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Add copy of templates and configs from subcell pipeline
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‎configs/free_barbed_end_final.cym‎

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% Fiber under compression to measure buckling force
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% how fast the end gets compressed (µm/s) 150 nm / 10 µs
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% fast: 1.5e2, 1.5e3, 1.5e4
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% slow: 0.0015, 0.015, 0.15, 1.5, 15
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% the time step (s)
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% how frequently the compression is applied (time steps)
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% frequency you save frames (s)
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% total fiber length
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% ratio of total length that gets compressed
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% total compression amount
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% total simulation time (s)
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% compression_velocity: 150
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% compression_distance: 0.15
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% total_time: 0.001
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% 200 repeats
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% 1 frames saved per repeat
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% translation = 0.00075
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set simul system
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{
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time_step = 5e-07
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viscosity = 0.01
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}
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set space cell
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{
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shape = sphere
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}
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new cell
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{
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radius = 2
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}
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set fiber filament
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{
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rigidity = 0.041
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segmentation = 0.001
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display = ( point=6,1; line=10,2; )
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}
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set hand binder
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{
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% 10 events per second, 0.05 um binding radius
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binding = 10, 0.005
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% 0 events per second, infinite unbinding force
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unbinding = 0, inf
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bind_also_end = 1
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display = ( width=3; size=12; color=green )
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}
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set single linker
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{
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hand = binder
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activity = fixed
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stiffness = 10000000
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}
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new filament
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{
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length = 0.5
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position = 0 0 0
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orientation = 1 0 0
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% attach1 = linker, 0, minus_end
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% attach2 = linker, 0, plus_end
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}
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new linker
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{
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position = -0.25 0 0
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attach = filament, 0, minus_end
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mark = 1
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}
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% make a second linker 5 nm from the first, to keep minus end rotationally fixed
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new linker
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{
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position = -0.24 0 0
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attach = filament, 0.01, minus_end
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mark = 2
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}
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% make a second linker 5 nm from the first, to keep minus end rotationally fixed
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% number of intervals for compression
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repeat 200
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{
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% this means you run one step and let it relax 9 time steps
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% and show it for 2 frames
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run 10 system { nb_frames = 1 }
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report fiber:points fiber_points.txt
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report single:position singles.txt
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}

‎configs/linkers_no_compression.cym‎

Lines changed: 148 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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1+
% Fiber under compression to measure buckling force
2+
3+
4+
% how fast the end gets compressed (µm/s) 150 nm / 10 µs
5+
6+
% fast: 1.5e2, 1.5e3, 1.5e4
7+
% slow: 0.0015, 0.015, 0.15, 1.5, 15
8+
9+
% the time step (s)
10+
11+
12+
% how frequently the compression is applied (time steps)
13+
14+
15+
% frequency you save frames (s)
16+
17+
18+
% total fiber length
19+
20+
21+
% ratio of total length that gets compressed
22+
23+
24+
25+
% total compression amount
26+
27+
28+
% total simulation time (s)
29+
30+
31+
% compression_velocity: 150
32+
% compression_distance: 0.15
33+
% total_time: 0.001
34+
% 200 repeats
35+
% 1 frames saved per repeat
36+
% translation = 0.00075
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set simul system
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{
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time_step = 5e-07
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viscosity = 0.01
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}
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set space cell
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{
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shape = sphere
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}
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new cell
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{
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radius = 2
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}
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set fiber filament
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{
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rigidity = 0.041
57+
segmentation = 0.001
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display = ( point=6,1; line=10,2; )
59+
}
60+
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set hand binder
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{
63+
% 10 events per second, 0.05 um binding radius
64+
65+
binding = 10, 0.005
66+
67+
% 0 events per second, infinite unbinding force
68+
69+
unbinding = 0, inf
70+
bind_also_end = 1
71+
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display = ( width=3; size=12; color=green )
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}
74+
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set single linker
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{
77+
hand = binder
78+
activity = fixed
79+
stiffness = 10000000
80+
}
81+
82+
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new filament
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{
85+
length = 0.5
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position = 0 0 0
87+
orientation = 1 0 0
88+
% attach1 = linker, 0, minus_end
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% attach2 = linker, 0, plus_end
90+
91+
}
92+
93+
new linker
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{
95+
position = -0.25 0 0
96+
attach = filament, 0, minus_end
97+
mark = 1
98+
}
99+
100+
% make a second linker 5 nm from the first, to keep minus end rotationally fixed
101+
102+
new linker
103+
{
104+
position = -0.24 0 0
105+
attach = filament, 0.01, minus_end
106+
mark = 2
107+
}
108+
109+
110+
new linker
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{
112+
position = 0.25 0 0
113+
attach = filament, 0, plus_end
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mark = 3
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}
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117+
% make a second linker 5 nm from the first, to keep minus end rotationally fixed
118+
119+
new linker
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{
121+
position = 0.24 0 0
122+
attach = filament, 0.01, plus_end
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mark = 4
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}
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% number of intervals for compression
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repeat 200
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{
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% this means you run one step and let it relax 9 time steps
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% and show it for 2 frames
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run 10 system { nb_frames = 1 }
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report fiber:points fiber_points.txt
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report single:position singles.txt
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move linker
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{
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translation = 0.00075 0 0
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mark = 1
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}
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move linker
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{
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translation = 0.00075 0 0
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mark = 2
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}
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}

