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config.cym.tpl
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config.cym.tpl
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% 2023/04/25
[[X = range(0, 1000, 100) ]] [[ Y = 1000 - X ]] % [[Y]]
set simul system
{
time_step = 0.005
viscosity = 0.01
}
set space cell
{
shape = circle
}
new cell
{
radius = 30
}
set fiber microtubule
{
rigidity = 20
segmentation = 0.2
total_polymer = 5000
activity = classic
growing_speed = 0.080
shrinking_speed = -0.250
catastrophe_rate = 0.005
rescue_rate = 0.06
growing_force = 1.67
min_length = 0.1
% steric = 1, 0.05
}
set hand kinesin5
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 1
unbinding_force = 3
activity = move
unloaded_speed = 0.05
stall_force = 6
display = { size=8; color=0x00FF00FF; }
}
set hand kinesin14
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.1
unbinding_force = 1
activity = move
unloaded_speed = -0.040
stall_force = 6
display = { size = 16; color=0x00FF00FF; }
}
set hand kinesin14_eb
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.1
unbinding_force = 10
activity = move
unloaded_speed = -0.040
stall_force = 10
display = { size = 16; color=0x0088FFFF; }
}
set hand eb
{
activity = track
bind_end = plus_end
bind_end_range = 0.2
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.05
unbinding_force = 5
bind_only_growing_end = 1
track_end = 1
bind_also_end = 1
display = { size = 16; color=0x0088FFFF; }
}
set couple kinesin5_pair
{
hand1 = kinesin5
hand2 = kinesin5
diffusion = 0.20
stiffness = 200
}
set couple kinesin14_pair
{
hand1 = kinesin14
hand2 = kinesin14
diffusion = 0.20
stiffness = 200
length = 0.01
}
set couple eb_complex
{
hand1 = eb
hand2 = kinesin14_eb
diffusion = 0.20
stiffness = 200
length = 0.01
}
set solid core
{
confine = 1, 100
display = ( style = 2 )
}
set aster centrosome
{
stiffness = 2000, 1000
nucleate = 1, microtubule, ( length = 0.75; plus_end = 1; )
}
new centrosome
{
solid = core
radius = 0.5
position = 1 0 0
fibers = 100, microtubule, ( plus_end=grow; length=2; )
}
new centrosome
{
solid = core
radius = 0.5
position = -1 0 0
fibers = 100, microtubule, ( plus_end=grow; length=2; )
}
%new 1000 kinesin_pair
new [[X]] kinesin14_pair
new [[Y]] eb_complex
run system
{
nb_steps = 200000
nb_frames = 1000
}