/** Configuration file for organization of PCM complexes and CAMSAP-kin14 complexes. The simulations were performed with Cytosim (www.cytosim.org) version June 2019. Author: f.m.berger@uu.nl */ set simul system { time_step = 0.01 kT = 0.0042 viscosity = 1 steric = 1, 1000 } set space cell { shape = sphere } new cell { radius = 10 } set hand dynein { binding_key = 3 binding_rate = 5 binding_range = 0.075 unbinding_rate = 0.1 unbinding_force = 2 activity = move unloaded_speed = -0.5 stall_force = 4 display = ( size = 0); %display = ( color = light_blue; size=7; ) hold_growing_end = 0 } set hand kin14 { binding_key = 3 binding_rate = 1 binding_range = 0.075 unbinding_rate = 1 unbinding_force = 3 activity = move unloaded_speed = -0.8 stall_force = 7 display = ( color = light_blue; size=0; ) hold_growing_end = 0 } set fiber microtubule { binding_key = 2 steric = 0 confine = inside, 100 rigidity = 20 segmentation = 0.5 activity = classic growing_speed = 0.13, 0 shrinking_speed = -0.272 catastrophe_rate = 0.026 growing_force = 1.7 display = ( color = red; end_style = 0; line_width = 0.5; ); rescue_rate = 0 min_length = 0.05 max_length = 7.5 } % To model adhesive interactions, we use a receptor (filament) and ligand (motor) binding interaction set fiber receptor { binding_key = 4 steric = 0 rigidity = 20 segmentation = 0.5 confine = inside, 100 min_length = 0.01 max_length = 0.01 %display = ( size = 0); display = ( line_width = 0; size=0; color = green) } set hand nucleation { activity = nucleate nucleate = 10, microtubule, (plus_end=grow; length = 0.05; ) display = ( size = 0; color = green); } set single anchored_nucsite { hand = nucleation stiffness = 1000 activity = fixed } set hand place_receptor { activity = nucleate nucleate = 1000000, receptor display = (size=0; color = green) } set single grafted_MT { hand = nucleation stiffness = 100 } set single grafted_receptor { hand = place_receptor stiffness = 100 } set single grafted_dynein { hand = dynein stiffness = 100 } set single grafted_kin14 { hand = kin14 stiffness = 100 } set sphere PCM { point_mobility = 0 steric = 1 display = { color=green; style=7; size=8 } } set sphere CAMSAP { point_mobility = 0 steric = 1 display = { color=blue; style=7; size=8 } } set hand anchor_ligand { binding_key = 4 binding_rate = 10 binding_range = 0.1 unbinding_rate = 0.01 unbinding_force = 3 display = ( size = 0;color=green); } set single grafted_ligand { hand = anchor_ligand stiffness = 100 activity = fixed } new 300 sphere PCM { radius = 0.05 point1 = 1, surface, 1 grafted_MT point2 = 1, surface, 1 grafted_dynein %To ignore adhesive interaction comment out the next two lines: point3 = 1, surface, 1 grafted_receptor point4 = 1, surface, 1 grafted_ligand %To use strong adhesive interactions use the following two lines instead of the preceeding ones: % point3 = 5, surface, 5 grafted_receptor % point4 = 5, surface, 5 grafted_ligand position = random } %PCMs that lost the MT new 0 sphere PCM { radius = 0.05 point1 = 1, surface, 1 grafted_dynein point2 = 1, surface, 1 grafted_receptor point3 = 1, surface, 1 grafted_ligand position = random } %CAMSAP-kin14 complexes new 0 sphere CAMSAP { radius = 0.05 point1 = 1, surface, 1 grafted_MT point2 = 5, surface, 1 grafted_kin14 %To include adhesive interaction, uncomment the following two lines point3 = 1, surface, 1 grafted_receptor point4 = 1, surface, 1 grafted_ligand position = random } % Microtubules can grow from these stationary nucleation sites randomly distributed in the cell new 0 anchored_nucsite { placement = all_inside } % Microtubules can grow from these stationary nucleation sites randomly distributed close to the periphery between 9 < r < 10 new 0 anchored_nucsite { placement = inside, cell, (r>9) } run system { nb_steps = 180000 nb_frames = 1000 }