Cytosim PI Cytoskeleton Simulator

- Main Page
- Related Pages
- Modules
- Namespaces
- Classes
- Files

Config Files - Set 3

# event.cym

% test stochastic events in function 'run simul *'
% F. Nedelec, 8 Feb 2011
set simul event
{
steric = 1, 100
steric_max_range = 0.5
time_step = 0.001
viscosity = 0.1
precondition = 0
}
set space cell
{
geometry = ( sphere 3 )
}
new space cell
set solid ball
{
confine = all_inside, 1000
steric = 1
display = ( style=4; coloring=1; )
}
new 100 bead ball
{
radius = 0.1
position = ( 0 0 0 )
mark = 1
}
new 100 bead ball
{
radius = 0.1
position = ( 0 0 0 )
mark = 2
}
run 200 simul *
delete bead *
{
mark = 2
}
run simul *
{
nb_steps = 2000
event = 100, ( new 1 bead ball { radius=0.15; position=(0 0 0); } )
}
delete bead *
{
mark = 1
}
run simul *
{
nb_steps = 1000
event = 50, ( new 1 bead ball { radius=0.20; position=(0 0 0); } )
}
run simul *
{
nb_steps = 1000
nb_frames = 10
event = 5, ( new 1 bead ball { radius=0.25; position=(0 0 0); } )
}

# fiber_anchor.cym

/**
@example fiber_anchor.cym
We use anchors to attach fibers to the substrate
F. Nedelec, 2010
*/
set simul demo
{
time_step = 0.005
viscosity = 0.02
}
set space cell
{
geometry = ( sphere 10 )
}
new space cell
set hand strong_hand
{
unbinding_rate = 0
unbinding_force = 1e6
display = ( size = 10 )
}
set single pivot
{
hand = strong_hand
stiffness = 1000
activity = fixed
}
set fiber tube
{
rigidity = 20
segmentation = 1
confine = inside, 100
}
new 32 fiber tube
{
orientation = 1 0.2 0
position = ( -6 0 0 )
length = 8
single = pivot, minus_dir
post_rotation = (1 0.2)
}
new 1 fiber tube
{
orientation = 1 0 0
position = ( 1.5 0 0 )
length = 3
single = pivot, minus_end
}
set hand kinesin
{
binding_rate = 10
binding_range = 0.05
unbinding_rate = 0.2
unbinding_force = 3
activity = move
max_speed = 1
stall_force = 6
display = ( size=8; color=0x00FF00FF; )
}
set couple complex
{
hand1 = kinesin
hand2 = kinesin
diffusion = 5
stiffness = 100
}
new 1000 couple complex
run simul *
{
nb_steps = 5000
nb_frames = 10
}

# aster_couple.cym

% Two asters interacting with hetero-complexes
% F. Nedelec, April 2010
set simul aster_couple
{
time_step = 0.005
viscosity = 0.1
}
set space cell
{
geometry = ( circle 7 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
}
set hand dynein
{
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=0xFF00FFFF; }
}
set hand kinesin
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.2
unbinding_force = 3
activity = move
max_speed = 0.8
stall_force = 6
display = { size=8; color=0x00FF00FF; }
}
set couple complex
{
hand1 = kinesin
hand2 = dynein
diffusion = 0.20
stiffness = 200
}
set solid core
{
confine = 1, 100
display = ( style=3 )
}
set aster centrosome
{
solid = core
fibers = microtubule
stiffness = 1000, 500
}
new 2 aster centrosome
{
radius = 1
nb_fibers = 32
length = 7
}
new 5001 couple complex
run simul *
{
nb_steps = 5000
nb_frames = 50
}

# steric.cym

% A test of steric interactions between fibers and beads
% F. Nedelec, 23 Jan 2010
set simul steric
{
steric = 1, 100
precondition = 0
time_step = 0.005
kT = 0.0042
steric_max_range = 0.5
display = ( point_value=0.01; delay=10; period=4; )
}
set space cell
{
geometry = ( sphere 3 )
}
new space cell
set fiber tube
{
rigidity = 1
confine = inside, 100
segmentation = 0.2
steric = 1, 0.05
activity = tubule
dynamic_model = 1, 1
dynamic_speed1 = 0.2, -0.8, 0.2, -0.8
dynamic_trans1 = 0.02, 0, 0.02, 0
fate = rescue
growing_force = 1.7
display = ( line_width=6; coloring=1 )
}
new 20 fiber tube
{
length = 0.05
}
set bead ball
{
steric = 1
confine = all_inside, 100
display = ( style=5; coloring=1; )
}
new 40 bead ball
{
radius = 0.25
}
run 100000 simul *
{
nb_frames = 100
}