Literature DB >> 28634292

Monte Carlo sampling for stochastic weight functions.

Daan Frenkel1, K Julian Schrenk2, Stefano Martiniani2.   

Abstract

Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here, we consider the case that the weight determining the acceptance probability itself is fluctuating. This situation is common in many numerical studies. We show that it is possible to construct a rigorous Monte Carlo algorithm that visits points in state space with a probability proportional to their average weight. The same approach may have applications for certain classes of high-throughput experiments and the analysis of noisy datasets.

Keywords:  Monte Carlo simulations; basin volumes; free-energy calculation; stochastic optimization; transition state

Year:  2017        PMID: 28634292      PMCID: PMC5502596          DOI: 10.1073/pnas.1620497114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  7 in total

1.  Parallel excluded volume tempering for polymer melts.

Authors:  A Bunker; B Dünweg
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2000-12-22

2.  Turning intractable counting into sampling: Computing the configurational entropy of three-dimensional jammed packings.

Authors:  Stefano Martiniani; K Julian Schrenk; Jacob D Stevenson; David J Wales; Daan Frenkel
Journal:  Phys Rev E       Date:  2016-01-25       Impact factor: 2.529

3.  Speed-up of Monte Carlo simulations by sampling of rejected states.

Authors:  Daan Frenkel
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-10       Impact factor: 11.205

4.  Statistically optimal analysis of samples from multiple equilibrium states.

Authors:  Michael R Shirts; John D Chodera
Journal:  J Chem Phys       Date:  2008-09-28       Impact factor: 3.488

5.  Direct determination of the size of basins of attraction of jammed solids.

Authors:  Ning Xu; Daan Frenkel; Andrea J Liu
Journal:  Phys Rev Lett       Date:  2011-06-17       Impact factor: 9.161

6.  Structural analysis of high-dimensional basins of attraction.

Authors:  Stefano Martiniani; K Julian Schrenk; Jacob D Stevenson; David J Wales; Daan Frenkel
Journal:  Phys Rev E       Date:  2016-09-15       Impact factor: 2.529

7.  Numerical calculation of granular entropy.

Authors:  Daniel Asenjo; Fabien Paillusson; Daan Frenkel
Journal:  Phys Rev Lett       Date:  2014-03-05       Impact factor: 9.161

  7 in total

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