Parallel tempering: Theory, applications, and new perspectives
We review the history of the parallel tempering simulation method. From its origins in data
analysis, the parallel tempering method has become a standard workhorse of …
analysis, the parallel tempering method has become a standard workhorse of …
Effects of confinement on freezing and melting
We present a review of experimental, theoretical, and molecular simulation studies of
confinement effects on freezing and melting. We consider both simple and more complex …
confinement effects on freezing and melting. We consider both simple and more complex …
On the inner workings of Monte Carlo codes
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 …
properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as …
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
Y Okamoto - Journal of Molecular Graphics and Modelling, 2004 - Elsevier
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 …
systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity …
Optimal allocation of replicas in parallel tempering simulations
N Rathore, M Chopra, JJ de Pablo - The Journal of chemical physics, 2005 - pubs.aip.org
We have studied the efficiency of parallel tempering simulations for a variety of systems
including a coarse-grained protein, an atomistic model polypeptide, and the Lennard-Jones …
including a coarse-grained protein, an atomistic model polypeptide, and the Lennard-Jones …
On the acceptance probability of replica-exchange Monte Carlo trials
DA Kofke - The Journal of chemical physics, 2002 - pubs.aip.org
An analysis is presented of the average probability of accepting an exchange trial in the
parallel-tempering Monte Carlo molecular simulation method. Arguments are given that this …
parallel-tempering Monte Carlo molecular simulation method. Arguments are given that this …
Coarse-grained simulations of macromolecules: from DNA to nanocomposites
JJ de Pablo - Annual review of physical chemistry, 2011 - annualreviews.org
This review discusses multiscale modeling and simulations of macromolecules and
macromolecular systems in the context of two specific examples. In the first, recent attempts …
macromolecular systems in the context of two specific examples. In the first, recent attempts …
The Monte Carlo method in science and engineering
JG Amar - Computing in science & engineering, 2006 - ieeexplore.ieee.org
Since 1953, researchers have applied the Monte Carlo method to a wide range of areas.
Specialized algorithms have also been developed to extend the method's applicability and …
Specialized algorithms have also been developed to extend the method's applicability and …
A bidimensional fluid system with competing interactions: spontaneous and induced pattern formation
A Imperio, L Reatto - Journal of physics: Condensed matter, 2004 - iopscience.iop.org
In this paper we present a study of pattern formation in bidimensional systems with
competing short-range attractive and long-range repulsive interactions. The interaction …
competing short-range attractive and long-range repulsive interactions. The interaction …
Microphase separation in two-dimensional systems with competing interactions
A Imperio, L Reatto - The Journal of chemical physics, 2006 - pubs.aip.org
The formation of clusters in condition of thermodynamic equilibrium can be easily observed
both in two and three dimensions. In two dimensions relevant cases include pattern …
both in two and three dimensions. In two dimensions relevant cases include pattern …