Brownian dynamics (BD) is a technique for carrying out computer simulations of physical
systems that are driven by thermal fluctuations. Biological systems at the macromolecular …

Identifying drug binding sites and elucidating drug action mechanisms are important
components in a drug discovery process. In this review, we briefly compared three different …

Coulomb interactions play a major role in determining the thermodynamics, structure, and
dynamics of condensed-phase systems, but often present significant challenges. Computer …

Coulomb interactions play a crucial role in a wide array of processes in aqueous solutions
but present conceptual and computational challenges to both theory and simulations. We …

We develop a hybrid approach that combines the Monte Carlo (MC) method, a variational
implicit-solvent model (VISM), and a binary level-set method for the simulation of …

In this article, we apply the binary level set method and techniques from image segmentation
to the variational implicit solvent model (VISM), a theoretical and computational setting for …

Existing computational models applied in the protein structure prediction process do not
sufficiently account for the presence of the aqueous solvent. The solvent is usually …

Coarse-grained modeling and efficient computer simulations are critical to the study of
complex molecular processes with many degrees of freedom and multiple spatiotemporal …