-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathSmoldyn_1.txt
264 lines (222 loc) · 5.13 KB
/
Smoldyn_1.txt
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
# Heterocyst model 1
graphics opengl_good
dim 3
species C N O2
time_start 0
time_stop 100000
time_step 0.1
color N red
color C green
color O2 blue
display_size * 2
boundaries x -640 635 r
boundaries y -70 70 r
boundaries z -70 70 r
start_surface cellmembrane_1
action all both reflect
color both purple 1
polygon both edge
panel sph -580 0 0 50 20 20
end_surface
start_surface cellmembrane_2
action all both reflect
color both purple 1
polygon both edge
panel sph -475 0 0 50 20 20
panel cyl -524 0 0 -531 0 0 2 10 3
end_surface
start_surface jumpsurface_123
action both all jump
color both blue
polygon both edge
panel disk -529 0 0 6 1 0 0 10 c1b
panel disk -524 0 0 6 1 0 0 10 c2a
panel disk -426 0 0 6 1 0 0 10 c2b
panel disk -419 0 0 6 1 0 0 10 c3a
jump c1b back <-> c2a front
jump c2b back <-> c3a front
end_surface
start_surface cellmembrane_3
action all both reflect
color both purple 1
polygon both edge
panel sph -370 0 0 50 20 20
panel cyl -419 0 0 -426 0 0 2 10 3
end_surface
start_surface cellmembrane_4
action all both reflect
color both purple 1
polygon both edge
panel sph -265 0 0 50 20 20
panel cyl -314 0 0 -321 0 0 2 10 3
end_surface
start_surface jumpsurface_345
action both all jump
color both blue
polygon both edge
panel disk -321 0 0 6 1 0 0 10 c3b
panel disk -314 0 0 6 1 0 0 10 c4a
panel disk -216 0 0 6 1 0 0 10 c4b
panel disk -209 0 0 6 1 0 0 10 c5a
jump c3b back <-> c4a front
jump c4b back <-> c5a front
end_surface
start_surface cellmembrane_5
action all both reflect
color both purple 1
polygon both edge
panel sph -160 0 0 50 20 20
panel cyl -209 0 0 -216 0 0 2 10 3
end_surface
start_surface cellmembrane_6
action all both reflect
colour both purple 1
polygon both edge
panel sph -55 0 0 50 20 20
panel cyl -104 0 0 -111 0 0 2 10 3
end_surface
start_surface jumpsurface_567
action both all jump
color both blue
polygon both edge
panel disk -111 0 0 6 1 0 0 10 c5b
panel disk -104 0 0 6 1 0 0 10 c6a
panel disk -6 0 0 6 1 0 0 10 c6b
panel disk +1 0 0 6 1 0 0 10 c7a
jump c5b back <-> c6a front
jump c6b back <-> c7a front
end_surface
start_surface cellmembrane_7
action all both reflect
color both purple 1
polygon both edge
panel sph 50 0 0 50 20 20
panel cyl 1 0 0 -6 0 0 2 10 3
panel cyl 99 0 0 106 0 0 2 10 3
end_surface
start_surface cellmembrane_8
action all both reflect
color both purple 1
polygon both edge
panel sph 155 0 0 50 20 20
panel cyl 204 0 0 211 0 0 2 10 3
end_surface
start_surface jumpsurface_789
action both all jump
color both blue
polygon both edge
panel disk +99 0 0 6 1 0 0 10 c7b
panel disk +116 0 0 6 1 0 0 10 c8a
panel disk +204 0 0 6 1 0 0 10 c8b
panel disk +211 0 0 6 1 0 0 10 c9a
jump c7b back <-> c8a front
jump c8b back <-> c9a front
end_surface
start_surface cellmembrane_9
action all both reflect
color both purple 1
polygon both edge
panel sph 260 0 0 50 20 20
panel cyl 309 0 0 316 0 0 2 10 3
end_surface
start_surface cellmembrane_10
action all both reflect
color both purple 1
polygon both edge
panel sph 365 0 0 50 20 20
panel cyl 414 0 0 421 0 0 2 10 3
end_surface
start_surface jumpsurface_91011
action both all jump
color both blue
polygon both edge
panel disk +309 0 0 6 1 0 0 10 c9b
panel disk +316 0 0 6 1 0 0 10 c10a
panel disk +414 0 0 6 1 0 0 10 c10b
panel disk +421 0 0 6 1 0 0 10 c11a
jump c9b back <-> c10a front
jump c10b back <-> c11a front
end_surface
start_surface cellmembrane_11
action all both reflect
color both purple 1
polygon both edge
panel sph 470 0 0 50 20 20
panel cyl 519 0 0 526 0 0 2 10 3
end_surface
start_surface cellmembrane_12
action all both reflect
color both purple 1
polygon both edge
panel sph 575 0 0 50 20 20
panel cyl 624 0 0 631 0 0 2 10 3
end_surface
start_surface jumpsurface_1112
action both all jump
color both blue
polygon both edge
panel disk +519 0 0 6 1 0 0 10 c11b
panel disk +526 0 0 6 1 0 0 10 c12a
jump c11b back <-> c12a front
end_surface
start_compartment cytoplasm_1
surface cellmembrane_1
point -575 0 0
end_compartment
start_compartment cytoplasm_2
surface cellmembrane_2
point -470 0 0
end_compartment
start_compartment cytoplasm_3
surface cellmembrane_3
point -365 0 0
end_compartment
start_compartment cytoplasm_4
surface cellmembrane_4
point -260 0 0
end_compartment
start_compartment cytoplasm_5
surface cellmembrane_5
point -155 0 0
end_compartment
start_compartment cytoplasm_6
surface cellmembrane_6
point -50 0 0
end_compartment
start_compartment cytoplasm_7
surface cellmembrane_7
point 50 0 0
end_compartment
start_compartment cytoplasm_8
surface cellmembrane_8
point 155 0 0
end_compartment
start_compartment cytoplasm_9
surface cellmembrane_9
point 260 0 0
end_compartment
start_compartment cytoplasm_10
surface cellmembrane_10
point 365 0 0
end_compartment
start_compartment cytoplasm_11
surface cellmembrane_11
point 470 0 0
end_compartment
start_compartment cytoplasm_12
surface cellmembrane_12
point 575 0 0
end_compartment
compartment_mol 100 N cytoplasm_6
compartment_mol 100 C cytoplasm_6
compartment_mol 100 O2 cytoplasm_7
difc N 5
difc C 5
difc O2 1
/*
reaction photosynthesis 0 -> C + O2 4e-4 # 2 s^-1
reaction respiration O2 + C -> 0 2e-4
reaction Nfixation 0 -> N 2e-4
reaction protein_turnover N -> 0 1e-4
*/
end_file