% "A Theory that Predicts Behaviors of Disordered Cytoskeletal Networks" (2017)
% JM Belmonte, M Leptin, F Nédélec
%
% Simulation file used to generate Fig. 4A
% Network of rigid filaments and connectors made of a motor and a binder
% 

set simul cytoskeleton
{ time_step = 0.001
  viscosity = 0.1
   kT = 0.0042 }

set space cell
{ geometry = ( sphere 15 ) }

new space cell

%--FIBERS-----------------------------------------------------

set fiber filament
{ rigidity = 22
  segmentation = 5
  display = ( line_width=0.5; end_style=0; color=white) }

%--HANDS------------------------------------------------------
set hand binder
{ binding = 10, 0.01
  unbinding = 0.3, inf
  display = ( color=gray; size = 2;) }

set hand motor_p
{ binding = 10, 0.01
  unbinding = 0.3, inf
  activity = move
  max_speed = 0
  stall_force = 6
  display = ( color=red; size = 2;) }

set hand motor_m
{ binding = 10, 0.01
  unbinding = 0.3, inf
  activity = move
  max_speed = 0
  stall_force = 6
  display = ( color=blue; size = 2;)}

set hand binder_p
{ binding = 10, 0.01
  unbinding = 0.3, inf
  activity = track
  bind_end = plus_end, 0.5
  display = ( color=red; size = 2;) }

set hand binder_m
{ binding = 10, 0.01
  unbinding = 0.3, inf
  activity = track
  bind_end = minus_end, 0.5
  display = ( color=blue; size = 2;) }

%--CONNECTORS-------------------------------------------------

set couple Connector
{ hand1 = binder
  hand2 = motor_p
  stiffness = 500
  diffusion = 1
  fast_diffusion = 1 }

%--INITIAL CONDITION------------------------------------------

new 1500 fiber filament { length = 5;  }

new 24000 couple Connector { }

%__RUNNING____________________________________________________________________

run 4000 simul * {solve=0;}

change hand motor_p { max_speed = 0.2}
change hand motor_m { max_speed = -0.2}

run 100000 simul * {
    nb_frames = 10}