267103/NTDiffusion.mod at master · ModelDBRepository/267103 · GitHub

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
COMMENT
ALE - 08.06.2011
NTDiffusion model using analytic solution [A1.2] of savtchenko - The optimal height of the synaptic cleft - 2007
ENDCOMMENT

DEFINE NDates 10
:DEFINE NDates 20

NEURON {
	POINT_PROCESS NTDiffusion
	RANGE Radius, CleftWidth, Diffusivity, BasalNTConcentration, NTi, k, Nused
	RANGE NTConcentration
	RANGE comp
	RANGE NTRatio
	RANGE tDiff
}

UNITS {
	(molar) = (1/liter)			: moles do not appear in units
	(mM)	= (millimolar)
	(um)	= (micron)
	(mA)	= (milliamp)
	(msM)	= (ms mM)
}

CONSTANT{
	PI = 3.1415926535897932384626433832795028841971693993751058209749445923078164062862089986280348253421170679
	Nav = 6.02214179e23
}

PARAMETER {
	Radius	= 1	(um)			: Radius, position of the receptor (DEFAULT 1) (50 nanometers is nominal)
	CleftWidth	= 0.02	(um)		: CleftWidth
	Diffusivity	= 0.33 (um.um/ms)	: Diffusivity coefficient of the NT in the cleft (DEFAULT 0.4)
	BasalNTConcentration = 0.0 (mM)	: resting NT concentration
	k = 1.0 					: variable d'ajustement
	comp = 0
	tRound = 0
	tDiff = 0
	NTRatio = 0
}

ASSIGNED {
	NTConcentration
	NTi
	tr[NDates]
	Nused
}

STATE {
	NT1
	NT2
	NT3
	NT4
	NT5
	NT6
	NT7
	NT8
	NT9
}

INITIAL {
	NTConcentration = BasalNTConcentration
	NTi = 0
	FROM i = 0 TO NDates-1{
		tr[i] = -1e12
	}
	Nused = 0

}

: LOCAL comp

BREAKPOINT {
	SOLVE state METHOD cnexp
	NTConcentration = BasalNTConcentration

	FROM i = 0 TO Nused-1{
		if(i == 0) {
			NTRatio = NT1
			tDiff = t-tr[i]
		} else if(i == 1) {
			NTRatio = NT2
		} else if(i == 2) {
			NTRatio = NT3
		} else if(i == 3) {
			NTRatio = NT4
		} else if(i == 4) {
			NTRatio = NT5
		} else if(i == 5) {
			NTRatio = NT6
		} else if(i == 6) {
			NTRatio = NT7
		} else if(i == 7) {
			NTRatio = NT8
		} else if(i == 8) {
			NTRatio = NT9
		} else {
			:printf("Warning: More NT events than expected")
			NTRatio = 0
		}

		if(Radius == 0){
		comp = NTRatio * 1e18 * NTi / (4 * PI * CleftWidth * Diffusivity) : en mM
		} else {
		comp = NTRatio * 1e18 * NTi / (4 * PI * CleftWidth * Diffusivity) * exp(- NTRatio * (Radius*Radius)/(4*Diffusivity)) : en mM
		}
		:printf("comp : %4.5f\n", comp)
		:printf("t = %f :\t %1.0f / %1.0f\t : comp = %f \n", t, i+1, Nused, comp)
		if(comp >= 0.001*NTConcentration){
			NTConcentration = NTConcentration + comp
		} else if(t==tr[i]){
			NTConcentration = BasalNTConcentration
		} else {
			Nused = i
			:printf("component used until %1.0f, %f / %f \n", Nused, comp, NTConcentration)
		}
	}

	: NTConcentration = NTConcentration/.06 : testing modifying the amplitude of glutamate

}

DERIVATIVE state {

	NT1' = - (NT1 * NT1)
	NT2' = - (NT2 * NT2)
	NT3' = - (NT3 * NT3)
	NT4' = - (NT4 * NT4)
	NT5' = - (NT5 * NT5)
	NT6' = - (NT6 * NT6)
	NT7' = - (NT7 * NT7)
	NT8' = - (NT8 * NT8)
	NT9' = - (NT9 * NT9)

}

NET_RECEIVE(w){

	if(flag == 0){ : external event coming from netcon object
		if(Nused < NDates){
			Nused = Nused +1
		} else {
			printf("Size of the NTDiffusion Glu array might be too small")
		}

		NTi = k*3000/Nav : en moles :  (Nav*PI*1e-9*ri*ri*CleftWidth)
		FROM i = 1 TO Nused{
			tr[Nused+1-i] = tr[Nused-i]

		}

		tr[0] = t
		NT9 = NT8
		NT8 = NT7
		NT7 = NT6
		NT6 = NT5
		NT5 = NT4
		NT4 = NT3
		NT3 = NT2
		NT2 = NT1
		NT1 = 1
		:printf("NTi : %4.5f\n", NTi)
	}
}