The calculation of a protein-ligand binding free energy based on molecular dynamics (MD)
simulations generally relies on a thermodynamic cycle in which the ligand is alchemically …

We present new scalable algorithms and a new implementation of our kernel-independent
fast multipole method (Ying et al. ACM/IEEE SC'03), in which we employ both distributed …

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 …

In this study, a modified multilevel fast multipole algorithm is constructed for investigating
large-scale particle systems. The algorithm expands the number of levels of the modified …

We review the mathematical and computational foundations for implicit-solvent models in
theoretical chemistry and molecular biophysics. These models are valuable theoretical tools …

We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of
solvated biomolecules described by the linear Poisson–Boltzmann equation. The method …

The coupled cluster (CC) ansatz is generally recognized as providing one of the best wave
function-based descriptions of electronic correlation in small-and medium-sized molecules …

We report on the development and validation of a new numerical wave tank (NWT) solving
fully nonlinear potential flow (FNPF) equations, as a more efficient variation of Grilli et al.'s …

This paper reports large-scale direct numerical simulations of homogeneous-isotropic fluid
turbulence, achieving sustained performance of 1.08 petaflop/s on gpu hardware using …

The calculation of binding free energies of charged species to a target molecule is a
frequently encountered problem in molecular dynamics studies of (bio‐) chemical …