-
Notifications
You must be signed in to change notification settings - Fork 1
/
dc-conf.lua
273 lines (245 loc) · 6.49 KB
/
dc-conf.lua
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
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
module(...,package.seeall)
require "chlib"
require "el_ph"
require 'lib'
--- Refs:
--- SE-model: Swarz-Eikhof model [cited from Rattay and Aberham, 1993]
--- MRG: McIntyre, Richardson, Grill model [MRG, 2002]
--- MRGAxon: MRG, but original NEURON files
local global_variable_values = {
K_o = 3.2, -- mM -- to check
Na_i = 12, -- mM
V_a = -87,
}
local temp = 37
local global_parameters = {
dNai_switch = 1, -- either 0 or 1
dKo_switch = 1,
rho_a = 0.07, -- KOhm*cm, axonal resistivity
T = temp + 273, -- temperature
celsius = temp,
V_leak = -80,
c_m = 2, -- uF/cm^2, membrane capacitance per cm^2
Na_o = 140, -- mM
Na_i = 9.5, -- mM
K_i = 155, -- mM -- to check
K_o = 3.2, -- mM -- to check
g_s = 1.0, -- mS, transmyelin conductivity, per lamella membrane
--ko_sig = lib.logistic(200, 12, 4.2, 1), -- (interesting)
--ko_sig = lib.logistic(137, 2.5, 6, 1), -- (normal?)
--ko_sig = lib.logistic(90, 2.5, 6.6, 1), --[poster]
ko_sig = lib.logistic(4, 3.5, 7.0, 1), --[paper sc1!]
--ko_sig = lib.logistic(4, 3.5, 7.0, 1),
--ko_sig = lib.hill(4, 25, 7.0, 1),
--ko_sig = lib.logistic(4, 4.0, 6.5, 1),
nak_pump = {
--jnamax = 0.15e-6, -- mmole/(cm^2*s) -- in kidney
jnamax = 0.03e-6, -- mmole/(cm^2*s) --
a_na = 0.5, -- mM
a_k = 0.1, -- mM
--a_k = 5.4, -- mM
b_na = 2.4e-2,
b_k = 5.4e-3,
},
nak_pump_a = {
jnamax =0.07e-6, --mmole/(cm^2*s)
a_na = 9,
b_na = 1e-2,
a_k = 0.1,
b_k = 1e-3,
},
nak_pump_g = {
jnamax =0.07e-6, --mmole/(cm^2*s)
a_na = 0.1,
b_na = 1e-2,
a_k = 4.5,
b_k = 1e-3,
}
}
segments={} -- compartment descriptions
segments.SC_mine = {
-- Geometry-based (2nd version) model
-- Some parameters are from HANA-2005
type = "SC_geom",
pars = {
stimulated = true,
node = {
c_m = 2, --uF/cm^2
l = 1e-4, d = 3.5e-4,
h = 9e-4, -- cm, height of the restricted space (was: 8)
g_lk = 2, V_lk = -80,
wavy = 9, -- account for 'wavyness' of glial membrane in node
pump_a = global_parameters.nak_pump_a,
tau_passive = 2e4, -- passive K exchange in the node char. time (ms)
currents = {
iNat = {
ion = "Na",
gp = {m_n = chlib.fsc.m.srb, h_n = chlib.fsc.h.srb},
g = 2800},
iNap = {
ion = "Na",
gp = {p_n = chlib.psc.p.hana},
g = 24},
iKs = {
ion = "K",
gp = {s_n = chlib.spc.s.my},
--g = 112,
g = 90}}},
int = { -- internode
c_m = 1, c_s = 0.1, l= 0.129, d = 8.8e-4,
lpara = 80e-4,
D = 10e-4, h = 4e-7, g_lk = 4.2e-3, --g_s = 1.0,
Nl = 140,
R_il = 50e3, -- internodal leakage, not yet based on
--geometry!!!
kparaw = 0.58, -- доля каналов в параноде.
