Literature DB >> 20701382

Efficient sampling of atomic configurational spaces.

Lívia B Pártay1, Albert P Bartók, Gábor Csányi.   

Abstract

We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling (AIP Conf. Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833) and allows us to explore the entire potential energy surface (PES) efficiently in an unbiased way. The algorithm has two parameters which directly control the trade-off between the resolution with which the space is explored and the computational cost. We demonstrate the use of nested sampling on Lennard-Jones (LJ) clusters. Nested sampling provides a straightforward approximation for the partition function; thus, evaluating expectation values of arbitrary smooth operators at arbitrary temperatures becomes a simple postprocessing step. Access to absolute free energies allows us to determine the temperature-density phase diagram for LJ cluster stability. Even for relatively small clusters, the efficiency gain over parallel tempering in calculating the heat capacity is an order of magnitude or more. Furthermore, by analyzing the topology of the resulting samples, we are able to visualize the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and suprabasins of the PES, allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.

Entities:  

Year:  2010        PMID: 20701382     DOI: 10.1021/jp1012973

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  5 in total

1.  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

2.  Mean Shift Cluster Recognition Method Implementation in the Nested Sampling Algorithm.

Authors:  Martino Trassinelli; Pierre Ciccodicola
Journal:  Entropy (Basel)       Date:  2020-02-06       Impact factor: 2.524

3.  Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.

Authors:  John A Keith; Valentin Vassilev-Galindo; Bingqing Cheng; Stefan Chmiela; Michael Gastegger; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 60.622

4.  Bayesian model comparison and parameter inference in systems biology using nested sampling.

Authors:  Nick Pullen; Richard J Morris
Journal:  PLoS One       Date:  2014-02-11       Impact factor: 3.240

5.  Thermodynamics of CuPt nanoalloys.

Authors:  K Rossi; L B Pártay; G Csányi; F Baletto
Journal:  Sci Rep       Date:  2018-06-14       Impact factor: 4.379

  5 in total

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