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 …

Metadynamics is an algorithm for accelerating rare events and reconstructing the associated
free energy surface. It works by biasing the evolution of the system by a history‐dependent …

Enhancing sampling and analyzing simulations are central issues in molecular simulation.
Recently, we introduced PLUMED, an open-source plug-in that provides some of the most …

A goal in the kinetic characterization of a macromolecular system is the description of its
slow relaxation processes via (i) identification of the structural changes involved in these …

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

The interaction of phthalic acid esters (PAEs) with DNA is known to be responsible for the
disruption of endocrine functions and the teratogenic and carcinogenic effects. However, the …

The use of free-energy landscapes rationalizes a wide range of aspects of protein behavior
by providing a clear illustration of the different states accessible to these molecules, as well …

Phosphatidylinositol 4, 5-bisphosphate (PI (4, 5) P2) lipids have been shown to stabilize an
active conformation of class A G-protein coupled receptors (GPCRs) through a conserved …

Abstract Na+/Ca2+ exchangers use the Na+ electrochemical gradient across the plasma
membrane to extrude intracellular Ca2+ and play a central role in Ca2+ homeostasis. Here …

Metadynamics is an enhanced sampling algorithm in which the normal evolution of the
system is biased by a history-dependent potential constructed as a sum of Gaussians …