Cytosim PI Cytoskeleton Simulator

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Config Files - Hands

# hand_track.cym

/**
@example hand_track.cym
We create a Tracker with `hand:activity=track`
F. Nedelec, June 2011
*/
set simul hand_track
{
time_step = 0.005
viscosity = 0.02
}
set space cell
{
geometry = ( capsule 10 2 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 500
display = { line_width=1; minus_end=4, 8; }
}
new 1 fiber microtubule
{
length = 19
position = ( 0 0 0 )
}
set hand tracker
{
binding_rate = 10
binding_range = 0.1
unbinding_rate = 0.1
unbinding_force = 10
activity = track
bind_end = plus_end, 1
display = { width=3; size=6; color=green }
}
set single protein
{
hand = tracker
diffusion = 10
}
new 1000 single protein
run simul *
{
nb_steps = 40000
nb_frames = 50
}

# hand_cut.cym

/**
@example hand_cut.cym
We create a Cutter with `hand:activity=cut`
F. Nedelec, October 2011
*/
set simul hand_cut
{
time_step = 0.005
viscosity = 0.1
}
set space cell
{
geometry = ( sphere 5 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.25
confine = inside, 100
}
new 1 fiber microtubule
{
length = 10
position = ( 0 0 0 )
}
set hand cutter
{
binding_rate = 10
binding_range = 0.05
unbinding_rate = 0
unbinding_force = 3
activity = cut
cutting_rate = 10
display = { size=8; color=green; }
}
set single protein
{
hand = cutter
diffusion = 1
}
new 100 single protein
run simul *
{
nb_steps = 5000
nb_frames = 10
}

# hand_slide.cym

/**
@example hand_slide.cym
We create a Slider with `hand:activity=slide`
F. Nedelec, June 2011
*/
set simul hand_slide
{
time_step = 0.005
viscosity = 0.02
}
set space cell
{
geometry = ( sphere 10 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 500
display = { line_width=3; minus_end=4, 8; }
}
new 1 fiber microtubule
{
length = 19
position = ( 0 0 0 )
}
set hand slider
{
binding_rate = 10
binding_range = 0.01
unbinding_rate = 0.1
unbinding_force = 10
activity = slide
mobility = 1
stiffness = 100
display = { width=3; size=6; color=green }
}
set single protein
{
hand = slider
activity = fixed
stiffness = 100
}
new 100 single protein
run simul *
{
nb_steps = 40000
nb_frames = 50
}

# hand_move.cym

/**
@example hand_move.cym
We create a Motor with `hand:activity=move`
F. Nedelec, April 2010
*/
set simul hand_move
{
time_step = 0.005
viscosity = 0.02
}
set space cell
{
geometry = ( sphere 10 )
}
new space cell
set fiber microtubule
{
rigidity = 30
segmentation = 0.5
confine = inside, 500
display = { line_width=2; minus_end=4, 8; }
}
new 1 fiber microtubule
{
length = 19
position = ( 0 0 0 )
}
set hand motor
{
binding_rate = 10
binding_range = 0.05
unbinding_rate = 0.2
unbinding_force = 3
hold_growing_end = 1
activity = move
max_speed = 1
stall_force = 5
display = { width=3; size=12; color=green }
}
set single protein
{
hand = motor
diffusion = 0.1
}
new 100 single protein
run simul *
{
nb_steps = 40000
nb_frames = 50
}

# hand_walk.cym

# hand_nucleate.cym

/**
@example hand_nucleate.cym
We create a Nucleator with `hand:activity=nucleate`
F. Nedelec, April 2011
*/
set simul hand_nucleate
{
time_step = 0.005
viscosity = 10
}
set space cell
{
geometry = ( capsule 3 1 )
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 100
}
new 1 fiber microtubule
{
length = 5
position = ( 0 0 0 )
orientation = horizontal
}
set hand activator
{
binding_rate = 1
binding_range = 0.05
unbinding_rate = 0
unbinding_force = 3
display = { size=8; color=white; }
}
set hand nucleator
{
unbinding_rate = 0
unbinding_force = 3
activity = nucleate
nucleate = 10, microtubule, ( fiber_length=1; )
specificity = parallel
display = { size=10; color=green; }
}
set couple complex
{
hand1 = activator
hand2 = nucleator
diffusion = 1
stiffness = 100
activity = crosslink
length = 0.1
trans_activated = 1
}
new 1000 couple complex
run simul *
{
nb_steps = 5000
nb_frames = 10
}

# hand_rescue.cym

/**
@example hand_rescue.cym
We create a Rescuer with `hand:activity=rescue`
F. Nedelec, September 2012
*/
set simul rescue
{
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, 200
activity = dynamic
unit_length = 0.008
growing_speed = 0.06
shrinking_speed = -0.15
hydrolysis_rate = 0.25
growing_force = 1.7
display = { line_width=2; plus_end=16, 2; }
}
new 5 fiber microtubule
{
length = 5
end_state = red
}
set hand rescue
{
binding_rate = 10
binding_range = 0.1
unbinding_rate = 0.1
unbinding_force = 10
activity = rescue
rescue_prob = 0.1
display = { width=3; size=6; color=green }
}
set single protein
{
hand = rescue
diffusion = 10
}
new 500 single protein
run simul *
{
nb_steps = 100000
nb_frames = 10
}