].startDeprLevel = initDeprLevel
        } else {
            gaba[c] = new DCNsyn(0.5)
        }
        gaba[c].tauRise = tauRiseGABA
        gaba[c].tauFall = tauFallGABA
        gaba[c].e = GABARevPot
        c+=1
    }

    // Excitatory synapses
    c = 0
    forsec excSynapseComps {

        ampa[c] = new DCNsyn(0.5)
        ampa[c].tauRise = tauRiseAMPA
        ampa[c].tauFall = tauFallAMPA
        ampa[c].e = ExcitSynRevPot

        fnmda[c] = new DCNsynNMDA(0.5)
        fnmda[c].tauRise = tauRisefNMDA
        fnmda[c].tauFall = tauFallfNMDA
        fnmda[c].e = ExcitSynRevPot
        fnmda[c].MgFactor = MgFactorfNMDA
        fnmda[c].gamma = gammafNMDA

        snmda[c] = new DCNsynNMDA(0.5)
        snmda[c].tauRise = tauRisesNMDA
        snmda[c].tauFall = tauFallsNMDA
        snmda[c].e = ExcitSynRevPot
        snmda[c].MgFactor = MgFactorsNMDA
        snmda[c].gamma = gammasNMDA

        c+=1
    }
} // end of proc insertSynapses()


proc fixCaIons() {
    // Set some specifications for the Ca and Cal ions. The following ion_style
    // statements don't affect the behaviour of the model but compared to not giving
    // them, speed up the simulation ca 5%, probably due to preventing eca from being
    // calculated each dt. ion_style has to be set for each compartment where the Ca ion
    // is used but gives no error when set for those compartments that don't use the ion.
    forall {
        ion_style("ca_ion", 2, 0, 0, 0, 1)
    }
    forall {
        ion_style("cal_ion", 2, 0, 0, 0, 1)
    }
    // Set the extracellular calcium concentrations (mM):
    cao0_ca_ion = 2
    calo0_cal_ion = 2
}

//DCNmechs()