We review a selection of methods for performing enhanced sampling in molecular dynamics
simulations. We consider methods based on collective variable biasing and on tempering …

This Perspective presents a personal overview of the current status of the theory of chemical
kinetics and mechanisms for complex processes. We attempt to assess the status of the field …

Enzymatic reactions are complex chemical processes taking place in complex dynamic
environments. Theoretical characterization of these reactions requires the determination of …

Theoretical and computational tools can provide a detailed knowledge of the mode of action
of enzymes. This knowledge can be systematized to be used as a guide for the design of …

Here we present a modified version of the on-the-fly string method for the localization of the
minimum free energy path in a space of arbitrary collective variables. In the proposed …

We describe a two-step approach for combining interactive molecular dynamics in virtual
reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological …

Irreversible epidermal growth factor receptor (EGFR) inhibitors can circumvent resistance to
first-generation ATP-competitive inhibitors in the treatment of nonsmall-cell lung cancer …

We combine molecular dynamics, statistical mechanics, and hybrid quantum
mechanics/molecular mechanics simulations to describe mechanistically the severe acute …

M. HhaI is a DNA methyltransferase from Haemophilus hemolyticus that catalyzes the
transfer of a methyl group from S-adenosyl-l-methionine (SAM) to the C5 position of a …

We present a combination of the string method and a path collective variable for the
exploration of the free energy surface associated to a chemical reaction in condensed …