Mirheo¶

Mesoscale flow solver for biological and medical applications.

Mirheo [alexeev2020] is designed as a classical molecular dynamics code adapted for inclusion of large (consisting of thousands of particles) rigid bodies and cells. The 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 [amoudruz2021],
viscoelastic cell membranes [economides2021], 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.

[alexeev2020]

Alexeev, Dmitry, et al. “Mirheo: High-performance mesoscale simulations for microfluidics.” Computer Physics Communications 254 (2020): 107298.

[economides2021]

Economides, Athena, et al. “Hierarchical Bayesian Uncertainty Quantification for a Model of the Red Blood Cell.” Physical Review Applied 15.3 (2021): 034062.

[amoudruz2021]

Amoudruz, Lucas, and Petros Koumoutsakos. “Independent Control and Path Planning of Microswimmers with a Uniform Magnetic Field.” Advanced Intelligent Systems (2021): 2100183.

User guide