This Review explores the dynamic behavior of water within nanopores and biological
channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside …

It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions,
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …

Chemical surfactants are omnipresent in consumer products, but they are the subject of
environmental concerns. For this reason, the complete replacement of petrochemical …

The goal of the present manuscript is to succinctly trace the key technological steps in the
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …

The binding free energy calculation of protein–ligand complexes is necessary for research
into virus–host interactions and the relevant applications in drug discovery. However, many …

Divalent metal ions play important roles in biological and materials systems. Molecular
dynamics simulation is an efficient tool to investigate these systems at the microscopic level …

Accurate modeling of the solvent environment for biological molecules is crucial for
computational biology and drug design. A popular approach to achieve long simulation time …

Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP)
remain a challenge: widely used,“general purpose” water models tend to favor overly …