‎configs/no_linkers_no_compression.cym‎

Lines changed: 104 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,104 @@
1+
% Fiber under compression to measure buckling force
2+
3+
4+
% how fast the end gets compressed (µm/s) 150 nm / 10 µs
5+
6+
% fast: 1.5e2, 1.5e3, 1.5e4
7+
% slow: 0.0015, 0.015, 0.15, 1.5, 15
8+
9+
% the time step (s)
10+
11+
12+
% how frequently the compression is applied (time steps)
13+
14+
15+
% frequency you save frames (s)
16+
17+
18+
% total fiber length
19+
20+
21+
% ratio of total length that gets compressed
22+
23+
24+
25+
% total compression amount
26+
27+
28+
% total simulation time (s)
29+
30+
31+
% compression_velocity: 150
32+
% compression_distance: 0.15
33+
% total_time: 0.001
34+
% 200 repeats
35+
% 1 frames saved per repeat
36+
% translation = 0.00075
37+
38+
set simul system
39+
{
40+
time_step = 5e-07
41+
viscosity = 0.01
42+
}
43+
44+
set space cell
45+
{
46+
shape = sphere
47+
}
48+
49+
new cell
50+
{
51+
radius = 2
52+
}
53+
54+
set fiber filament
55+
{
56+
rigidity = 0.041
57+
segmentation = 0.001
58+
display = ( point=6,1; line=10,2; )
59+
}
60+
61+
set hand binder
62+
{
63+
% 10 events per second, 0.05 um binding radius
64+
65+
binding = 10, 0.005
66+
67+
% 0 events per second, infinite unbinding force
68+
69+
unbinding = 0, inf
70+
bind_also_end = 1
71+
72+
display = ( width=3; size=12; color=green )
73+
}
74+
75+
set single linker
76+
{
77+
hand = binder
78+
activity = fixed
79+
stiffness = 10000000
80+
}
81+
82+
83+
new filament
84+
{
85+
length = 0.5
86+
position = 0 0 0
87+
orientation = 1 0 0
88+
% attach1 = linker, 0, minus_end
89+
% attach2 = linker, 0, plus_end
90+
91+
}
92+
93+
% number of intervals for compression
94+
repeat 200
95+
{
96+
97+
% this means you run one step and let it relax 9 time steps
98+
% and show it for 2 frames
99+
run 10 system { nb_frames = 1 }
100+
101+
report fiber:points fiber_points.txt
102+
report single:position singles.txt
103+
104+
}

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