Single-molecule force spectroscopy with the atomic force microscope provides molecular
level insights into protein function, allowing researchers to reconstruct energy landscapes …

With the advent of faster computer processors and especially graphics processing units
(GPUs) over the last few decades, the use of data-intensive machine learning (ML) and …

Protein folding occurs as a set of transitions between structural states within an energy
landscape. An oversimplified view of the folding process emerges when transiently …

To meet the challenge of modeling the conformational dynamics of biological
macromolecules over long time scales, much recent effort has been devoted to constructing …

We construct coarse master equations for peptide folding dynamics from atomistic molecular
dynamics simulations. A maximum-likelihood propagator-based method allows us to extract …

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 …

The definition of reaction coordinates for the characterization of a protein-folding reaction
has long been a controversial issue, even for the “simple” case in which one single free …

A method for obtaining appropriate reaction coordinates is required to identify transition
states distinguishing the product and reactant in complex molecular systems. Recently …

Reducing the complexity of large systems described as complex networks is key to
understanding them and a crucial issue is to know which properties of the initial system are …

Reaction coordinates are widely used throughout chemical physics to model and
understand complex chemical transformations. We introduce a definition of the natural …