Cytosim PI Cytoskeleton Simulator

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Config Files - Set 2

# glide_stripe.cym

% A gliding assay, with stripes of two motors of opposite directionality
% run in 2D
set simul glide_stripe
{
time_step = 0.005
viscosity = 0.5
display = { window_size=800,400 }
}
set space cell
{
geometry = ( periodic 10 5 )
}
new space cell
set fiber microtubule
{
%taxol-stabilized microtubule are more flexible
rigidity = 10
segmentation = 0.5
display = { line_width=6 }
}
set hand kinesin
{
binding_rate = 5
binding_range = 0.01
unbinding_rate = 0.3
unbinding_force = 3
activity = move
max_speed = 0.6
stall_force = 6
display = { color=0x0000FF99; size=8 }
}
set hand dynein
{
binding_rate = 5
binding_range = 0.01
unbinding_rate = 0.3
unbinding_force = 3
activity = move
max_speed = -0.6
stall_force = 6
display = { color=0xFF990099; size=8 }
}
set single gKinesin
{
hand = kinesin
stiffness = 100
activity = fixed
}
set single gDynein
{
hand = dynein
stiffness = 100
activity = fixed
}
new 2 fiber microtubule
{
length = 12
}
new 2500 single gKinesin ( stripe -5 5 )
new 1200 single gDynein ( stripe 5 10 )
new 1200 single gDynein ( stripe -10 -5 )
set simul:display gliding
{
label = (Motor stripes -)
delay = 10
tiled = 1, 1
style = 2
}
run simul *
{
nb_steps = 10000
nb_frames = 50
}

# solid.cym

% Francois Nedelec, August, 2010
set simul solid
{
time_step = 0.01
viscosity = 0.01
steric = 1, 500
}
set space cell
{
geometry = ( sphere 15 )
}
new space cell
set hand protein
{
binding = 10, 0.05
unbinding = 0, 3
display = { size=8; color=green; }
}
set single gprotein
{
hand = protein
stiffness = 100
}
set solid blob
{
confine = all_inside, 100
steric = 1
display = ( style=7; coloring=1; visible=transparent; )
}
new 10 solid blob
{
nb_points = 4
radius = 0.5
shape = surface
singles = 2 gprotein
}
new 5 solid blob
{
nb_points = 10
shape = inside
radius = 1.5
single = gprotein
}
new 10 solid blob
{
nb_points = 3
point0 = -1 0 0, 1
point1 = 0 0 0, 0.75, gprotein
point2 = 1 0 0, 1
}
new 10 solid blob
{
radius = 2
nb_points = 4
point0 = 0 0 0, 2
point1 = inside, 0.1, gprotein
point2 = inside, 0.1, gprotein
point3 = inside, 0.1
}
new 3 solid blob
{
nb_points = 3
point0 = 0 0 0, 1
point1 = 0.95 0.1 0, 0, 2 gprotein
point2 = 0.95 -0.1 0, 0, 2 gprotein
}
run simul *
{
nb_steps = 10000
nb_frames = 100
}

# bead.cym

set simul bead
{
steric = 1, 100
time_step = 0.001
viscosity = 0.1
precondition = 0
}
set space cell
{
geometry = ( sphere 3 )
}
new space cell
set hand kinesin
{
binding_rate = 10
binding_range = 0.02
unbinding_rate = 2
unbinding_force = 3
display = ( color=blue; size=10; )
}
set single grafted
{
hand = kinesin
stiffness = 100
}
set bead balls
{
confine = all_inside, 1000
steric = 1
display = ( coloring=1; style=5 )
}
new 320 bead balls
{
radius = 0.05
single = grafted
}
new 160 bead balls
{
radius = 0.1
single = grafted
}
new 40 bead balls
{
radius = 0.25
}
new 10 solid balls
{
nb_points = 10
shape = surface
radius = 0.5
}
run simul *
{
nb_steps = 5000
nb_frames = 10
}

# cut_fibers.cym

% A test for cuting fiber
% F. Nedelec, April 2011
set simul fiber
{
time_step = 0.01
viscosity = 0.02
}
set space cell
{
geometry = ( capsule 4 3 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 100
display = ( plus_tip=16,2; line_style=2; speckles=1, 0.25 )
}
new 1 fiber microtubule
{
length = 12
position = ( 0 0 0 )
}
set hand binder
{
binding_rate = 50
binding_range = 0.01
unbinding_rate = 0.2
unbinding_force = 3
display = ( width=3; size=10; color=green )
}
set single protein
{
hand = binder
diffusion = 0.1
stiffness = 100
}
new 100 single protein
run simul *
{
nb_steps = 100
nb_frames = 5
}
cut fiber *
{
plane = 1 0 0, 0
}
cut fiber *
{
plane = 1 0 0, 3
}
cut fiber *
{
plane = 1 0 0, -3
}
run simul *
{
nb_steps = 1000
nb_frames = 1
}