For a number of years, we have been exploring the underpinnings of algorithms for
simulating molecular dynamics from a mathematics perspective, ie as outsiders. We have …

DL_MESO is a parallel mesoscale simulation package capable of dissipative particle
dynamics and the lattice Boltzmann equation method. It has been developed at Daresbury …

We design and implement a scalable hard particle Monte Carlo simulation toolkit (HPMC),
and release it open source as part of HOOMD-blue. HPMC runs in parallel on many CPUs …

The study of viscous fluid flow coupled with rigid or deformable solids has many applications
in biological and engineering problems, eg, blood cell transport, drug delivery, and …

Dissipative particle dynamics (DPD) is a coarse-grained particle-based simulation method
that offers microscopic-scale insights into soft matter systems. We present an efficient …

We review and compare numerical methods that simultaneously control temperature while
preserving the momentum, a family of particle simulation methods commonly used for the …

Calcium (Ca2+) sparks are the elementary events of excitation–contraction coupling, yet
they are not explicitly represented in human ventricular myocyte models. A stochastic …

We present simulations of blood and cancer cell separation in complex microfluidic
channels with subcellular resolution, demonstrating unprecedented time to solution …

A parallel implementation of the Shardlow splitting algorithm (SSA) for Dissipative Particle
Dynamics (DPD) simulations is presented. The isothermal and isoenergetic SSA …

Cardiovascular disease is the leading cause of death worldwide due in a large part to
arrhythmia. In order to understand how calcium dynamics play a role in arrhythmogenesis …