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Code: Select all

//-----------------------------------------------------------------------------
// setIonParameters()
//-----------------------------------------------------------------------------
// sets the ion parameters for each segment inserting mechanisms given in mod files

proc setIonParameters() {

  // set the soma parameters
  forsec somatic {

    // insert the ion mechanisms
    insert k_ion
    insert na_ion
    insert hco3_ion
    insert cl_ion
    insert ca_ion

    insert pas
    	e_pas = el_soma
    	g_pas = gl_soma
  }

  // set the proximal apical dendrite parameters
  forsec proximal {

    // insert the ion mechanisms
    insert k_ion
    insert na_ion
    insert hco3_ion
    insert cl_ion
    insert ca_ion

    insert pas
    	e_pas = el_prox
    	g_pas = gl_prox
  }

  // set the middle apical dendrite parameters
  forsec middle {

    // insert the ion mechanisms
    insert k_ion
    insert na_ion
    insert hco3_ion
    insert cl_ion
    insert ca_ion

    insert pas
    	e_pas = el_mid
    	g_pas = gl_mid
  }

  // set the distal apical dendrite parameters
  forsec distal {

    // insert the ion mechanisms
    insert k_ion
    insert na_ion
    insert hco3_ion
    insert cl_ion
    insert ca_ion     

    insert pas
    	e_pas = el_dist
    	g_pas = gl_dist
  }
}

//////////////////// procedure calls /////////////////////////////////////
// register the new ions with NEURON
forall{
  cltype      = ion_register("cl",-1)
  hco3type    = ion_register("hco3",-1)
  catype      = ion_register("ca",2)
}

// set the ion parameters throughout the cell
setIonParameters()

// tell neuron how to treat them during the simulation
                            //ion_style("name", c_style, e_style, einit, eadvance, cinit)
                             // c_style-concentration: [0, 1, 2, 3] (UNUSED, PARAMETER, ASSIGNED, STATE)
                              // e_style - reversal pot: [0, 1, 2, 3] (UNUSED, PARAMETER, ASSIGNED, STATE)
                              // einit: [0, 1] (If 1 then reversal potential computed by Nernst equation on call to finitialize() using values of concentrations.)
                              // eadvance: [0, 1] (If 1 then reversal potential computed every call to fadvance() using the values of the concentrations)
                              //cinit: [0, 1] (If 1 then a call to finitialize() sets the concentrations to the values of the global initial concentrations. eg. nai set to nai0_na_ion and nao set to nao0_na_ion.)
forall {

	kstyle      = ion_style("k_ion",1,2,1,0,1)            // k, na, hco3 all parameters; set and forget
	nastyle     = ion_style("na_ion",1,2,1,0,1)           // cl is a state variable
	clstyle     = ion_style("cl_ion",3,2,1,1,1)
	hco3style   = ion_style("hco3_ion",1,2,1,0,1)
	castyle     = ion_style("ca_ion",3,2,1,0,1)
}

forall {
	ki = ki0_k_ion        
	ko = ko0_k_ion        
	nai = nai0_na_ion      
	nao = nao0_na_ion           
	hco3i = hco3i0_hco3_ion  
	hco3o = hco3o0_hco3_ion     
}

Code: Select all

NEURON {
    POINT_PROCESS GABAa
    RANGE trans_pres, nevents, g, gmax
    USEION cl READ ecl WRITE icl VALENCE -1
    USEION hco3 READ ehco3 WRITE ihco3 VALENCE -1
    GLOBAL clprm, C, D, alpha, beta
}

:------------------------------------------------------------------------------
UNITS {
    (nA) = (nanoamp)
    (mV) = (millivolt)
    (uS) = (microsiemens)
    (M)  = (1/liter)
    (mM) = (milliM)
}

:------------------------------------------------------------------------------
PARAMETER {
    clprm   = 0.8               : chloride permeability (hco3prm is 1-clprm)
    C       = 1       (mM)      : max transmitter concentration (From Mainen & Sejnowski 1998)
    D       = 1       (ms)      : transmitter duration (rising phase) (From Mainen & Sejnowski 1998)
    alpha   = 5       (/ms mM)  : forward (binding) rate (From Mainen & Sejnowski 1998)
    beta    = 0.18    (/ms)     : backward (unbinding) rate (From Mainen & Sejnowski 1998)
    gmax    = 0.003   (uS)      : maximum synaptic conductance
}

:------------------------------------------------------------------------------
ASSIGNED {
    v       (mV)    : postsynaptic voltage
    g       (uS)    : synaptic conductance
    rinf            : steady state channels open
    rtau    (ms)    : time constant of channel binding
    rdelta          : decay term for release vars
    trans_pres      : indicates whether transmitter is present (1 = yes, 0 = no)
    nevents         : counts the number of transmitter events
    icl     (nA)    : chloride current
    ecl     (mV)    : chloride reversal
    ihco3   (nA)    : bicarbonate current
    ehco3   (mV)    : bicarbonate reversal
}

:------------------------------------------------------------------------------
STATE { ron roff }

:------------------------------------------------------------------------------
INITIAL {
    ron = 0
    roff = 0
    rinf = C*alpha / (C*alpha + beta)
    rtau = 1 / ((alpha * C) + beta)
    rdelta = rinf*(1 - exp(-D/rtau))
    trans_pres = 0
    nevents = 0
}

:------------------------------------------------------------------------------
BREAKPOINT {
    SOLVE release METHOD cnexp
    g     = gmax * (ron + roff)
    icl   = g * clprm * (v - ecl)
    ihco3 = g * (1 - clprm) * (v - ehco3) 
}

:------------------------------------------------------------------------------
DERIVATIVE release {
    ron'  = (trans_pres*rinf - ron)/rtau
    roff' = -beta*roff
}

:------------------------------------------------------------------------------
NET_RECEIVE (w) { : the NetCon weight is ignored in this model
    if(flag == 0) { : spike event, increment events counter
        nevents = nevents + 1
        if (trans_pres == 0) {                              : this is a new event, turn conductance to on mode
            ron = roff
            roff = 0
        }
        trans_pres = 1
        net_send(D, 1)                                      : send a signal D later to turn to off mode
    } 
    else {                                                  : received an off signal, decrement the events counter
        nevents = nevents - 1
        if (nevents == 0) {                                 : no remaining events, turn conductance to off mode
            trans_pres = 0
            ron = 0
            roff = rdelta
        }
    }
}

Code: Select all

  USEION cl READ icl, ecl, clo WRITE cli VALENCE -1