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figure5.hoc
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figure5.hoc
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/////////////////////////////////
//
// Figure 5 - varying peak calcium concentration by varying beta parameter
// High calcium configuration
// Jaffe, Wang, and Brenner (2011)
//
// Original code based on Aradi and Holmes (1999)
//
/////////////////////////////////
load_file("nrngui.hoc")
v_init = -70
tstart = 0
tstop = 30
dt = 0.025
celsius = 35
load_file("channels.ses")
objref p
p = new PWManager()
for i = 2,5 {p.hide(i)}
proc celldef() {
topol()
subsets()
geom()
biophys()
geom_nseg()
}
create soma, axon[4], GCL[2], prox[2], middle[2], distal[2]
proc topol() { local i
connect axon(0), soma(1)
for i = 1, 3 connect axon[i](0), axon[i-1](1)
for i = 0, 1 connect GCL[i](0), soma(0)
for i = 0, 1 connect prox[i](0), GCL[i](1)
for i = 0, 1 connect middle[i](0), prox[i](1)
for i = 0, 1 connect distal[i](0), middle[i](1)
basic_shape()
}
proc basic_shape() {
soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
axon {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(30, 0, 0, 1)}
axon[1] {pt3dclear() pt3dadd(30, 0, 0, 1) pt3dadd(45, 0, 0, 1)}
axon[2] {pt3dclear() pt3dadd(45, 0, 0, 1) pt3dadd(60, 0, 0, 1)}
axon[3] {pt3dclear() pt3dadd(60, 0, 0, 1) pt3dadd(120, 0, 0, 1)}
GCL {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-29, 30, 0, 1)}
GCL[1] {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-29, -29, 0, 1)}
prox {pt3dclear() pt3dadd(-29, 30, 0, 1) pt3dadd(-44, 30, 0, 1)}
prox[1] {pt3dclear() pt3dadd(-29, -29, 0, 1) pt3dadd(-44, -29, 0, 1)}
middle {pt3dclear() pt3dadd(-44, 30, 0, 1) pt3dadd(-59, 30, 0, 1)}
middle[1] {pt3dclear() pt3dadd(-44, -29, 0, 1) pt3dadd(-59, -29, 0, 1)}
distal {pt3dclear() pt3dadd(-59, 30, 0, 1) pt3dadd(-119, 30, 0, 1)}
distal[1] {pt3dclear() pt3dadd(-59, -29, 0, 1) pt3dadd(-119, -29, 0, 1)}
}
objref all, dendrites, GCLs, proxs, middles, distals, allaxon
proc subsets() { local i
objref all, dendrites, GCLs, proxs, middles, distals, allaxon
all = new SectionList()
soma all.append()
for i=0, 3 axon[i] all.append()
for i=0, 1 GCL[i] all.append()
for i=0, 1 prox[i] all.append()
for i=0, 1 middle[i] all.append()
for i=0, 1 distal[i] all.append()
dendrites = new SectionList()
for i=0, 1 GCL[i] dendrites.append()
for i=0, 1 prox[i] dendrites.append()
for i=0, 1 middle[i] dendrites.append()
for i=0, 1 distal[i] dendrites.append()
GCLs = new SectionList()
for i=0, 1 GCL[i] GCLs.append()
proxs = new SectionList()
for i=0, 1 prox[i] proxs.append()
middles = new SectionList()
for i=0, 1 middle[i] middles.append()
distals = new SectionList()
for i=0, 1 distal[i] distals.append()
allaxon = new SectionList()
for i=0, 3 axon[i] allaxon.append()
}
proc geom() {
forsec dendrites { L = 150 diam = 3 }
forsec GCLs { L = 50 }
forsec allaxon { L = 50 }
axon.diam = 0.9
axon[1].diam = 0.7
axon[2].diam = 0.5
axon[3].diam = 0.4
soma { L = 16.8 diam = 16.8 }
axon[3] { L = 1400 }
}
proc geom_nseg() {
forsec dendrites { nseg = 4 }
forsec GCLs { nseg = 2 }
forsec allaxon { nseg = 1 }
soma { nseg = 2 }
axon[3] { nseg = 28 }
}
proc biophys() {
forsec all {
Ra = 210
cm = 1
insert pas
g_pas = 2.5e-05
e_pas = -70
}
forsec dendrites {
cm = 1.6
insert pas
g_pas = 4e-05
e_pas = -70
}
forsec GCLs {
cm = 1
insert pas
g_pas = 2.5e-05
e_pas = -70
insert Na
gmax_Na = 0.018
insert fKDR
gmax_fKDR = 0.004
insert sKDR
gmax_sKDR = 0.003
}
forsec proxs {
insert Na
gmax_Na = 0.013
insert fKDR
gmax_fKDR = 0.004
insert sKDR
gmax_sKDR = 0.003
}
forsec middles {
insert Na
gmax_Na = 0.008
insert fKDR
gmax_fKDR = 0.001
insert sKDR
gmax_sKDR = 0.003
}
forsec distals {
insert fKDR
gmax_fKDR = 0.001
insert sKDR
gmax_sKDR = 0.004
}
forsec allaxon {
insert Na
gmax_Na = 0.21
insert fKDR
gmax_fKDR = 0.028
}
soma {
insert Ca // Ca Channesl
gtcabar_Ca = 0
gncabar_Ca = 0
glcabar_Ca = 0.0018
insert aabBK // BK Channels
gakbar_aabBK = 0
gabkbar_aabBK = 0
cascale_aabBK = .01 // Beta factorg
tau_aabBK = 1
base_aabBK = 4
insert Na
gmax_Na = 0.12
insert fKDR
gmax_fKDR = 0.016
insert sKDR
gmax_sKDR = 0.003
}
}
access soma
celldef()
forsec all {
if (ismembrane("Na")) {ena = 45}
ek = -85
}
// insert current clamp at the soma
objref stim
stim = new IClamp(0.5)
stim.del = 5
stim.dur = 1
stim.amp = 2
proc init() {local i
finitialize(v_init)
fcurrent()
t = tstart
}
init()
access soma
proc advance() {
// output is in four columns: time, soma.v, calcium, I-BK
fprint("%g %g %g %g\n",t,soma.v,cal_aabBK, (gak_aabBK+gabk_aabBK)*(soma.v+85))
fadvance()
}
strdef tname
proc DualSimulate() { // Perform two simulations, one with alphabeta4 and one with alpha
// Calcium channels
gtcabar_Ca = 0
gncabar_Ca = 0
glcabar_Ca = 0.0045
// BK Channels - alphabeta4 on
gakbar_aabBK = 0
gabkbar_aabBK = .05
sprint(tname,"trace_ab_%d.dat",$1) // output file name
wopen(tname)
run()
// BK Channels - alpha on
gakbar_aabBK = .05
gabkbar_aabBK = 0
sprint(tname,"trace_a_%d.dat",$1) // output file name
wopen(tname)
run()
wopen()
}
// Loop through parameter file systematically varying beta
ropen("varybeta.parm") // beta parameter file
for i=0,7 {
cascale_aabBK = fscan()
DualSimulate(i)
}
cascale_aabBK = 0
DualSimulate(8)