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 …

Metadynamics is an atomistic simulation technique that allows, within the same framework,
acceleration of rare events and estimation of the free energy of complex molecular systems …

This Review illustrates the evaluation of permeability of lipid membranes from molecular
dynamics (MD) simulation primarily using water and oxygen as examples. Membrane …

Metadynamics is an enhanced sampling method of great popularity, based on the on-the-fly
construction of a bias potential that is a function of a selected number of collective variables …

Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …

In adaptive-bias enhanced sampling methods, a bias potential is added to the system to
drive transitions between metastable states. The bias potential is a function of a few …

Proteins are dynamic molecules that can transition between a potentially wide range of
structures comprising their conformational ensemble. The nature of these conformations and …

Molecular simulations are commonly used to understand the mechanism of membrane
permeation of small molecules, particularly for biomedical and pharmaceutical applications …

Lipid droplet (LD) formation from the endoplasmic reticulum (ER) is accompanied by the
targeting and accumulation of specific hydrophobic, membrane-embedded proteins on LDs …

Performing alchemical transformations, in which one molecular system is nonphysically
changed to another system, is a popular approach adopted in performing free energy …