% This is a configuration file for cytosim (www.cytosim.org)
% Please, used it with the Open Source code available on:
% http://www.github.com/nedelec/cytosim
%
% Simulation of nuclear dynamics in multinucleated hyphae of Ashbya gossypii
% R. Gibeaux, A. Politi, F. Nedelec -  06/2012-08/2014
    

set simul Ashbya
{
    time_step = 0.05
    % 'viscosity=0.9' from Tolic-Norrelykke et al. 2004.
    viscosity = 0.9
    steric = 1, 100
    precondition = 0
    display = ( back_color=dark_gray; inner_color=black; style=3; size=1280,256; )
    steric_max_range = 1.5
    flow = 0 0 0
}

%%%% The hypha %%%%%%%%%%%%%%%%%

set space cell
{
    geometry = (cylinderP 15 1.5)
    display = { color=black; }
}

new space cell

%%%% Microtubules %%%%%%%%%%%%%%%%%%%

% Values for MT dynamics in Ashbya gossypii from Grava and Philippsen MBoC 2010 21, 3680-3692
% Assumption that catastrophe rate = growing speed / average MT length
% MT length obtained from raw data of Grava and Philippsen MBoC 2010 21, 3680-3692
% Fit on trucated exponential distribution, Fraile and Garcia-Ortega JoAM 2005 44, 1620-25
% Only MT between 1 to 20 um considered for fit as high number of very short MT observed by ET in Gibeaux et al. JCS 2012

set fiber microtubule
{ 
    rigidity = 20
    segmentation = 0.5
    growing_force = 1.7
    steric = 1, 0.025
    confine =  inside, 100
    activity = classic
    growing_speed = 0.108, 0
    shrinking_speed = -0.272
    catastrophe_rate = 0.023
    min_length = 0
    display = ( plus_end=8,2; color=white; line=2.5; )
}

%%%% Dynein %%%%%%%%%%%%%%%%%%%%%%%%%%%%

set hand dynein
{
    binding_rate = 5
    unbinding_rate = 0.64 % 0.64 in King and Schroer, NCB 2000, 2
    binding_range = 0.075
    unbinding_force  = 7
    activity = motor
    % Unloaded speed ~ 0.05 um/s from Gennerich et al. Cell 2007, 131, 952-965
    max_speed = -0.025
    limit_speed = 1
    hold_shrinking_end = 0
    bind_also_end = 1
    % 'stall_force=6 pN' from Shingyoji et al. Nature 1998, 393
    % 'stall_force=7 pN' from Gennerich et al. Cell 2007, 131, 952-965
    stall_force = 7
    display = ( color=green; size=7; )
}

set single dyneinNum1
{
    hand = dynein
    stiffness = 500
    activity = fixed
}

%%%% Nucleus %%%%%%%%%%%%%%%%%%%%%%

set sphere nucleus
{
    confine = all_inside, 100
    point_mobility = 0.1
    steric = 1
    display = ( color=0x7700CCFF; style=3; )
}

set hand nucleator
{
    binding_rate = 10
    binding_range = 0.05
    unbinding_rate = 0
    unbinding_force = 3
    activity = nucleate
    nucleate = 1, microtubule, ( fiber_length=0.5 )
    display = ( size=12; color=orange; )
    specificity = none
}

set single handle
{
    hand = nucleator
    stiffness = 500
}

%%%% Congestion %%%%%%%%%%%%%%%%%%%

% Congestion data from Gibeaux et al. 2013

set bead mito
{
    confine = all_inside, 100
    steric = 1 
    display = ( color=0xFF993333 ; style=1; )
}

set bead vacuole
{
    confine = all_inside, 100
    steric = 1 
    display = ( color=0x3399FF33 ; style=1; )
}

%----------------------------------------
%----------- Simulation -----------------
%----------------------------------------

% Spacing between nuclei of 3-6 um, Fig1. Lang et al. MBoC 2010, 21, 753-766

new 5 sphere nucleus
{
    radius = 0.7
    point0 = surface, 3 handle
}

new 200 single dyneinNum1
{
    position = surface
}

% to be around 8.8% of the full volume
new 550 bead mito
{
    radius = 0.2
}

% to be around 2.5% of the full volume
new 50 bead vacuole
{
    radius = 0.3
}

%%%% Equilibrate & RUN %%%%%%%%%%%%

run simul *
{
    nb_steps = 6000
    nb_frames = 0
}

% Speed of flow 0.15 - 1.28 um/min from Table 1 Lang et al. 2010 MBoC, 21, 18-28
% Speed used for mutant comparison around 0.75 um/min in Grava and Philippsen 2010 MBoC 21, 3680-3692; Grava et al. 2011 EC, 10, 7, 902-915.
% The flow should be slightly higher to compensate for brownian and set in um/s.

change simul * { flow = 0.009 0 0 }

run simul *
{
    nb_steps = 6000
    nb_frames = 0
}

run simul *
{
    nb_steps = 36000
    nb_frames = 900
}