-
Notifications
You must be signed in to change notification settings - Fork 2
/
reD_vc.oc
246 lines (169 loc) · 5.57 KB
/
reD_vc.oc
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
/*----------------------------------------------------------------------------
VOLTAGE-CLAMP SIMULATIONS OF RE CELLS
=====================================
- passive and structural parameters estimated from SimFit
- electrode with adjustable series resistance
- simulations at 24 degC
- special run procedure for calculating the peak current
- calcium diffusion
- Q10=2.5
** voltage-clamp in dissociated RE cell with 8 compartment **
For more details, see:
Destexhe, A., Contreras, D., Steriade, M., Sejnowski, T.J. and Huguenard,
J.R. In vivo, in vitro and computational analysis of dendritic calcium
currents in thalamic reticular neurons. J. Neurosci. 16: 169-185, 1996.
See also:
http://www.cnl.salk.edu/~alain
http://cns.fmed.ulaval.ca
----------------------------------------------------------------------------*/
//----------------------------------------------------------------------------
// load and define general graphical procedures
//----------------------------------------------------------------------------
// xopen("$(NEURONHOME)/lib/hoc/stdrun.hoc")
load_file("nrngui.hoc")
objectvar g[20] // max 20 graphs
ngraph = 0
proc addgraph() { local ii // define subroutine to add a new graph
// addgraph("variable", minvalue, maxvalue)
ngraph = ngraph+1
ii = ngraph-1
g[ii] = new Graph()
g[ii].size(tstart,tstop,$2,$3)
g[ii].xaxis()
g[ii].yaxis()
g[ii].addvar($s1,1,0)
g[ii].save_name("graphList[0].")
g[ii].exec_menu("Keep Lines")
graphList[0].append(g[ii])
}
if(ismenu==0) {
nrnmainmenu() // create main menu
nrncontrolmenu() // create control menu
}
//----------------------------------------------------------------------------
// transient time
//----------------------------------------------------------------------------
trans = 1000
print " "
print ">> Transient time of ",trans," ms"
print " "
//----------------------------------------------------------------------------
// create multi-compartment geometry and insert currents
//----------------------------------------------------------------------------
xopen("cells/reD.geo") // read geometry file
corrD = 1 // dendritic surface correction
forall { // insert passive current everywhere
insert pas
g_pas = 5e-5 * corrD // (from simfit)
e_pas = -72.843 // (from simfit)
cm = 1 * corrD // (from simfit)
Ra = 260 // (from simfit)
L = L
}
soma {
g_pas = 5e-5 // (from simfit)
cm = 1 // (from simfit)
}
forall {
insert it2 // T-current everywhere
cai = 2.4e-4
cao = 2
eca = 120
shift_it2 = 0 // no shift of ITs
gcabar_it2 = corrD * 0.0002
qm_it2 = 2.5 // low q10
qh_it2 = 2.5
insert cad // calcium diffusion everywhere
depth_cad = corrD // NEED TO BE RESCALED
kt_cad = 0 // no pump
kd_cad = 1e-4
taur_cad = 5
cainf_cad = 2.4e-4
}
xopen("locD.oc") // load procedure for localizing T-current
localize (0.000045, 0.000045) // initial distribution of T-current
//----------------------------------------------------------------------------
// insert electrode in the soma
//----------------------------------------------------------------------------
// note load_file command only executed if not executed yet for that file in current session
load_file("El.oc") // Electrode with series resistance
access soma
objectvar El // insert electrode
El = new Electrode()
electrodes_present=1
//
// VOLTAGE-CLAMP MODE
//
forall { g_pas = 0 } // remove passive current everywhere
soma El.vc.loc(0.5) // put electrode in voltage-clamp mode
El.vc.dur[0] = trans-20
El.vc.dur[1] = 10
El.vc.dur[2] = 1000
El.vc.amp[0] = -110
El.vc.amp[1] = -110
El.vc.amp[2] = -30
El.vc.rs = 5 // series resistance
// 49.79 megohm from simfit
//----------------------------------------------------------------------------
// setup simulation parameters
//----------------------------------------------------------------------------
Dt = 0.2
npoints = 2000
objectvar Sim // create vector of simulation points
Sim = new Vector(npoints)
dt = 0.1 // must be submultiple of Dt
tstart = trans-100
tstop = trans + npoints * Dt
runStopAt = tstop
steps_per_ms = 1/Dt
celsius = 24
v_init = -70
//----------------------------------------------------------------------------
// procedures for voltage-clamp protocol
//----------------------------------------------------------------------------
proc run2() { // new run procedure
run()
peak_current = Sim.min()
print "Peak current = ",peak_current
}
proc init() { // initialization procedure
finitialize(v_init)
fcurrent()
index = 0 // add definition of an index
peak_current = 0 // define peak current
}
proc step() {local i // advance-one-step (Dt) procedure
Plot()
if(t >= trans) {
Sim.set(index,El.vc.i) // memorize data only after trans
index = index + 1
}
for i=1,nstep_steprun {
advance()
}
}
vmin = -110 // values of protocol
vmax = -40
vstep = 5
proc run_vc() { // general procedure for v-clamp
for(vhold=vmin; vhold<vmax+vstep; vhold=vhold+vstep) {
El.vc.amp[0] = vhold
run2()
}
}
proc make_VCpanel() { // make panel
xpanel("VC")
xpvalue("Start holding potential",&vmin)
xpvalue("End holding potential",&vmax)
xpvalue("Step potential",&vstep)
xbutton("Start protocol","run_vc()")
xpanel()
}
make_VCpanel()
//----------------------------------------------------------------------------
// add graphs
//----------------------------------------------------------------------------
addgraph("El.vc.i",-0.16,0.0001)
addgraph("soma.v(0.5)",-120,0)
addgraph("dend1[3].v(0.5)",-120,0) // for dissociated cell
//addgraph("dend3[6].v(0.5)",-120,0) // for intact cell