// ReConv algorithm for reconstructing evoked LFP in cerebellar granular layer
// Uses Multicompartmental GrC model (see http://senselab.med.yale.edu/ModelDb/showmodel.asp?model=116835)
// Last updated 11-June-2011
// Model developer: Shyam Diwakar M.
// Developed at Amrita School of Biotechnology (India) and at Prof. Egidio D'Angelo's Lab at Univ of Pavia (Italy)
// Amrita School of Biotechnology, Amritapuri
// Clappana P.O., Kollam, 690 525, Kerala, India.
// http://research.amrita.edu/compneuro
// Email:shyam@amrita.edu
/* Model published as [Diwakar et al., 2011, manuscript accepted, PLoS ONE]
Shyam Diwakar, Paola Lombardo, Sergio Solinas, Giovanni Naldi, Egidio D'Angelo. "Local field potential modeling predicts dense activation in cerebellar granule cells clusters under LTP and LTD control", PLoS ONE, 2011.
*/
begintemplate GrC
ndend = 4
nsg = 5
naxon = 30
public soma,synA,synNS,synG,Area,CC,dend_1,dend_2,dend_3,dend_4,hillock,axon
public connect_pre,rescale,Us
public list_go_grc,list_con_inhib
public branch0,branch1,branch2,branch3
public SpikeTrain
create soma,hillock[1],axon[1],dend_1[1],dend_2[1],dend_3[1],dend_4[1],branch0,branch1,branch2,branch3
objref synNS[4],synA[4],synG[4]
objref list_go_grc,list_con_inhib
objref Inhib[4],CC
objref SpikeTrain,nil,netcon
proc init() {
list_go_grc=new List()
list_con_inhib=new List()
if(numarg()==4){ndend=$1 nsg =$2 nbut=$3 naxon=$4} else {ndend=4 nsg=5 nbut=20 naxon=30}
create soma, hillock[nsg], axon[naxon], dend_1[ndend], dend_2[ndend], dend_3[ndend], dend_4[ndend],branch0,branch1,branch2,branch3
soma {
access soma
nseg = 1
diam = 5.8//6.06
L = 5.8//6.16
cm = 1
Ra = 100
celsius=30
// Soma Channels
insert GRC_LKG1
insert GRC_LKG2
ggaba_GRC_LKG2 = 3e-05
insert GRC_KIR
insert GRC_KA
insert GRC_KM
usetable_GRC_KA = 0
usetable_GRC_KIR = 0
usetable_GRC_KM = 0
insert GRC_NA
insert GRC_KV
usetable_GRC_NA = 0
usetable_GRC_KV = 0
insert GRC_KCA
usetable_GRC_KCA = 0
gkbar_GRC_KCA = 0
insert GRC_CA
usetable_GRC_CA = 0
gcabar_GRC_CA = 0
insert GRC_CALC
beta_GRC_CALC = 1.5
ena = 87.39
ek = -84.69
eca = 129.33
ecl = -65
}
// Hillock definition
for(w1=0;w1<nsg;w1=w1+1) {
hillock[w1] {
access hillock[w1]
nseg = 1
diam = 2.3-0.5*w1
L = 0.5
cm = 1
Ra = 100
// Hillock Channels
insert GRC_LKG1
insert GRC_NA
insert GRC_KV
usetable_GRC_NA = 0
usetable_GRC_KV = 0
\
ena = 87.39
ek = -84.69
}
}
for(w3=0;w3<naxon;w3=w3+1) {
axon[w3] { // Axon definition
access axon[w3]
nseg = 1
diam = 0.3
L = 2.3367
cm = 1
Ra = 100
// Axon Channels
insert GRC_LKG1
insert GRC_NA
insert GRC_KV
usetable_GRC_NA = 0
usetable_GRC_KV = 0
ena = 87.39
ek = -84.69
}
}
// Dendrite definition: first compartment
for(w2=0;w2<ndend;w2=w2+1) {
dend_1[w2] {
access dend_1[w2]
nseg = 1
diam = 0.75
L = 5
cm = 1
Ra = 100
// Dendritic Channels
insert GRC_LKG1
insert GRC_LKG2
ggaba_GRC_LKG2 = 3e-05
insert GRC_KIR
usetable_GRC_KIR = 0
gkbar_GRC_KIR=0
