By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

Biomolecules are the prime information processing elements of living matter. Most of these
inanimate systems are polymers that compute their own structures and dynamics using as …

The recent availability of long equilibrium simulations of protein folding in atomistic detail for
more than 10 proteins allows us to identify the key interactions driving folding. We find that …

Markov State Models (MSMs) provide an automated framework to investigate the dynamical
properties of high-dimensional molecular simulations. These models can provide a human …

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven
to be an effective means of capturing the functionally important long-time and large-length …

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

We present a multiscale method for the determination of collective reaction coordinates for
macromolecular dynamics based on two recently developed mathematical techniques …

Protein folding has been viewed as a difficult problem of molecular self-organization. The
search problem involved in folding however has been simplified through the evolution of …

Coarse-grained models are emerging as a practical alternative to all-atom simulations for
the characterization of protein folding mechanisms over long time scales. While a decade …

Diffusion on a low-dimensional free-energy surface is a remarkably successful model for the
folding dynamics of small single-domain proteins. Complicating the interpretation of both …