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 …

Dynamical reweighting techniques aim to recover the correct molecular dynamics from a
simulation at a modified potential energy surface. They are important for unbiasing …

Simulations of biomolecules have enormous potential to inform our understanding of biology
but require extremely demanding calculations. For over 20 years, the Folding@ home …

Variational autoencoder frameworks have demonstrated success in reducing complex
nonlinear dynamics in molecular simulation to a single nonlinear embedding. In this work …

Ever since Clausius in 1865 and Boltzmann in 1877, the concepts of entropy and of its
maximization have been the foundations for predicting how material equilibria derive from …

We review here Maximum Caliber (Max Cal), a general variational principle for inferring
distributions of paths in dynamical processes and networks. Max Cal is to dynamical …

The modeling of atomistic biomolecular simulations using kinetic models such as Markov
state models (MSMs) has had many notable algorithmic advances in recent years. The …

In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM)
methodologies have made possible accurate and efficient estimation of kinetic rates and …

Kinases are ubiquitous enzymes involved in the regulation of critical cellular pathways.
However, in silico modelling of the conformational ensembles of these enzymes is difficult …

This review discusses successful strategies and key open problems in the kinetic and
thermodynamic characterization of complex biomolecular systems by computer simulations …