Modelling microbial motion: the case of Chlamydomonas reinhardtii

This is a numerical implementation of a mathematical model that represents the motion of the unicellular eukaryotic organism Chlamydomonas Reinhardtii. All the parameters of the model and the simulation can be found (and modified) in the folder "parameters". Slides briefly showing the model and the results of the simulation can be found here

How to make it work

Tested on linux ubuntu.

Install dependencies

The first step is to obtain the necessary libraries: This is the official location of the Kaldi project.

GNU Scientific Library

• obtain GNU scientific library for generating random numbers:
  • on ubuntu you can maybe try: apt-get install libgsl0ldbl or apt-get install libgsl0-dev or apt-get install gsl-bin libgsl0-dev
  • you can also download the source code from ftp://ftp.gnu.org/gnu/gsl/ ("gsl-latest.tar.gz") and compile it following the instruction in "INSTALL"

SDL2

• obtain SDL2 libraries for the visualization:
  • graphics: apt-get install libsdl2-dev (maybe only apt-get install libsdl2-2)
  • fonts: apt-get install libsdl2-image-dev and apt-get install libsdl-ttf2-dev (maybe only apt-get install libsdl2-image and apt-get install libsdl-ttf2)

meson

• Meson for building the project: pip3 install meson

Compile and run

Build the project:

• meson build

and run with:

• ./initializer.py

Profiling

• install Valgrind: apt-get install valgrind
• install kcachegrind: apt-get install kcachegrind
• memory leaks check: valgrind --leak-check=yes build/swimmers-brownian-simulation <input file>
• profiling: ⋅⋅* valgrind --tool=callgrind build/swimmers-brownian-simulation <input file> ⋅⋅* callgrind_annotate callgrind.out.<pid>