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
}