Cytosim PI Cytoskeleton Simulator

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Config Files - Set 4

# overlap_walk.cym

# aster_texas.cym

% A confined aster with cortical pulling motors
% F. Nedelec, April 2010
set simul aster_texas
{
time_step = 0.005
viscosity = 0.1
}
set space texas
{
geometry = ( polygon texas.txt 2 )
}
new space texas
set fiber microtubule
{
rigidity = 30
segmentation = 0.5
confine = inside, 100
activity = classic
growing_speed = 0.2
shrinking_speed = -0.5
catastrophe_rate = 0.05
rescue_rate = 0
growing_force = 1.67
fate = rescue
min_length = 0.25
}
set solid core
{
display = ( style=3 )
}
set aster centrosome
{
solid = core
fibers = microtubule
stiffness = 1000, 500
}
new 1 aster centrosome
{
radius = 1
nb_fibers = 32
length = 2
}
run simul *
{
nb_steps = 20000
nb_frames = 10
}

# fiber_glue.cym

/**
@example fiber_glue.cym
Parameter fiber:glue is set link fiber with the boundaries:
- it creates a Single, everytime a fiber contacts the surface.
- the Single is deleted if the associated Hand detaches.
.
F. Nedelec, February 2011
*/
set simul fiber_glue
{
time_step = 0.01
viscosity = 0.1
display = { delay=4; }
}
set space cell
{
geometry = ( sphere 5 )
}
new space cell
set hand strong_hand
{
unbinding_rate = 0
unbinding_force = 1e6
hold_growing_end = 1
hold_shrinking_end = 1
display = { size=8 }
}
set single cortical_glue
{
hand = strong_hand
stiffness = 10
activity = fixed
}
set fiber microtubule
{
rigidity = 30
segmentation = 0.5
confine = inside, 100
glue = 3, cortical_glue
activity = tubule
dynamic_model = 3
dynamic_speed1 = 0.51, -0.84
dynamic_trans1 = 0.01
dynamic_trans2 = 5
fate = rescue
growing_force = 1.7
min_length = 0.5
display = { line=8, 2; point=1; speckles=2, 0.25; rainbow=-0.1 }
}
set solid core
{
display = ( style=3 )
}
set aster centrosome
{
solid = core
fibers = microtubule
stiffness = 1000, 500
}
new 1 aster centrosome
{
radius = 0.5
nb_fibers = 20
fiber_length = 2
position = 0 0 0
}
run simul *
{
nb_steps = 10000
nb_frames = 50
}

# motif.cym

% Francois Nedelec, July 24, 2009
set simul motif
{
time_step = 0.01
}
set space cell
{
geometry = ( sphere 8 )
}
new space cell
set fiber tube
{
segmentation = 0.5
rigidity = 20
confine = inside, 100
}
new 10 fiber tube
{
length = 10
}
set hand kinesin
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.5
unbinding_force = 2
activity = move
max_speed = 0.8
stall_force = 6
display = { color=0x0000FFFF }
}
set single gKinesin
{
hand = kinesin
stiffness = 100
activity = fixed
}
set hand dynein
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.5
unbinding_force = 2
activity = move
max_speed = -0.8
stall_force = 6
display = { color=0xFFFFFFFF }
}
set single gDynein
{
hand = dynein
stiffness = 100
activity = fixed
}
% female motif
new 3000 single gKinesin ( circle 3 0.2 at -3 2 )
new 500 single gKinesin ( rectangle 0.1 2 0.1 at -3 -3.0 )
new 500 single gKinesin ( rectangle 2 0.1 0.1 at -3 -2.9 )
% male motif
new 3000 single gDynein ( circle 3 0.2 at +3 -2 )
new 500 single gDynein ( rectangle 1.5 0.1 at 4.5 0 turn 1 1.5 at 3 -2 )
new 500 single gDynein ( rectangle 1.0 0.1 at -1.0 0 turn 1 +1 at 6 0 turn 1 1.5 at 3 -2 )
new 500 single gDynein ( rectangle 1.0 0.1 at -1.0 0 turn 1 -1 at 6 0 turn 1 1.5 at 3 -2 )
% cortical pool
new 500 single gKinesin ( edge 0.1 )
new 500 single gDynein ( surface 0.1 )
run simul *
{
nb_steps = 5000
nb_frames = 50
}

# wash.cym

% A confined fiber
% F. Nedelec, April 2010
set simul anchor
{
time_step = 0.01
viscosity = 0.02
steric = 1, 100
}
set space cell
{
geometry = ( sphere 10 )
}
new space cell
set hand strong_hand
{
unbinding = 0, 1e6
}
set single pivot
{
hand = strong_hand
stiffness = 1000
activity = fixed
}
set fiber tube
{
rigidity = 20
segmentation = 1
confine = inside, 100
}
new 20 fiber tube
{
orientation = 0.8 0.5 0
position = ( -5 0 0 )
length = 9
single = pivot, minus_dir, 0.5
post_rotation = ( 0.8 0.25 )
}
set hand kinesin
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.2
unbinding_force = 3
activity = move
max_speed = 1
stall_force = 6
display = ( size=8; color=0x00FF00FF; )
}
set single grafted
{
hand = kinesin
stiffness = 100
}
set solid dirty
{
confine = all_inside, 100
steric = 1
display = ( coloring=1; )
}
new 301 bead dirty
{
single = grafted
radius = 0.4
}
run simul *
{
nb_steps = 5000
nb_frames = 100
}