Config Files - Set 4

overlap_walk.cym

aster_texas.cym

% A confined aster with cortical pulling motors
% F. Nedelec, April 2010

set simul aster_texas 
{
    time_step = 0.005
    viscosity = 0.1
}

set space texas
{
    geometry = ( polygon texas.txt 2 )
}

new space texas

set fiber microtubule
{
    rigidity = 30
    segmentation = 0.5
    confine = inside, 100
    
    activity         = classic
    growing_speed    = 0.2
    shrinking_speed  = -0.5
    catastrophe_rate = 0.05
    rescue_rate      = 0
    growing_force    = 1.67
    fate             = rescue
    min_length       = 0.25
}

set solid core
{
    display = ( style=3 )
}

set aster centrosome
{
    solid = core
    fibers = microtubule
    stiffness = 1000, 500
}

new 1 aster centrosome
{
    radius = 1
    nb_fibers = 32
    length = 2
}

run simul *
{
    nb_steps = 20000
    nb_frames = 10
}

fiber_glue.cym

/**
 @example fiber_glue.cym
 Parameter fiber:glue is set link fiber with the boundaries:
 - it creates a Single, everytime a fiber contacts the surface.
 - the Single is deleted if the associated Hand detaches.
 .
 F. Nedelec, February 2011
*/

set simul fiber_glue
{
    time_step = 0.01
    viscosity = 0.1
    display = { delay=4; }
}

set space cell
{
    geometry = ( sphere 5 )
}

new space cell

set hand strong_hand
{
    unbinding_rate = 0
    unbinding_force = 1e6
    hold_growing_end = 1
    hold_shrinking_end = 1
    display = { size=8 }
}

set single cortical_glue
{
    hand = strong_hand
    stiffness = 10
    activity = fixed
}

set fiber microtubule
{
    rigidity = 30
    segmentation = 0.5
    confine = inside, 100
    glue = 3, cortical_glue

    activity        = tubule
    dynamic_model   = 3
    dynamic_speed1  = 0.51,  -0.84
    dynamic_trans1  = 0.01
    dynamic_trans2  = 5 
    fate            = rescue
    growing_force   = 1.7
    min_length      = 0.5
    
    display = { line=8, 2; point=1; speckles=2, 0.25; rainbow=-0.1 }
}

set solid core
{
    display = ( style=3 )
}

set aster centrosome
{
    solid = core
    fibers = microtubule
    stiffness = 1000, 500
}

new 1 aster centrosome
{
    radius = 0.5
    nb_fibers = 20
    fiber_length = 2
    position = 0 0 0
}


run simul *
{
    nb_steps = 10000
    nb_frames = 50
}

motif.cym

% Francois Nedelec, July 24, 2009 


set simul motif 
{
    time_step = 0.01
}


set space cell
{
    geometry = ( sphere 8 )
}

new space cell

set fiber tube
{
    segmentation = 0.5
    rigidity = 20
    confine = inside, 100
}

new 10 fiber tube
{
    length = 10
}

set hand kinesin
{
    binding_rate = 10
    binding_range = 0.01
    unbinding_rate = 0.5
    unbinding_force = 2
    
    activity = move
    max_speed = 0.8
    stall_force = 6

    display = { color=0x0000FFFF }
}

set single gKinesin
{
    hand = kinesin
    stiffness = 100
    activity = fixed
}
    

set hand dynein
{
    binding_rate = 10
    binding_range = 0.01
    unbinding_rate = 0.5
    unbinding_force = 2
    
    activity = move
    max_speed = -0.8
    stall_force = 6

    display = { color=0xFFFFFFFF }
}


set single gDynein
{
    hand = dynein
    stiffness = 100
    activity = fixed
}


% female motif
new 3000  single gKinesin ( circle 3 0.2 at -3 2 )
new  500  single gKinesin ( rectangle 0.1 2 0.1 at -3 -3.0 )
new  500  single gKinesin ( rectangle 2 0.1 0.1 at -3 -2.9 )


% male motif
new 3000  single gDynein ( circle 3 0.2 at +3 -2 )
new  500  single gDynein ( rectangle 1.5 0.1 at 4.5 0 turn 1 1.5 at 3 -2 )

new  500  single gDynein ( rectangle 1.0 0.1 at -1.0 0 turn 1 +1 at 6 0 turn 1 1.5 at 3 -2 )
new  500  single gDynein ( rectangle 1.0 0.1 at -1.0 0 turn 1 -1 at 6 0 turn 1 1.5 at 3 -2 )

% cortical pool
new 500  single gKinesin ( edge 0.1 )
new 500  single gDynein  ( surface 0.1 )


run simul *
{
    nb_steps = 5000
    nb_frames = 50
}

wash.cym

% A confined fiber
% F. Nedelec, April 2010

set simul anchor 
{
    time_step = 0.01
    viscosity = 0.02
    steric = 1, 100
}

set space cell
{
    geometry = ( sphere 10 )
}

new space cell

set hand strong_hand
{
    unbinding = 0, 1e6
}

set single pivot
{
    hand = strong_hand
    stiffness = 1000
    activity = fixed
}

set fiber tube
{
    rigidity = 20
    segmentation = 1
    confine = inside, 100
}

new 20 fiber tube
{
    orientation = 0.8 0.5 0 
    position = ( -5 0 0 )
    length = 9
    single = pivot, minus_dir, 0.5
    post_rotation = ( 0.8 0.25 )
}

set hand kinesin 
{
    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=0x00FF00FF; )
}

set single grafted 
{
    hand = kinesin
    stiffness = 100
}

set solid dirty
{
    confine = all_inside, 100
    steric = 1
    display = ( coloring=1; )
}

new 301 bead dirty
{
    single = grafted
    radius = 0.4
}

run simul *
{
    nb_steps = 5000
    nb_frames = 100
}