Cytosim PI Cytoskeleton Simulator

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Config Files - Set 1

# aster.cym

% A confined aster
% F. Nedelec, April 2010
set simul aster
{
time_step = 0.001
viscosity = 0.01
}
set space cell
{
geometry = ( sphere 10 )
}
new space cell
set fiber microtubule
{
rigidity = 30
segmentation = 1
confine = inside, 100
display = { line_width=3; }
}
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 = 32
length = 12
}
run simul *
{
nb_steps = 20000
nb_frames = 100
}

# pombe_classic.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
display = { window_size=800,400 }
}
set space pombe
{
geometry = ( capsule 3.5 1.6 )
}
new space pombe
set fiber microtubule
{
rigidity = 30
segmentation = 0.5
confine = inside, 200
activity = classic
growing_speed = 0.06
shrinking_speed = -0.15
catastrophe_rate = 0.004, 0.04
rescue_rate = 0
growing_force = 1.67
fate = rescue
min_length = 0.5
display = {show_average=2}
}
set sphere envelope
{
point_mobility = 0.05
confine = all_inside, 200
piston_effect = 1
display = { color=0x0000FF55 }
}
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 )
length = 0.5
}
run simul *
{
nb_steps = 50000
nb_frames = 100
}

# self.cym

% One of the oldest simulation
% F. Nedelec
set simul self
{
time_step = 0.01
viscosity = 0.05
}
set space cell
{
geometry = ( circle 16 )
}
new space cell
set fiber microtubule
{
rigidity = 30
segmentation = 1.5
confine = inside, 100
display = { line_width=1; }
}
set hand kinesin
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.1
unbinding_force = 3
activity = move
max_speed = 0.8
stall_force = 5
hold_growing_end = 1
display = { size=8 }
}
set couple complex
{
hand1 = kinesin
hand2 = kinesin
stiffness = 100
diffusion = 10
}
new 80 fiber microtubule
{
length = 14
}
new 2000 couple complex
set simul:display *
{
label = (Nedelec et al. 1998 -)
}
run simul *
{
nb_frames = 100
nb_steps = 4000
}

# glide.cym

% Gliding assay with realistic Kinesin and Microtubule parameters,
% cf. Bourdieu et al. PRL Vol 75/N 1/Page 176-179
% the parameters for motor density are also taken from there
set simul glide
{
time_step = 0.005
viscosity = 0.1
precondition = 0
display = ( style=2 )
}
set space cell
{
geometry = ( periodic 2 2 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.25
display = {
line_width = 2
line_style = 1
point_size = 8
point_style = 2
}
}
set hand kinesin
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.3
unbinding_force = 2.5
activity = move
max_speed = 0.4
stall_force = 6
}
set single grafted
{
hand = kinesin
stiffness = 200
activity = fixed
}
new fiber microtubule
{
length = 5
orientation = horizontal
}
new 16000 single grafted
set simul:display gliding
{
label = (Gliding assay -)
delay = 10
%tiled = 1
point_size = 6
style = 2
}
run simul *
{
nb_steps = 5000
nb_frames = 50
}

# overlap.cym

% An antiparallel bundle extending under the action of crosslinking motors
% Francois Nedelec, July 24, 2009
set simul overlap
{
time_step = 0.01
viscosity = 0.1
display = (
window_size = 768, 256;
zoom=1.4;
style = 2
point_size = 5
line_width = 2
label = (Sliding bundle -)
)
}
set space cell
{
geometry = ( rectangle 6 1.5 1.5 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
display = ( line=3,2; speckles=1; point_size=8; end_section=0,1; end_size=5,5 )
}
set hand kinesin
{
binding_rate = 10
binding_range = 0.06
unbinding_rate = 0.3
activity = motor
max_speed = 0
stall_force = 6
unbinding_force = 3
hold_growing_end = 0
hold_shrinking_end = 0
}
set couple complex
{
hand1 = kinesin
hand2 = kinesin
stiffness = 100
diffusion = 20
activity = bridge
length = 0.05
}
new 10 fiber microtubule
{
length = 5
position = 0 -0.50
post_translation = 0 0.1 0
orientation = +1 0
}
new 10 fiber microtubule
{
length = 5
position = 0 -0.45
post_translation = 0 0.1 0
orientation = -1 0
}
new 1000 couple complex
run simul *
{
nb_steps = 100
solve = 0
}
change hand kinesin { max_speed = 0.1 }
run 5000 simul *
{
nb_frames = 100
}