It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …

Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

Adequate sampling of conformation space remains challenging in atomistic simulations,
especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up …

An understanding of molecular interactions is essential for insight into biological systems at
the molecular scale. Among the various components of molecular interactions, electrostatics …

This paper reviews various enhanced conformational sampling methods and explicit/implicit
solvent/membrane models, as well as their recent applications to the exploration of the …

Histone tails play an important role in gene transcription and expression. We present here a
systematic computational study of the role of histone tails in the nucleosome, using replica …

The evidence is now overwhelming that partially assembled nucleosome states (PANS) are
as important as the canonical nucleosome structure for the understanding of how …

We investigate the effect of solvent models on the computed thermodynamics of protein
folding. Atomistic folding simulations of a fast-folding mini-protein, CLN025, were employed …

Molecular dynamics (MD) simulations based on the implicit solvent generalized Born (GB)
models can provide significant computational advantages over the traditional explicit solvent …

We propose an approach for approximating electrostatic charge distributions with a small
number of point charges to optimally represent the original charge distribution. By …