Literature DB >> 11384401

Mathematical analysis of coupled parallel simulations.

M R Shirts1, V S Pande.   

Abstract

A set of parallel replicas of a single simulation can be statistically coupled to closely approximate long trajectories. In many cases, this produces nearly linear speedup over a single simulation ( M times faster with M simulations), rendering previously intractable problems within reach of large computer clusters. Interestingly, by varying the coupling of the parallel simulations, it is possible in some systems to obtain greater than linear speedup. The methods are generalizable to any search algorithm with long residence times in intermediate states.

Year:  2001        PMID： 11384401     DOI： 10.1103/PhysRevLett.86.4983

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


  27 in total

1.  On the simulation of protein folding by short time scale molecular dynamics and distributed computing.

Authors:  Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2002-10-18       Impact factor: 11.205

2.  The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation.

Authors:  Jun Shimada; Eugene I Shakhnovich
Journal:  Proc Natl Acad Sci U S A       Date:  2002-08-06       Impact factor: 11.205

3.  Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.

Authors:  A Xayaphoummine; T Bucher; F Thalmann; H Isambert
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-15       Impact factor: 11.205

4.  Multiplexed-replica exchange molecular dynamics method for protein folding simulation.

Authors:  Young Min Rhee; Vijay S Pande
Journal:  Biophys J       Date:  2003-02       Impact factor: 4.033

5.  Analysis of the distributed computing approach applied to the folding of a small beta peptide.

Authors:  Emanuele Paci; Andrea Cavalli; Michele Vendruscolo; Amedeo Caflisch
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-18       Impact factor: 11.205

6.  Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations.

Authors:  Eric J Sorin; Young Min Rhee; Bradley J Nakatani; Vijay S Pande
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

7.  Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy.

Authors:  Christopher D Snow; Linlin Qiu; Deguo Du; Feng Gai; Stephen J Hagen; Vijay S Pande
Journal:  Proc Natl Acad Sci U S A       Date:  2004-03-12       Impact factor: 11.205

8.  Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations.

Authors:  G Settanni; J Gsponer; A Caflisch
Journal:  Biophys J       Date:  2004-03       Impact factor: 4.033

9.  Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder.

Authors:  Hui-Hsu Gavin Tsai; Meital Reches; Chung-Jung Tsai; Kannan Gunasekaran; Ehud Gazit; Ruth Nussinov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-27       Impact factor: 11.205

10.  Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding.

Authors:  Yunhui Ge; Elias Borne; Shannon Stewart; Michael R Hansen; Emilia C Arturo; Eileen K Jaffe; Vincent A Voelz
Journal:  J Biol Chem       Date:  2018-10-04       Impact factor: 5.157
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.