Cytosim PI Cytoskeleton Simulator

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Config Files - Fibers

# fiber.cym

% A confined fiber
% F. Nedelec, April 2010
set simul fiber
{
time_step = 0.005
viscosity = 0.02
}
set space cell
{
geometry = ( sphere 5 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 200
}
new 1 fiber microtubule
{
length = 12
}
run 5000 simul *
{
nb_frames = 10
}

# fiber_dynamic.cym

/**
@example fiber_dynamic.cym
We create a dynamic fiber with activity=dynamic
F. Nedelec, February 2011
*/
set simul demo
{
time_step = 0.01
viscosity = 1
}
set space cell
{
geometry = ( capsule 2 2 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 100
activity = dynamic
unit_length = 0.008
growing_speed = 0.06
shrinking_speed = -0.15
hydrolysis_rate = 0.06
growing_force = 1.7
display = { line_width=4; plus_end=16, 2; }
}
new 5 fiber microtubule
{
length = 1
plus_end_state = 1
}
new 5 fiber microtubule
{
length = 2
plus_end_state = 4
}
run simul *
{
nb_steps = 100000
nb_frames = 10
}

# fiber_treadmill.cym

/**
@example fiber_treadmill.cym
We create a dynamic fiber with activity=treadmill
F. Nedelec, February 2011
*/
set simul demo
{
time_step = 0.001
viscosity = 1
}
set space cell
{
geometry = ( capsule 2 2 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 200
activity = treadmill
growing_speed = 0.1, 0.05
shrinking_speed = -0.05, -0.1
growing_force = 2, 2
display = ( speckles=1, 0.1; line_width=4; line_style=2; )
}
new 1 fiber microtubule
{
length = 3
end_state = 1, 4
}
new 1 fiber microtubule
{
length = 1
end_state = 1, 1
}
new 1 fiber microtubule
{
length = 3
end_state = 4, 1
}
new 1 fiber microtubule
{
length = 6
end_state = 4, 4
}
run simul *
{
nb_steps = 100000
nb_frames = 10
}

# fiber_both.cym

/**
@example fiber_both.cym
We create two classes of fibers and associated motors
F. Nedelec, October 2011
*/
set simul demo
{
time_step = 0.001
viscosity = 0.05
display = ( window_size=900,300 )
}
set space cell
{
geometry = ( capsule 2 1 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
binding_key = 1
confine = inside, 200
display = ( line_width=8 )
}
new 1 fiber microtubule
{
length = 3
}
set hand kinesin
{
binding_key = 1
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.1
unbinding_force = 3
activity = move
max_speed = 0.8
stall_force = 5
display = ( size=10; color=orange; )
}
set single singleK
{
hand = kinesin
diffusion = 0.01
stiffness = 100
}
set fiber actin
{
rigidity = 0.05
segmentation = 0.05
binding_key = 2
confine = inside, 100
display = ( line_width=5; plus_end=5,5; minus_end=5,5; )
}
new 3 fiber actin
{
length = 1
}
set hand myosin
{
binding_key = 2
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.1
unbinding_force = 4
activity = move
max_speed = -0.8
stall_force = 5
display = ( size=10; color=sky_blue )
}
set single singleM
{
hand = myosin
diffusion = 0.01
stiffness = 100
}
new 100 single singleK
new 100 single singleM
run simul *
{
nb_steps = 10000
nb_frames = 100
}