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Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements
Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5713141/ https://www.ncbi.nlm.nih.gov/pubmed/29217989 http://dx.doi.org/10.1107/S1600576717013292 |
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author | Anada, Masato Nakanishi-Ohno, Yoshinori Okada, Masato Kimura, Tsuyoshi Wakabayashi, Yusuke |
author_facet | Anada, Masato Nakanishi-Ohno, Yoshinori Okada, Masato Kimura, Tsuyoshi Wakabayashi, Yusuke |
author_sort | Anada, Masato |
collection | PubMed |
description | Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes’ theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO(3) film fabricated on top of SrTiO(3). The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites. |
format | Online Article Text |
id | pubmed-5713141 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-57131412017-12-07 Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements Anada, Masato Nakanishi-Ohno, Yoshinori Okada, Masato Kimura, Tsuyoshi Wakabayashi, Yusuke J Appl Crystallogr Research Papers Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes’ theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO(3) film fabricated on top of SrTiO(3). The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites. International Union of Crystallography 2017-10-20 /pmc/articles/PMC5713141/ /pubmed/29217989 http://dx.doi.org/10.1107/S1600576717013292 Text en © Masato Anada et al. 2017 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/2.0/uk/ |
spellingShingle | Research Papers Anada, Masato Nakanishi-Ohno, Yoshinori Okada, Masato Kimura, Tsuyoshi Wakabayashi, Yusuke Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements |
title | Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements |
title_full | Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements |
title_fullStr | Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements |
title_full_unstemmed | Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements |
title_short | Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements |
title_sort | bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5713141/ https://www.ncbi.nlm.nih.gov/pubmed/29217989 http://dx.doi.org/10.1107/S1600576717013292 |
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