M1_yeast_Ang180_mdxx.cym

% Neha Khetan, Athale Lab
% 2020 - 2021 : Budding cell
% Geomtery of cell: file in the path: ./input/CellCoors.out
% Geometry of spindle: elliposidal and dumbell
% Models for dynein localization:
%				1. uniform arc: "yeast_bud_mdX.cym"
%				2. offloading: Offloading_1 => same mt on both spbs
%				3. offloading:           _2 => off-loading only at the bud-cortex
%               4. => Create MT asymmetry: microtubule1 and microtubule2 : in this file.
% CYTOSIM PI version ed5c1f1                              
% =============================================================

set simul INVIVO
{
	time_step = 0.001
	steric = 1, 100
	viscosity = 0.5
	tolerance = 0.01
	kT = 0.0042
}


set space cell
{
    shape = polygon
    display = ( visible=1; style = 3)
}

new cell
{
    file = ./input/cellCoors.out   
    
}


set fiber microtubule1
{
    rigidity       = 20
    segmentation   = 0.5
    confine        = 1 ,  500 , cell
    min_length     = 0.5  
    activity       = classic
    
    % first column if for PLUS end; second one for MINUS end
    growing_speed            = 0.03  %,   0 
    shrinking_speed          = -0.05   %,  0
    catastrophe_rate         = 0.023 , 1   %,  0
    %catastrophe_rate_stalled = 0.04 %,   0
    rescue_rate              = 0.03 %,      0
    growing_force            = 1.67%,   1.67
    steric = 1, 0.05
    %display = ( plus_end=6, 2;  )
    persistent  = 1 
}



set fiber microtubule2
{
    rigidity       = 20
    segmentation   = 0.5
    confine        = 1 ,  500 , cell
    min_length     = 0.5  
    activity       = classic
    
    % first column if for PLUS end; second one for MINUS end
    growing_speed            = 0.03  %,   0 
    shrinking_speed          = -0.05   %,  0
    catastrophe_rate         = 0.023 , 1   %,  0
    %catastrophe_rate_stalled = 0.04 %,   0
    rescue_rate              = 0.03 %,      0
    growing_force            = 1.67%,   1.67
    steric = 1, 0.05
    %display = ( plus_end=6, 2;  )
    persistent  = 1 
}



set hand nucleator1
{
	unbinding_rate   = 0
	unbinding_force  = Inf
	activity         = nucleate
	nucleate         = 10, microtubule1, ( fiber_length= 0.5 ;  plus_end = grow;  )
	display          = ( size=4; color= grey; )
}



set hand nucleator2
{
	unbinding_rate  = 0
	unbinding_force = Inf
	activity        = nucleate
	nucleate        = 10, microtubule2, ( fiber_length= 1.0 ;  plus_end = grow ;)
	display         = ( size=4; color= orange; )
}


set single spindleNucleator1
{
	hand = nucleator1
	stiffness = 1000
    
}

set single spindleNucleator2
{
	hand = nucleator2
	stiffness = 1000
}


set solid spindle
{
	confine = 4 , 10000, cell
	steric = 1
   	 
}



new 1 solid spindle
{

    nb_points   = 13
    point1 =   -0.85      0      0  , 0 , spindleNucleator1
    point2 =    0.85      0      0  , 0 , spindleNucleator2
    

    point10 = -0.6  0   0,0.0
    point11 = -0.45 0   0,0.4

    point3  = -0.3  0   0,0.52
    point4  = -0.15 0   0,0.58
    point5  = 0.0   0   0,0.6
    point6  = 0.15  0   0,0.58
    point7  = 0.3   0   0,0.52
    point8  = 0.45  0   0,0.4
    point9  = 0.6   0   0,0.0

    
    point12 =    0.85     0.01   0  , 0 , spindleNucleator2
    point13 =   -0.85     0.01   0  , 0 , spindleNucleator1
    position 	= 1 0 0 %at 0.1 0
    orientation = 1 0 0 %Places the solid in absolute space
}





%% ==========================================
set hand binder
{
    binding 	= 0, 0
    unbinding 	= 0, Inf
    display  = ( size =0.18 ; color = white;)
}

set single grafted
{
    hand 		= binder
    stiffness 	= 200
    activity 	= fixed

   
}

new 5000 grafted
{
    position = surface % gradient 3 5

    
}
%% =========================================



set hand dynein
{
    binding_rate     = 5
    binding_range    = 0.075
    unbinding_rate   = 0.04
    unbinding_force  = 3
        
    activity 		 = move
    unloaded_speed   =   -0.08
    stall_force 	 = 4.8
    display  = ( size = 25 ; color = red ;)
}


set single graftedDyn
{
    hand = dynein
    stiffness = 200
    activity = fixed
}

% Dynein 
new 1 graftedDyn	 (3.25	-1.7) 
new 1 graftedDyn	 (3.40	-1.69) 
new 1 graftedDyn	 (3.51	-1.68) 
new 1 graftedDyn	 (3.64	-1.66) 
new 1 graftedDyn	 (3.77	-1.62) 
new 1 graftedDyn	 (3.89	-1.58) 
new 1 graftedDyn	 (4.01	-1.53) 
new 1 graftedDyn	 (4.12	-1.47) 
new 1 graftedDyn	 (4.24	-1.4) 
new 1 graftedDyn	 (4.30	-1.33) 
new 1 graftedDyn	 (4.44	-1.25) 
new 1 graftedDyn	 (4.53	-1.16) 
new 1 graftedDyn	 (4.62	-1.06) 
new 1 graftedDyn	 (4.68	-0.96) 
new 1 graftedDyn	 (4.75	-0.85) 
new 1 graftedDyn	 (4.80	-0.74) 
new 1 graftedDyn	 (4.88	-0.62) 
new 1 graftedDyn	 (4.92	-0.5) 
new 1 graftedDyn	 (4.94	-0.38) 
new 1 graftedDyn	 (4.98	-0.25) 
new 1 graftedDyn	 (5.0	-0.10) 
new 1 graftedDyn	 (5.0	0.0) 
new 1 graftedDyn	 (5.0	0.10) 
new 1 graftedDyn	 (4.98	0.25) 
new 1 graftedDyn	 (4.94	0.38) 
new 1 graftedDyn	 (4.92	0.5) 
new 1 graftedDyn	 (4.88	0.61) 
new 1 graftedDyn	 (4.83	0.74) 
new 1 graftedDyn	 (4.75	0.85) 
new 1 graftedDyn	 (4.7	0.96) 
new 1 graftedDyn	 (4.60	1.06) 
new 1 graftedDyn	 (4.53	1.16) 
new 1 graftedDyn	 (4.40	1.25) 
new 1 graftedDyn	 (4.30	1.33) 
new 1 graftedDyn	 (4.24	1.4) 
new 1 graftedDyn	 (4.12	1.47) 
new 1 graftedDyn	 (4.01	1.53) 
new 1 graftedDyn	 (3.89	1.58) 
new 1 graftedDyn	 (3.77	1.62) 
new 1 graftedDyn	 (3.62	1.66) 
new 1 graftedDyn	 (3.51	1.68) 
new 1 graftedDyn	 (3.41	1.69) 
new 1 graftedDyn	 (3.25	1.7) 	 

%% ==========================================
run simul *
{
	nb_steps = 1200000
	nb_frames = 1200
}