YMeRo

Mesoscale flow solver for biological and medical applications

Introduction

The YMeRo code is designed as a classical molecular dynamics code adapted for inclusion of large (consisting of thousands of particles) rigid bodies and cells. Main features of the code include:

  • fluids represented as free particles interacting with different pairwise potentials (i.e. DPD or Lennard-Jones),
  • static walls of arbitrary complexity and size,
  • rigid bodies with arbitrary shapes and sizes,
  • viscoelastic cell membranes, that can separate inner from outer fluids

The multi-process GPU implementation enables very fast time-to-solution without compromising physical complexity and Python front-end ensures fast and easy simulation setup. Some benchmarks are listed in Benchmarks.

The following documentation is aimed at providing users a comprehensive simulation guide as well as exposing code internals for the developers wishing to contribute to the project.