Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …

Computer simulations play an important role in the study of transformation processes of
condensed matter, including phase transitions, chemical reactions, and conformational …

We develope a new free-energy method, based on the combination of parallel tempering
and metadynamics, and apply this method to the calculation of the free-energy landscape of …

We present a new approach for calculating reaction coordinates in complex systems. The
new method is based on transition path sampling and likelihood maximization. It requires …

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several
features with larger globular proteins. Although the system has been intensively investigated …

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 …

An understanding of the thermodynamics and kinetics of protein folding requires a
knowledge of the free energy surface governing the motion of the polypeptide chain …

Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of
complex molecular events. However, these simulations can rarely sample the required time …

We review two recently developed efficient methods for calculating rate constants of
processes dominated by rare events in high-dimensional complex systems. The first is …

While experiments can yield a wealth of insight into protein folding, it is difficult for
experiments to describe the process of folding in atomic detail. Typically, experiments …