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
}