Literature DB >> 11289852

Efficient, multiple-range random walk algorithm to calculate the density of states.

F Wang1, D P Landau.   

Abstract

We present a new Monte Carlo algorithm that produces results of high accuracy with reduced simulational effort. Independent random walks are performed (concurrently or serially) in different, restricted ranges of energy, and the resultant density of states is modified continuously to produce locally flat histograms. This method permits us to directly access the free energy and entropy, is independent of temperature, and is efficient for the study of both 1st order and 2nd order phase transitions. It should also be useful for the study of complex systems with a rough energy landscape.

Year:  2001        PMID: 11289852     DOI: 10.1103/PhysRevLett.86.2050

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  162 in total

1.  Configurational temperature density of states simulations of proteins.

Authors:  Nitin Rathore; Thomas A Knotts; Juan J de Pablo
Journal:  Biophys J       Date:  2003-12       Impact factor: 4.033

2.  Escaping free-energy minima.

Authors:  Alessandro Laio; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-23       Impact factor: 11.205

3.  Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS".

Authors:  Ravi Radhakrishnan; Tamar Schlick
Journal:  J Chem Phys       Date:  2004-08-01       Impact factor: 3.488

4.  Re-entrant melting as a design principle for DNA-coated colloids.

Authors:  Stefano Angioletti-Uberti; Bortolo M Mognetti; Daan Frenkel
Journal:  Nat Mater       Date:  2012-04-29       Impact factor: 43.841

5.  Exploring the energy landscapes of protein folding simulations with Bayesian computation.

Authors:  Nikolas S Burkoff; Csilla Várnai; Stephen A Wells; David L Wild
Journal:  Biophys J       Date:  2012-02-21       Impact factor: 4.033

6.  GxxxG motifs, phenylalanine, and cholesterol guide the self-association of transmembrane domains of ErbB2 receptors.

Authors:  Anupam Prakash; Lorant Janosi; Manolis Doxastakis
Journal:  Biophys J       Date:  2011-10-19       Impact factor: 4.033

7.  Isotropic-nematic phase transition in the Lebwohl-Lasher model from density of states simulations.

Authors:  Raj Shekhar; Jonathan K Whitmer; Rohit Malshe; J A Moreno-Razo; Tyler F Roberts; Juan J de Pablo
Journal:  J Chem Phys       Date:  2012-06-21       Impact factor: 3.488

8.  Electric field-driven disruption of a native beta-sheet protein conformation and generation of a helix-structure.

Authors:  Pedro Ojeda-May; Martin E Garcia
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

9.  Generalized replica exchange method.

Authors:  Jaegil Kim; Thomas Keyes; John E Straub
Journal:  J Chem Phys       Date:  2010-06-14       Impact factor: 3.488

10.  Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

Authors:  Xinqiang Ding; Jonah Z Vilseck; Ryan L Hayes; Charles L Brooks
Journal:  J Chem Theory Comput       Date:  2017-05-26       Impact factor: 6.006

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