Cytosim PI Cytoskeleton Simulator

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Config Files - Set 5

# beat.cym

# motile_bead.cym

% F. Nedelec, April 2010
set simul motile_bead
{
time_step = 0.02
viscosity = 0.2
kT = 0.0042
steric = 1, 100
}
set space cell
{
geometry = ( square 10 10 10 )
}
new space cell
set fiber actin
{
rigidity = 5
segmentation = 0.5
steric = 1, 0.02
activity = treadmill
growing_speed = 0.1, 0
shrinking_speed = -0.05, -0.01
growing_force = 2, 2
display = { color=white; point_size=5; speckles=1; line_style=1; line_width=1 }
}
set hand formin
{
binding = 0, 0.02
unbinding = 0, 3
activity = nucleate
nucleate = 1, actin
hold_growing_end = 1
hold_shrinking_end = 0
track_end = plus_end
nucleation_spec = ( length=0.01; end_state=1, 4 )
}
set single grafted
{
hand = formin
stiffness = 100
}
set sphere bead
{
point_mobility = 1
steric = 1
display = { color=0xFFFF0055; style=8; size=8 }
}
new sphere bead
{
radius = 1
nb_points = 10
singles = 100 grafted
position = ( 0 0 0 )
}
set simul:display * { track_fibers=1 }
run simul *
{
nb_steps = 2500
nb_frames = 50
}

# pombe.cym

% Microtubules in interphase S.pombe
% Francois Nedelec, Aug. 4, 2009
% NOTE: parameters use units of picoNewton, micrometer, second
set simul pombe
{
time_step = 0.01
kT = 0.0042
viscosity = 0.9
precondition = 0
display = ( window_size=800,400 )
}
set space pombe
{
geometry = ( capsule 3.5 1.6 )
display = ( color=0xFFFFFF55; )
}
new space pombe
set fiber microtubule
{
rigidity = 30
segmentation = 0.5
confine = inside, 200
activity = dynamic
unit_length = 0.008
growing_speed = 0.06
shrinking_speed = -0.15
hydrolysis_rate = 0.058
growing_force = 1.7
fate = rescue
min_length = 0.5
display = ( line_width=5; plus_end=15; minus_end=15; )
}
set sphere envelope
{
point_mobility = 0.05
confine = all_inside, 200
piston_effect = 1
display = ( color=0xFFFFFF55; size=12; style=12 )
}
set bundle microtubule_bundle
{
fibers = microtubule
nb_fibers = 4
overlap = 0.5
stiffness = 1000
}
set nucleus nucleus
{
sphere = envelope
nb_bundles = 4
bundles = microtubule_bundle
stiffness = 200
}
new nucleus nucleus
{
radius = 1.3
position = ( 3.5 0 0 )
fiber_length = 0.5
}
run simul *
{
nb_steps = 50000
nb_frames = 100
}

# contract.cym

% A contractile actin gel
% F. Nedelec Dec. 2010
set simul contract
{
time_step = 0.001
viscosity = 0.05
}
set space cell
{
geometry = ( circle 8 )
}
new space cell
set fiber actin
{
rigidity = 0.1
segmentation = 0.25
confine = inside, 100
display = ( line=2,2; )
}
set hand myosin
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.01
unbinding_force = 3
activity = move
max_speed = 1
stall_force = 5
display = ( size = 4; color=green )
}
set hand binder
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.01
unbinding_force = 3
display = ( size = 2; color=blue )
}
set couple motor
{
hand1 = myosin
hand2 = myosin
stiffness = 250
diffusion = 10
fast_diffusion = 1
}
set couple crosslinker
{
hand1 = binder
hand2 = binder
stiffness = 250
diffusion = 10
fast_diffusion = 1
}
new 150 fiber actin
{
length = 5
}
new 5000 couple motor
new 5000 couple crosslinker
run simul *
{
nb_frames = 100
nb_steps = 10000
}