Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Rare events are ubiquitous in many different fields, yet they are notoriously difficult to
simulate because few, if any, events are observed in a conventional simulation run. Over the …

Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …

For a number of years, we have been exploring the underpinnings of algorithms for
simulating molecular dynamics from a mathematics perspective, ie as outsiders. We have …

We present a detailed theoretical analysis of the reaction mechanism of proteolysis
catalyzed by the main protease of SARS-CoV-2. Using multiscale simulation methods, we …

In this note we propose a method based on artificial neural network to study the transition
between states governed by stochastic processes. In particular, we aim for numerical …

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and
molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of …

In recent years atomistic simulations have become increasingly important in providing
molecular insight to complement experiments. Even for the seemingly simple case of ion …

We introduce a method to obtain one-dimensional collective variables for studying rarely
occurring transitions between two metastable states separated by a high free energy barrier …

The long-timescale dynamics of macromolecular systems can be oftentimes viewed as a
reaction connecting metastable states of the system. In the past decade, various approaches …