Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Unsupervised learning is becoming an essential tool to analyze the increasingly large
amounts of data produced by atomistic and molecular simulations, in material science, solid …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

Cluster analysis is aimed at classifying elements into categories on the basis of their
similarity. Its applications range from astronomy to bioinformatics, bibliometrics, and pattern …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

Highlights•Liquid-liquid phase separation underlies the formation of membraneless
organelles within cells.•Theory and molecular simulations help to relate interactions at the …

Metadynamics is a powerful technique for enhancing sampling in molecular dynamics
simulations and reconstructing the free‐energy surface as a function of few selected …

Metadynamics is a commonly used and successful enhanced sampling method. By the
introduction of a history dependent bias which depends on a restricted number of collective …

Molecular permeation through lipid membranes is a fundamental biological process that is
important for small neutral molecules and drug molecules. Precise characterization of free …