Literature DB >> 20550390

Generalized replica exchange method.

Jaegil Kim1, Thomas Keyes, John E Straub.   

Abstract

We present a powerful replica exchange method, particularly suited to first-order phase transitions associated with the backbending in the statistical temperature, by merging an optimally designed generalized ensemble sampling with replica exchanges. The key ingredients of our method are parametrized effective sampling weights, smoothly joining ordered and disordered phases with a succession of unimodal energy distributions by transforming unstable or metastable energy states of canonical ensembles into stable ones. The inverse mapping between the sampling weight and the effective temperature provides a systematic way to design the effective sampling weights and determine a dynamic range of relevant parameters. Illustrative simulations on Potts spins with varying system size and simulation conditions demonstrate a comprehensive sampling for phase-coexistent states with a dramatic acceleration of tunneling transitions. A significant improvement over the power-law slowing down of mean tunneling times with increasing system size is obtained, and the underlying mechanism for accelerated tunneling is discussed.

Entities:  

Mesh:

Year:  2010        PMID: 20550390      PMCID: PMC2896417          DOI: 10.1063/1.3432176

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  46 in total

1.  Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram.

Authors:  F Wang; D P Landau
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2001-10-17

2.  Replica-exchange method using the generalized effective potential.

Authors:  Soonmin Jang; Seokmin Shin; Youngshang Pak
Journal:  Phys Rev Lett       Date:  2003-08-01       Impact factor: 9.161

3.  Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights.

Authors:  Jae Gil Kim; Yoshifumi Fukunishi; Akinori Kidera; Haruki Nakamura
Journal:  J Chem Phys       Date:  2004-09-22       Impact factor: 3.488

4.  Microcanonical replica exchange molecular dynamics simulation of proteins.

Authors:  Parimal Kar; Walter Nadler; Ulrich H E Hansmann
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-11-18

5.  Optimized parallel tempering simulations of proteins.

Authors:  Simon Trebst; Matthias Troyer; Ulrich H E Hansmann
Journal:  J Chem Phys       Date:  2006-05-07       Impact factor: 3.488

6.  Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.

Authors:  Pu Liu; Xuhui Huang; Ruhong Zhou; B J Berne
Journal:  J Phys Chem B       Date:  2006-09-28       Impact factor: 2.991

7.  Resolution exchange simulation.

Authors:  Edward Lyman; F Marty Ytreberg; Daniel M Zuckerman
Journal:  Phys Rev Lett       Date:  2006-01-18       Impact factor: 9.161

8.  Relationship between protein folding thermodynamics and the energy landscape.

Authors:  Jaegil Kim; Thomas Keyes; John E Straub
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-03-04

9.  Microcanonical versus canonical analysis of protein folding.

Authors:  J Hernández-Rojas; J M Gomez Llorente
Journal:  Phys Rev Lett       Date:  2008-06-25       Impact factor: 9.161

Review 10.  Parallel tempering: theory, applications, and new perspectives.

Authors:  David J Earl; Michael W Deem
Journal:  Phys Chem Chem Phys       Date:  2005-12-07       Impact factor: 3.676

View more
  16 in total

1.  Generalized simulated tempering for exploring strong phase transitions.

Authors:  Jaegil Kim; John E Straub
Journal:  J Chem Phys       Date:  2010-10-21       Impact factor: 3.488

2.  Enhanced sampling and applications in protein folding in explicit solvent.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2010-06-28       Impact factor: 3.488

3.  Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables.

Authors:  Jaegil Kim; Thomas Keyes; John E Straub
Journal:  J Chem Phys       Date:  2011-08-14       Impact factor: 3.488

4.  Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

Authors:  Emilio Gallicchio; Junchao Xia; William F Flynn; Baofeng Zhang; Sade Samlalsingh; Ahmet Mentes; Ronald M Levy
Journal:  Comput Phys Commun       Date:  2015-11       Impact factor: 4.390

5.  Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.

Authors:  Xiongwu Wu; Milan Hodoscek; Bernard R Brooks
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

6.  Parallel continuous simulated tempering and its applications in large-scale molecular simulations.

Authors:  Tianwu Zang; Linglin Yu; Chong Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2014-07-28       Impact factor: 3.488

7.  Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.

Authors:  Junichi Higo; Jinzen Ikebe; Narutoshi Kamiya; Haruki Nakamura
Journal:  Biophys Rev       Date:  2012-01-11

8.  Optimal updating magnitude in adaptive flat-distribution sampling.

Authors:  Cheng Zhang; Justin A Drake; Jianpeng Ma; B Montgomery Pettitt
Journal:  J Chem Phys       Date:  2017-11-07       Impact factor: 3.488

9.  From data to noise to data for mixing physics across temperatures with generative artificial intelligence.

Authors:  Yihang Wang; Lukas Herron; Pratyush Tiwary
Journal:  Proc Natl Acad Sci U S A       Date:  2022-08-04       Impact factor: 12.779

10.  Using a sequence-specific coarse-grained model for studying protein liquid-liquid phase separation.

Authors:  Roshan Mammen Regy; Wenwei Zheng; Jeetain Mittal
Journal:  Methods Enzymol       Date:  2020-08-17       Impact factor: 1.600

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.