Parallel tempering: Theory, applications, and new perspectives

DJ Earl, MW Deem - Physical Chemistry Chemical Physics, 2005 - pubs.rsc.org
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 …

Generalized‐ensemble algorithms for molecular simulations of biopolymers

A Mitsutake, Y Sugita, Y Okamoto - Peptide Science: Original …, 2001 - Wiley Online Library
In complex systems with many degrees of freedom such as peptides and proteins, there
exists a huge number of local‐minimum‐energy states. Conventional simulations in the …

Random heteropolymers preserve protein function in foreign environments

B Panganiban, B Qiao, T Jiang, C DelRe, MM Obadia… - Science, 2018 - science.org
The successful incorporation of active proteins into synthetic polymers could lead to a new
class of materials with functions found only in living systems. However, proteins rarely …

Equilibration of long chain polymer melts in computer simulations

R Auhl, R Everaers, GS Grest, K Kremer… - The Journal of chemical …, 2003 - pubs.aip.org
Several methods for preparing well equilibrated melts of long chains polymers are studied.
We show that the standard method in which one starts with an ensemble of chains with the …

ESPResSo—an extensible simulation package for research on soft matter systems

HJ Limbach, A Arnold, BA Mann, C Holm - Computer Physics …, 2006 - Elsevier
We describe a new program package that is designed to perform numerical Molecular
Dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in …

[HTML][HTML] Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their …

A Bunker, A Magarkar, T Viitala - Biochimica et Biophysica Acta (BBA) …, 2016 - Elsevier
Combined experimental and computational studies of lipid membranes and liposomes, with
the aim to attain mechanistic understanding, result in a synergy that makes possible the …

Molecular dynamics simulations of glassy polymers

JL Barrat, J Baschnagel, A Lyulin - Soft Matter, 2010 - pubs.rsc.org
We review recent results from computer simulation studies of polymer glasses, from the
chain dynamics around the glass transition temperature Tg to the mechanical behaviour …

Computer simulations of supercooled polymer melts in the bulk and in confinedgeometry

J Baschnagel, F Varnik - Journal of Physics: Condensed Matter, 2005 - iopscience.iop.org
We survey results of computer simulations for the structure and dynamics of supercooled
polymer melts and films. Our survey is mainly concerned with features of a coarse grained …

Ductile-to-brittle transition and yielding in soft amorphous materials: perspectives and open questions

T Divoux, E Agoritsas, S Aime, C Barentin, JL Barrat… - Soft Matter, 2024 - pubs.rsc.org
Soft amorphous materials are viscoelastic solids ubiquitously found around us, from clays
and cementitious pastes to emulsions and physical gels encountered in food or biomedical …

Extended ensemble monte carlo

Y Iba - International Journal of Modern Physics C, 2001 - World Scientific
" Extended Ensemble Monte Carlo" is a generic term that indicates a set of algorithms, which
are now popular in a variety of fields in physics and statistical information processing …