Enhanced sampling methods for molecular dynamics simulations

J Hénin, T Lelièvre, MR Shirts, O Valsson… - arXiv preprint arXiv …, 2022 - arxiv.org
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 …

Thermodynamically driven assemblies and liquid–liquid phase separations in biology

H Falahati, A Haji-Akbari - Soft matter, 2019 - pubs.rsc.org
The sustenance of life depends on the high degree of organization that prevails through
different levels of living organisms, from subcellular structures such as biomolecular …

Modeling and simulations of polymers: a roadmap

TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …

Signatures of a liquid–liquid transition in an ab initio deep neural network model for water

TE Gartner III, L Zhang, PM Piaggi… - Proceedings of the …, 2020 - National Acad Sciences
The possible existence of a metastable liquid–liquid transition (LLT) and a corresponding
liquid–liquid critical point (LLCP) in supercooled liquid water remains a topic of much …

On the inner workings of Monte Carlo codes

D Dubbeldam, A Torres-Knoop, KS Walton - Molecular Simulation, 2013 - Taylor & Francis
We review state-of-the-art Monte Carlo (MC) techniques for computing fluid coexistence
properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as …

Adaptive biasing force method for scalar and vector free energy calculations

E Darve, D Rodríguez-Gómez… - The Journal of chemical …, 2008 - pubs.aip.org
In free energy calculations based on thermodynamic integration, it is necessary to compute
the derivatives of the free energy as a function of one (scalar case) or several (vector case) …

A new approach to Monte Carlo simulations in statistical physics: Wang-Landau sampling

DP Landau, SH Tsai, M Exler - American Journal of Physics, 2004 - pubs.aip.org
We describe a Monte Carlo algorithm for doing simulations in classical statistical physics in
a different way. Instead of sampling the probability distribution at a fixed temperature, a …

Direct calculation of liquid–vapor phase equilibria from transition matrix Monte Carlo simulation

JR Errington - The Journal of chemical physics, 2003 - pubs.aip.org
An approach for directly determining the liquid–vapor phase equilibrium of a model system
at any temperature along the coexistence line is described. The method relies on transition …

[HTML][HTML] Phase diagrams—Why they matter and how to predict them

PY Chew, A Reinhardt - The Journal of Chemical Physics, 2023 - pubs.aip.org
Understanding the thermodynamic stability and metastability of materials can help us to, for
example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to …

Fast algorithm to calculate density of states

RE Belardinelli, VD Pereyra - Physical Review E—Statistical, Nonlinear, and …, 2007 - APS
An algorithm to calculate the density of states, based on the well-known Wang-Landau
method, is introduced. Independent random walks are performed in different restricted …