Actin polymerization simulation

A simple code to simulate actin monomer diffusion and reaction with filaments.

Installation

You need a working python environment. Then install pandas, numpy, and yaml :

$ pip3 install numpy --user  
$ pip3 install yaml --user  
$ pip3 install pandas --user

Then download actin_polymerization.py from this github repo.

Usage

Run actin_polymerization.py with a config file, e.g. :

$ python3 actin_polymerization.py config.yaml

Configuration files

config.yaml is a suitable yaml-type config file, e.g.

simulation:
    Tmax: 1000
    N_monomers: 100000
    box: [150,120,120]
    success_frac: 1.0
filaments:
    f0:
        position: [60,19]
        orientation: [1,0]
        length: 50
    f1:
        position: [60,20]
        orientation: [1,0]
        length: 100

Parameters

Misc

success_frac : success rate of the polymerization reaction, from 0 to 1

Filament orientation

Values for orientation can be :

Single protofilament

[0,0]

Two protofilaments :

[1,0] : horizontal
[0,1] : vertical

Two prototfilaments, diffusion grid size : half monomer :

[2,0] : horizontal
[0,2] : vertical

SergeDmi/actin_polym