Markov state models (MSMs) are a powerful framework for analyzing dynamical systems,
such as molecular dynamics (MD) simulations, that have gained widespread use over the …

Machine learning encompasses tools and algorithms that are now becoming popular in
almost all scientific and technological fields. This is true for molecular dynamics as well …

The development of enhanced sampling methods has greatly extended the scope of
atomistic simulations, allowing long-time phenomena to be studied with accessible …

Identifying a reduced set of collective variables is critical for understanding atomistic
simulations and accelerating them through enhanced sampling techniques. Recently …

Markov state models (MSMs) based on molecular dynamics (MD) simulations are routinely
employed to study protein folding, however, their application to functional conformational …

MSMBuilder is a software package for building statistical models of high-dimensional time-
series data. It is designed with a particular focus on the analysis of atomistic simulations of …

A significant challenge faced by atomistic simulations is the difficulty, and often impossibility,
to sample the transitions between metastable states of the free-energy landscape …

Often the analysis of time-dependent chemical and biophysical systems produces high-
dimensional time-series data for which it can be difficult to interpret which individual features …

Metadynamics is a powerful enhanced molecular dynamics sampling method that
accelerates simulations by adding history-dependent multidimensional Gaussians along …

Markov state models (MSMs) and master equation models are popular approaches to
approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in …