insert GRC_KA
usetable_GRC_KA = 0
gkbar_GRC_KA=0
insert GRC_KCA
usetable_GRC_KCA = 0
gkbar_GRC_KCA = 0
insert GRC_CA
usetable_GRC_CA = 0
gcabar_GRC_CA = 0
insert GRC_CALC
beta_GRC_CALC = 1.5
eca = 129.33
ek = -84.69
}
}
// Dendrite definition: second compartment
for(w2=0;w2<ndend;w2=w2+1) {
dend_2[w2] {
access dend_2[w2]
nseg = 1
diam = 0.75
L = 5
cm = 1
Ra = 100
// Dendritic Channels
insert GRC_LKG1
insert GRC_LKG2
ggaba_GRC_LKG2 = 3e-05
insert GRC_KIR
usetable_GRC_KIR = 0
gkbar_GRC_KIR=0
insert GRC_KA
usetable_GRC_KA = 0
gkbar_GRC_KA=0
insert GRC_KCA
usetable_GRC_KCA = 0
gkbar_GRC_KCa = 0
insert GRC_CA
usetable_GRC_CA = 0
gcabar_GRC_CA = 0
insert GRC_CALC
beta_GRC_CALC = 1.5
eca = 129.33
ek = -84.69
}
}
// Dendrite definition: third compartment
for(w2=0;w2<ndend;w2=w2+1) {
dend_3[w2] {
access dend_3[w2]
nseg = 1
diam = 0.75
L = 2.5
cm = 1
Ra = 100
// Dendritic Channels
insert GRC_LKG1
insert GRC_LKG2
ggaba_GRC_LKG2 = 3e-05
insert GRC_KIR
usetable_GRC_KIR = 0
gkbar_GRC_KIR=0
insert GRC_KA
usetable_GRC_KA = 0
gkbar_GRC_KA=0
insert GRC_KCA
usetable_GRC_KCA = 0
gkbar_GRC_KCA = 0
insert GRC_CA
usetable_GRC_CA = 0
gcabar_GRC_CA = 0
insert GRC_CALC
beta_GRC_CALC = 1.5
eca = 129.33
ek = -84.69
synG[w2] = new GRC_GABA(0.5)
}
}
// Dendrite definition: fourth compartment
for(w2=0;w2<ndend;w2=w2+1) {
dend_4[w2] {
access dend_4[w2]
nseg = 1
diam = 0.75
L = 2.5
cm = 1
Ra = 100
// Dendritic Channels
insert GRC_LKG1
insert GRC_LKG2
ggaba_GRC_LKG2 = 3e-05
insert GRC_CA
insert GRC_KIR
usetable_GRC_KIR = 0 // 1
gkbar_GRC_KIR=0
insert GRC_KA
usetable_GRC_KA = 0 // 1
gkbar_GRC_KA=0
insert GRC_KCA
usetable_GRC_KCA = 0 // 1
insert GRC_CA
usetable_GRC_CA = 0 // 1
insert GRC_CALC
beta_GRC_CALC = 1.5
eca = 129.33
ek = -84.69
synA[w2] = new AmpaCOD(0.5)
synNS[w2] = new NMDAS(0.5)
}
}
//Passive compartments -to maintain propagation delay and to avoid spike reflection
branch0 {
access branch0
nseg = 1
diam = 0.3
L = 3
cm = 0.5
Ra = 100
celsius=30
insert GRC_LKG1
}
branch1 {
access branch1
nseg = 1
diam = 0.2
L = 5
cm = 0.45
Ra = 100
celsius=30
insert GRC_LKG1
}
branch2 {
access branch2
nseg = 1
diam = 0.1
L = 10
cm = 1
Ra = 90
celsius=30
insert GRC_LKG1
}
branch3 {
access branch3
nseg = 1
diam = 0.1
L = 200
cm = 1
Ra = 100
celsius=30
insert GRC_LKG1
}
//Connect all compartments
for(i=0;i<ndend;i=i+1){
connect dend_4[i](1), dend_3[i](0)
connect dend_3[i](1), dend_2[i](0)
connect dend_2[i](1), dend_1[i](0)
connect dend_1[i](1), soma(0)
}
connect soma(1), hillock[0](0)
connect hillock[0](1), hillock[1](0)
connect hillock[1](1), hillock[2](0)
connect hillock[2](1), hillock[3](0)
connect hillock[3](1), hillock[4](0)
connect hillock[4](1), axon[0](0)
for(i=0;i<naxon-1;i=i+1) {
connect axon[i](1), axon[i+1](0)
}
connect axon[naxon-1](1),branch0(0)
connect branch0(1),branch1(0)
connect branch1(1),branch2(0)
connect branch2(1),branch3(0)
}
endtemplate GrC
