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 …

It has recently become practical to construct Markov state models (MSMs) that reproduce the
long-time statistical conformational dynamics of biomolecules using data from molecular …

Markov (state) models (MSMs) and related models of molecular kinetics have recently
received a surge of interest as they can systematically reconcile simulation data from either …

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

Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding
have long been considered a holy grail of computational biology. Due to the large system …

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

Markov state models provide a framework for understanding the fundamental states and
rates in the conformational dynamics of biomolecules. We describe an improved protocol for …

The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer
operator) contain the essential information about the molecular thermodynamics and …

The slow processes of metastable stochastic dynamical systems are difficult to access by
direct numerical simulation due to the sampling problems. Here, we suggest an approach for …

The statistical analysis of molecular dynamics simulations requires dimensionality reduction
techniques, which yield a low-dimensional set of collective variables (CVs){xi}= x that in …