naparaw = 0.06,
tau_passive_K = 2e3, -- passive K exchange char. time (ms)
tau_passive_Na = 5e3, -- passive Na exchange char. time (ms)
tau_sw = 1000, -- tau for sw changes
g_Kglia = 2, -- total V-independent K conductance in Glion
g_lk_glia = 0.01,
V_lk_glia = -85,
currents = {
iKs = {
ion = "K",
gp = {s_i = chlib.spc.s.my},
g = 0.23},
iKf = {
ion = "K",
gp = {n_i = chlib.fpc.n.hana},
g = 3}}},
},
state = {V_n = -80, V_int = -80, V_g = -90,
m_n = 0.2, h_n = 0.2, p_n = 0.2, -- nonsense values
s_n = 0.1, s_i = 0.2, n_i = 0.2,
Ko_n = 3.2, Ko_p = 3.2, Ko_i = 3.2, Nai_n = 9, Nai_p = 9,
Nai_i = 9,
sw = 1.0,
},
virtuals = {ipump_p = 0, iKfp = 0, iKfi = 0}
}
segments.SC_mine.pars.node.pump_a.jnamax = global_parameters.nak_pump_a.jnamax*1.0
segments.Hana = { -- Based on HAA-2005 paper
type = "SC_simple",
pars = {
stimulated = true,
C_n = 0.22e-6, -- uF
C_my = 0.17e-6,
C_i = 379e-6,
G_lk_i = 1.7e-6,
R_il = 41e3,
node_currents = {
iNat = {
ion = "Na",
gp = {m_n = chlib.fsc.m.hana, h_n = chlib.fsc.h.hana},
G = 276e-6},
iNap = {
ion = "Na",
gp = {p_n = chlib.psc.p.hana},
--G = 7.1e-6},
G = 2.5e-5},
iKs = {
ion = "K",
gp = {s_n = chlib.spc.s.hana},
G = 17.4e-6},
iKf = {
ion = "K",
gp = {n_n = chlib.fpc.n.hana},
G = 4.1e-6}
},
internode_currents = {
iKs = {
ion = "K",
gp = {s_i = chlib.spc.s.hana},
G = 87.1e-6}
},
},
state = {
V_n = -86, V_int = -86,
h_n = 0.2, m_n = 0.2, p_n = 0.2,s_n = 0.2,
n_n = 0.2, s_i = 0.2,
},
virtuals = {ipump=0},
}
segments.Hana2 = {
-- Based on HANA-2005 paper, other currents, closer
-- to my own model
-- As well as Hana1 is a strangely hyperpolarized
type = "SC_simple",
pars = {
stimulated = true,
C_n = 0.22e-6, -- uF
C_my = 0.17e-6,
C_i = 379e-6,
--
G_lk_i = 1.7e-6,
--
R_il = 41e3,
--R_il = 120e3,
--
node_currents = {
iNat = {
ion = "Na",
gp = {m_n = chlib.fsc.m.srb, h_n = chlib.fsc.h.srb},
G = 276e-6},
iNap = {
ion = "Na",
gp = {p_n = chlib.psc.p.my},
G = 7.1e-6},
iKs = {
ion = "K",
gp = {s_n = chlib.spc.s.my},
G = 17.4e-6},
iKf = {
ion = "K",
gp = {n_n = chlib.fpc.n.hana},
G = 0.1e-6}
},
internode_currents = {
iKs = {
ion = "K",
gp = {s_i = chlib.spc.s.hana},
G = 87.1e-6},
iKf = {
ion = "K",
gp = {n_i = chlib.fpc.n.hana},
G = 100e-6}}
},
state = {
V_n = -86, V_int = -86,
h_n = 0.2, m_n = 0.2, p_n = 0.2,s_n = 0.2,
n_n = 0.2, s_i = 0.2, n_i = 0.2,
},
virtuals = {ipump=0},
}
sc1 = {tag='sc1', description = "A space-clamped model",
rule = {'SC_mine'}}
hana1 = {tag='hana1', description = "A space-clamped model (Hana)",
rule = {'Hana'}}
hana2 = {tag='hana2', description = "A space-clamped model (Hana)",
rule = {'Hana2'}}
--for k, gp in pairs(segments.Node.pars.gating_particles) do
--io.stderr:write(string.format('k is %s\n', k))
-- if segments.Node.state[k] then
-- segments.Node.state[k] = gp.inf(global_variable_values.V_a)
-- end
--end
for _,segment in pairs(segments) do
for key,val in pairs(global_variable_values) do
if segment.state[key] then -- only for those with such a variable
segment.state[key] = val
end
end
end
for _,segment in pairs(segments) do
for key,val in pairs(global_parameters) do
if not segment.pars[key] then
segment.pars[key] = val
end
end
end
numerics = {
--stepper = 'rkc'
stepper = 'rkc_a'
}