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 …

Molecular simulation allows researchers unique insight into the structures and interactions
at play in fluids. Since publication of the first edition of Molecular Simulation of Fluids, novel …

In complex systems with many degrees of freedom such as spin glass and biomolecular
systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity …

Alzheimer's disease is understood to be caused by amyloid fibrils and oligomers formed by
aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) …

A multibaric‐multithermal molecular dynamics (MD) simulation of a 10‐residue protein,
chignolin, was performed. All‐atom model with the Amber parm99SB force field was used for …

We propose a new method for molecular dynamics and Monte Carlo simulations, which is
referred to as the replica-permutation method (RPM), to realize more efficient sampling than …

We present a method for performing multithermal-multibaric molecular dynamics simulations
that sample entire regions of the temperature-pressure (TP) phase diagram. The method …

In biomolecular systems (especially all-atom models) with many degrees of freedom such as
proteins and nucleic acids, there exist an astronomically large number of local-minimum …

We applied the multibaric− multithermal (MUBATH) molecular dynamics (MD) algorithm to
an alanine dipeptide in explicit water. The MUBATH MD simulation covered a wide range of …

We give general formulations of the multidimensional multicanonical algorithm, simulated
tempering, and replica-exchange method. We generalize the original potential energy …