-
Notifications
You must be signed in to change notification settings - Fork 1
/
calyx.mdl
123 lines (98 loc) · 4.42 KB
/
calyx.mdl
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
/******************************************************/
/* A simple model of a single AZ at the calyx of Held */
/* */
/* Main simulation script */
/* */
/* Matthias Hennig */
/* mhennig@inf.ed.ac.uk */
/******************************************************/
/* source: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=85981 */
/* Used by D.Kufel */
/* time step */
dt = 1.0e-6
/* number of iterations */
it = 3000
TIME_STEP = dt
ITERATIONS = it
EFFECTOR_GRID_DENSITY = 10000
RADIAL_SUBDIVISIONS = 2^10
RADIAL_DIRECTIONS = 2^14 /* FULLY_RANDOM would be 2^15 */
/* this file contains the relative diameter of the fusion pore */
/* it is constantly updated during the run time of the simulation */
INCLUDE_FILE = "pore_scale"
pore_scale = 1-EXP(-(abs_time/10)*0.1)
CHECKPOINT_INFILE = "chkpt_pos"
CHECKPOINT_OUTFILE = "chkpt_pos"
CHECKPOINT_ITERATIONS = check_time
/* load simulation parameters */
INCLUDE_FILE = "parameters.mdl"
/* SIMULATION *********************/
INCLUDE_FILE = "effectors.mdl"
INCLUDE_FILE = "geometry.mdl"
/**********************************/
/* the synapse, here one PSD */
INSTANTIATE coh OBJECT {
/* relase site/point source of glutamate in the centre of the vesicle */
transmitter_release_site SPHERICAL_RELEASE_SITE {
LOCATION = [-Rex*vesicle_pos,0,cleft/2+fpL+vDiam/2]
LIGAND = Glu
NUMBER_TO_RELEASE = n
SITE_DIAMETER = 0.0
}
/* insert objects that constitute the synaptic cleft */
cleft1 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,Rex/2,0 ] }
cleft2 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,-3*Rex/2,0 ] }
cleft3 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,-Rex/2,0 ] }
cleft4 OBJECT synaptic_cleft_element { TRANSLATE=[-Rex/2,-3*Rex/2,0 ] }
cleft5 OBJECT synaptic_cleft_element { TRANSLATE=[-Rex/2,Rex/2,0 ] }
cleft6 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,-3*Rex/2,0,0 ] }
cleft7 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,Rex/2,0,0 ] }
cleft8 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,-Rex/2,0,0 ] }
cleft9 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,Rex/2,0 ] }
cleft10 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,-3*Rex/2,0 ] }
cleft11 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,-3*Rex/2,0,0 ] }
cleft12 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,Rex/2,0,0 ] }
cleft13 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,3*Rex/2,0 ] }
cleft14 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,-5*Rex/2,0 ] }
cleft15 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,3*Rex/2,0 ] }
cleft16 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,-5*Rex/2,0 ] }
cleft17 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,3*Rex/2,0 ] }
cleft18 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,-5*Rex/2,0 ] }
cleft19 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,3*Rex/2,0 ] }
cleft20 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,-5*Rex/2,0 ] }
cleft25 OBJECT synaptic_cleft_element {
SCALE=[2,9,1]
TRANSLATE=[-9*Rex/2,-9*Rex/2,0 ]
}
cleft26 OBJECT synaptic_cleft_element {
SCALE=[2,9,1]
TRANSLATE=[5*Rex/2,-9*Rex/2,0 ]
}
cleft27 OBJECT synaptic_cleft_element {
SCALE=[5,2,1]
TRANSLATE=[-5*Rex/2,-9*Rex/2,0 ]
}
cleft28 OBJECT synaptic_cleft_element {
SCALE=[5,2,1]
TRANSLATE=[-5*Rex/2,5*Rex/2,0 ]
}
/* the postsynaptic densities */
psd OBJECT psd {}
/* if these are removed, only the central PSD is active */
psd2 OBJECT psd {TRANSLATE=[-2*Rex, 0 ,0 ] }
psd3 OBJECT psd {TRANSLATE=[2*Rex, 0 ,0 ] }
psd4 OBJECT psd {TRANSLATE=[0, -2*Rex ,0 ] }
psd5 OBJECT psd {TRANSLATE=[0, 2*Rex ,0 ] }
/* These replace the four PSDs psd2-psd5 if only one PSD is to be simulated:
cleftp1 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,Rex/2,0 ] }
cleftp2 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,Rex/2,0 ] }
cleftp3 OBJECT synaptic_cleft_element { TRANSLATE=[-1*Rex/2,-4*Rex/2,0 ] }
cleftp4 OBJECT synaptic_cleft_element { TRANSLATE=[-1*Rex/2,5*Rex/2,0 ] }
*/
vesicle OBJECT vesicle {TRANSLATE=[-Rex*vesicle_pos, 0 ,0 ] }
pore OBJECT pore {TRANSLATE=[-Rex*vesicle_pos, 0 ,0 ] }
}
/* write simulation results to a file */
INCLUDE_FILE = "output.mdl"
/* uncomment to create a movie of the simulation */
/* INCLUDE_FILE = "3dout.mdl" */