Config Files - Fibers

fiber.cym

% A confined fiber
% F. Nedelec, April 2010

set simul fiber 
{
    time_step = 0.005
    viscosity = 0.02
}

set space cell
{
    geometry = ( sphere 5 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    confine = inside, 200
}

new 1 fiber microtubule
{
    length = 12
}

run 5000 simul *
{
    nb_frames = 10
}

fiber_dynamic.cym

/**
 @example fiber_dynamic.cym
 We create a dynamic fiber with activity=dynamic

 F. Nedelec, February 2011
*/


set simul demo
{
    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, 100
    
    activity        = dynamic
    unit_length     = 0.008
    growing_speed   = 0.06
    shrinking_speed = -0.15
    hydrolysis_rate = 0.06
    growing_force   = 1.7
    display = { line_width=4; plus_end=16, 2; }
}

new 5 fiber microtubule
{
    length = 1
    plus_end_state = 1
}

new 5 fiber microtubule
{
    length = 2
    plus_end_state = 4
}

run simul *
{
    nb_steps = 100000
    nb_frames = 10
}

fiber_treadmill.cym

/**
 @example fiber_treadmill.cym
 We create a dynamic fiber with activity=treadmill

 F. Nedelec, February 2011
*/


set simul demo
{
    time_step = 0.001
    viscosity = 1
}

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

new space cell

set fiber microtubule
{
    rigidity     = 20
    segmentation = 0.5
    confine      = inside, 200
    
    activity        = treadmill
    growing_speed   =   0.1,  0.05
    shrinking_speed = -0.05, -0.1
    growing_force   =     2,  2

    display = ( speckles=1, 0.1; line_width=4; line_style=2; )
}

new 1 fiber microtubule
{
    length = 3
    end_state = 1, 4
}

new 1 fiber microtubule
{
    length = 1
    end_state = 1, 1
}

new 1 fiber microtubule
{
    length = 3
    end_state = 4, 1
}

new 1 fiber microtubule
{
    length = 6
    end_state = 4, 4
}

run simul *
{
    nb_steps = 100000
    nb_frames = 10
}

fiber_both.cym

/**
 @example fiber_both.cym
 We create two classes of fibers and associated motors

 F. Nedelec, October 2011
*/

set simul demo
{
    time_step = 0.001
    viscosity = 0.05
    display = ( window_size=900,300 )
}

set space cell
{
    geometry = ( capsule 2 1 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    binding_key = 1
    confine = inside, 200
    display = ( line_width=8 )
}

new 1 fiber microtubule
{
    length = 3
}

set hand kinesin
{
    binding_key = 1
    binding_rate = 10
    binding_range = 0.01
    unbinding_rate = 0.1
    unbinding_force = 3
    
    activity = move
    max_speed = 0.8
    stall_force = 5
    display = ( size=10; color=orange; )
}

set single singleK
{
    hand = kinesin
    diffusion = 0.01
    stiffness = 100
}


set fiber actin
{
    rigidity = 0.05
    segmentation = 0.05
    binding_key = 2
    confine = inside, 100
    display = ( line_width=5; plus_end=5,5; minus_end=5,5; )
}

new 3 fiber actin
{
    length = 1
}

set hand myosin
{
    binding_key = 2
    binding_rate = 10
    binding_range = 0.01
    unbinding_rate = 0.1
    unbinding_force = 4
    
    activity = move
    max_speed = -0.8
    stall_force = 5
    display = ( size=10; color=sky_blue )
}

set single singleM
{
    hand = myosin
    diffusion = 0.01
    stiffness = 100
}

new 100 single singleK
new 100 single singleM

run simul *
{
    nb_steps  = 10000
    nb_frames = 100
}