NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel …

An important and computationally demanding part of molecular dynamics simulations is the
calculation of long-range electrostatic interactions. Today, the prevalent method to compute …

Aiming at the current problems that most physical hosts in the cloud data center are so
overloaded that it makes the whole cloud data center'load imbalanced and that existing load …

We present a fast, petaflop-scalable algorithm for Stokesian particulate flows. Our goal is the
direct simulation of blood, which we model as a mixture of a Stokesian fluid (plasma) and …

This article is mainly devoted to a review on fast BEMs for elastodynamics, with particular
attention on time-harmonic fast multipole methods (FMMs). It also includes original results …

We describe our implementation of a parallel fast multipole method for evaluating potentials
for discrete and continuous source distributions. The first requires summation over the …

This paper throws a small “wet blanket” on the hot topic of GPGPU acceleration, based on
experience analyzing and tuning both multithreaded CPU and GPU implementations of …

From molecular dynamics and quantum chemistry, to plasma physics and computational
astrophysics, Poisson solvers in the unit cube are used in many applications in …

Molecular dynamics (MD) has experienced a significant growth in the recent decades.
Simulating systems consisting of hundreds of thousands of atoms is a routine task of …

This paper focuses on the use of GPGPU-based clusters for hierarchical N-body simulations.
Whereas the behavior of these hierarchical methods has been studied in the past on CPU …