% "A Theory that Predicts Behaviors of Disordered Cytoskeletal Networks" (2017)
% JM Belmonte, M Leptin, F Nédélec
%
% Simulation file used to generate Fig. 5E 
% Actomyosin contraction with filament turnover leads to pulsatile behavior
% 

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

set space cell
{ geometry = ( periodic 8 8 ) }

new space cell

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

set fiber actin
{ rigidity = 0.075
  segmentation = 0.15
  display = ( line_width=1.0; 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;) }

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

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

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

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

new 1400 fiber actin { length = 2 }

new 22400 couple Motor
new 5600 couple Xlink

%__RUNNING____________________________________________________________________

run 4000 simul * { solve=0; }

change hand motor_p { max_speed = 0.2}

run 600000 simul * { nb_frames = 150
  event = 64, {delete 1 fiber actin 
	       	     new 1 fiber actin { length = 2} } }