Config Files - Set 1

aster.cym

% A confined aster
% F. Nedelec, April 2010

set simul aster 
{
    time_step = 0.001
    viscosity = 0.01
}

set space cell
{
    geometry = ( sphere 10 )
}

new space cell

set fiber microtubule
{
    rigidity = 30
    segmentation = 1
    confine = inside, 100

    display = { line_width=3; }
}

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 = 32
    length = 12
}


run simul *
{
    nb_steps = 20000
    nb_frames = 100
}

pombe_classic.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
    display = { window_size=800,400 }
}

set space pombe
{
    geometry = ( capsule 3.5 1.6 )
}

new space pombe

set fiber microtubule
{
    rigidity       = 30
    segmentation   = 0.5
    confine        = inside, 200
    
    activity         = classic
    growing_speed    = 0.06
    shrinking_speed  = -0.15
    catastrophe_rate = 0.004,  0.04
    rescue_rate      = 0
    growing_force    = 1.67
    fate             = rescue
    min_length       = 0.5
    
    display = {show_average=2}
}

set sphere envelope
{
    point_mobility = 0.05
    confine        = all_inside, 200
    piston_effect  = 1
    
    display = { color=0x0000FF55 }
}

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 )
    length = 0.5
}

run simul *
{
    nb_steps   = 50000
    nb_frames  = 100
}

self.cym

% One of the oldest simulation
% F. Nedelec

set simul self 
{
    time_step = 0.01
    viscosity = 0.05
}


set space cell
{
    geometry = ( circle 16 )
}

new space cell

set fiber microtubule
{
    rigidity = 30
    segmentation = 1.5
    confine = inside, 100
    display = { line_width=1; }
}

set hand kinesin
{
    binding_rate = 10
    binding_range = 0.01
    unbinding_rate = 0.1
    unbinding_force = 3
    
    activity = move
    max_speed = 0.8
    stall_force = 5
    
    hold_growing_end = 1
    display = { size=8 }
}

set couple complex
{
    hand1 = kinesin
    hand2 = kinesin
    stiffness = 100
    diffusion = 10
}

new 80 fiber microtubule
{
    length = 14
}

new 2000 couple complex

set simul:display *
{
    label = (Nedelec et al. 1998 -)
}

run simul *
{
    nb_frames  = 100
    nb_steps   = 4000
}

glide.cym

% Gliding assay with realistic Kinesin and Microtubule parameters, 
% cf. Bourdieu et al. PRL Vol 75/N 1/Page 176-179
% the parameters for motor density are also taken from there

set simul glide 
{
    time_step = 0.005
    viscosity = 0.1
    precondition = 0
    display = ( style=2 )
}

set space cell
{
    geometry = ( periodic 2 2 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.25
    display = {
        line_width = 2
        line_style = 1
        point_size = 8
        point_style = 2
    }
}

set hand kinesin
{
    binding_rate = 10
    binding_range = 0.01
    unbinding_rate = 0.3
    unbinding_force = 2.5
    
    activity = move
    max_speed = 0.4
    stall_force = 6
}

set single grafted
{
    hand = kinesin
    stiffness = 200
    activity = fixed
}

new fiber microtubule
{
    length = 5
    orientation = horizontal
}

new 16000 single grafted

set simul:display gliding
{
    label = (Gliding assay -)
    
    delay = 10
    %tiled = 1
    point_size = 6
    style = 2
}

run simul *
{
    nb_steps = 5000
    nb_frames = 50
}

overlap.cym

% An antiparallel bundle extending under the action of crosslinking motors
% Francois Nedelec, July 24, 2009

set simul overlap 
{
    time_step = 0.01
    viscosity = 0.1
    display = (
        window_size = 768, 256;
        zoom=1.4;
        style = 2
        point_size = 5
        line_width = 2
        label = (Sliding bundle -)
    )
}

set space cell 
{
    geometry = ( rectangle 6 1.5 1.5 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    display = ( line=3,2; speckles=1; point_size=8; end_section=0,1; end_size=5,5 )
}

set hand kinesin
{
    binding_rate = 10
    binding_range = 0.06
    unbinding_rate = 0.3
    
    activity = motor
    max_speed = 0
    stall_force = 6
    
    unbinding_force = 3
    hold_growing_end = 0
    hold_shrinking_end = 0
}

set couple complex
{
    hand1 = kinesin
    hand2 = kinesin
    stiffness = 100
    diffusion = 20
    activity = bridge
    length = 0.05
}

new 10 fiber microtubule
{
    length = 5
    position = 0 -0.50
    post_translation = 0 0.1 0
    orientation = +1 0
}
    
new 10 fiber microtubule
{
    length = 5
    position = 0 -0.45
    post_translation = 0 0.1 0 
    orientation = -1 0
}
    
new 1000 couple complex

run simul * 
{
    nb_steps = 100
    solve = 0
}
    
change hand kinesin { max_speed = 0.1 }

run 5000 simul *
{
    nb_frames = 100
}