Hydrophobic interactions are driven by the combined influence of the direct attraction
between oily solutes and an additional water-mediated interaction whose magnitude (and …

In modern-day simulations of many-body systems, much of the computational complexity is
shifted to the identification of slowly changing molecular order parameters called collective …

Molecular dynamics (MD) simulations have become a tool of immense use and popularity
for simulating a variety of systems. With the advent of massively parallel computer resources …

In this work, we demonstrate how to leverage our recent iterative deep learning–all atom
molecular dynamics (MD) technique “Reweighted autoencoded variational Bayes for …

Given the importance of water-mediated hydrophobic interactions in a wide range of
biological and synthetic self-assembly processes, it is remarkable that both the sign and the …

A key factor influencing a drug's efficacy is its residence time in the binding pocket of the
host protein. Using atomistic computer simulation to predict this residence time and the …

Water plays a crucial part in virtually all protein–ligand binding processes in and out of
equilibrium. Here, we investigate the role of water in the binding kinetics of a ligand to a …

As standard unbiased molecular dynamics (MD) simulations become impractical for
sampling rare events,“targeted MD” employs a moving distance constraint to enforce rare …

We introduce a machine-learning-based coarse-grained molecular dynamics model that
faithfully retains the many-body nature of the intermolecular dissipative interactions. Unlike …

The dynamics of colloids and proteins in dense suspensions is of fundamental importance,
from a standpoint of understanding the biophysics of proteins in the cytoplasm and for the …