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ca3_paper.hoc
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ca3_paper.hoc
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// **********************************************************
//
// This simulation is based on the following paper:
//
// Maciej T. Lazarewicz, Michele Migliore, Giorgio A. Ascoli,
// "A new bursting model of CA3 pyramidal cell physiology suggests multiple
// locations for spike initiation",
// Biosystems, 67(2002), 129-137
//
// Questions on how to use this model with NEURON should be directed to
// Maciej Lazarewicz (mailto:[email protected])
//
// Thanks to Leif Finkel and Elliot Menschik, UPENN, for valuable discussions on the model
//
// **********************************************************
load_file("nrngui.hoc")
// Set variable time step integration mehod
cvode_active(1)
Rm = 60000 // [ohm cm2]
RmDend = Rm / 2 // spines on dendrites are not implicitly simulated, but additional membrane area was accounted by dividing Rm by 2 and mulitplying Cm by 2
RmSoma = Rm
Cm = 1
CmSoma = Cm // [uF/cm2]
CmDend = Cm * 2
RaAll = 200 // [ohm cm]
RaSoma = 200
Vrest = -65 // [mV]
celsius = 25.0 // [C deg]
xopen("ca3a.geo")
Mesh_th = 0.4
gNa = 0.035 // [S/cm2]
gKdr = 0.002 // [S/cm2]
gKa = 0.011 // [S/cm2]
KaDt = 11.0 / (7.0 * 100 )
gKc = 0.004 // [S/cm2]
gKahp = 0.0005 // [S/cm2]
gKm = 0.0001 // [S/cm2]
gKh = 0.0001 // [S/cm2]
gKd = 0.00025 // [S/cm2]
gCaL = 0.0013 // [S/cm2]
gCaN = 0.0015 // [S/cm2]
gCaT = 0.001 // [S/cm2]
xopen("mesh.hoc")
xopen("fitness.hoc")
xopen("utilities.hoc")
access soma
// Set up current pulse
objref inj
inj = new IClamp(0.5)
inj.del = 2
inj.dur = 5
inj.amp = 1
// Set up passive parameters
proc ins_pasive() {
forall if(issection("soma")) {
insert pas
e_pas = Vrest
g_pas = 1 / RmSoma
Ra = RaSoma
cm = CmSoma
} else {
insert pas
e_pas = Vrest
g_pas = 1 / RmDend
Ra = RaAll
cm = CmDend
}
}
// Functions for set up distributions of ion channels
proc dist_Na() {
forall gbar_NaM99SL = gNa
}
proc dist_Kdr() {
forall gbar_KdrM99SL = gKdr
}
proc dist_Ka() {
forall for (x) {
xdist = abs(distance(x))
gbar_KaDistM99SL(x) = gKa * ( 1.0 + KaDt * xdist ) * ( xdist > 100.0 )
gbar_KaProxM99SL(x) = gKa * ( 1.0 + KaDt * xdist ) * ( xdist <= 100.0 )
}
}
proc dist_Km() {
forall if(issection("soma.*") || issection("dend2[0]") || issection("dend2[1]") || issection("dend3[0]") || issection("dend3[2]") || issection("dend3[37]") || issection("dend3[38]") ) gbar_KmM95 = gKm else gbar_KmM95 = 0
}
proc dist_Kahp() {
forall {
gbar_KahpM95 = gKahp * 0.2
if(issection("dend4.*") || issection("dend5.*") || issection("dend6.*") || issection("dend7.*") || issection("dend8.*") || issection("dend9.*") || issection("dend10.*") || issection("basal.*")) gbar_KahpM95 = gKahp
if(issection("soma.*")) gbar_KahpM95 = 0
}
}
proc dist_CaN() {
forall gbar_CAnM95 = gCaN
}
proc dist_CaT() {
forall gbar_CAtM95 = gCaT
}
proc dist_CaL() {
forall if( abs( distance(x) ) < 50 ) gbar_CAlM95 = gCaL else gbar_CAlM95 = 0
}
proc dist_Kc() {
forall for(x) if( abs( distance(x) ) < 150 ) gbar_KctBG99(x) = gKc * ( 150.0 - abs( distance(x) ) ) / 150.0 else gbar_KctBG99 = 0
}
proc dist_Khd() {
ehd_KhdM01 = -30
forall for (x){
xdist = abs( distance(x) )
ghdbar_KhdM01(x) = gKh * ( 1 + 3 / 100 * xdist )
if (xdist > 100) vhalfl_KhdM01 = -90 else vhalfl_KhdM01 = -82
}
}
proc dist_Kd() {
forall gbar_KdBG = gKd
}
// Set up active conductances
proc ins_active() {
forall {
insert KdrM99SL
insert KaProxM99SL
insert KaDistM99SL
insert caM95
insert NaM99SL
insert KmM95
insert CAlM95
insert CAnM95
insert CAtM95
insert KahpM95
insert KctBG99
insert KhdM01
insert KdBG
}
}
proc dist_active() {
dist_Na()
dist_Kdr()
dist_Ka()
dist_Km()
dist_CaL()
dist_CaN()
dist_CaT()
dist_Kahp()
dist_Kc()
dist_Kd()
dist_Khd()
}
// Initialization
proc init() {
forall {
v = Vrest
ek = -91
}
finitialize(Vrest)
fcurrent()
// Here is implemented the assumption that at steady state there is no current crossing the cell membrane
// by setting nonhomogenous reversal potential for leakage current
forall for (x) e_pas(x) = v(x) + ( ina(x) + ik(x) + ica(x) + i_KhdM01(x) ) / g_pas(x)
finitialize(Vrest)
}
// Main program
ins_pasive()
proc mesh_init() {
//compartmentalization function.
//To have compartments with a lambda length < $2
//at $1 (Hz) - the value for $2 should be less than 0.1-0.3.
//To speedup the demo simulation a value of 0.4@100Hz is used.
//Slightly different values for the conductances would be needed
//to obtain the same results when using a different compartmentalization.
//Contact the author for more information.
nra = fast_mesh(100,Mesh_th)
soma nseg = 1
print "Number of Comp: ",nra
// Set up origin in soma
soma distance()
access soma
// Set conductances
dist_active()
}
// Insert active conductances
ins_active()
mesh_init()
xopen("ses1.ses")
PlotShape[0].exec_menu("Shape Plot")
PlotShape[0].show(0)
tstop = 140
steps_per_ms = 40
dt = 0.025
init()
run()