Atom’s Dynamics and Crystal Structure: An Ordinal Pattern Method

Rafał Abram; Roman Nowak; Dariusz Chrobak

doi:10.1021/acs.jpca.4c06151

Atom’s Dynamics and Crystal Structure: An Ordinal Pattern Method

Rafał Abram
, Roman Nowak
, Dariusz Chrobak^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Scientific › peer-review

1 Citation (Scopus)

47 Downloads (Pure)

Abstract

The ubiquitous nature of thermal fluctuations poses a limitation on the identification of crystal structures. However, the trajectory of an atom carries a fingerprint of its surroundings. This rationalizes the search for a method that can determine the local atomic configuration via the analysis of the movement of an individual atom. Here, we report, while using molecular modeling, how a statistical analysis of a single-atom speed trajectory, represented by ordinal patterns, distinguishes between actual crystal structures. Using the Shannon entropy of ordinal patterns enabled discernment of the studied high-pressure silicon phases. Identification of the atoms occupying the 2(c) and 6(f) Wyckoff positions of the r8 crystal revealed an increase in the developed method’s accuracy with trajectory length. The proposed concept of studying the structure of crystals offers new opportunities in solid-solid phase transformation studies.

Original language	English
Pages (from-to)	1136–1142
Journal	Journal of Physical Chemistry A
Volume	129
Issue number	4
Early online date	17 Jan 2025
DOIs	https://doi.org/10.1021/acs.jpca.4c06151
Publication status	Published - 30 Jan 2025
MoE publication type	A1 Journal article-refereed

Funding

Our simulations used resources provided by the CSC-IT Centre for Science, Finland, which we gratefully acknowledge. RN expresses appreciation to Prof. Koichi Niihara (Nagaoka University of Technology), Prof. Tohru Sekino (Osaka University), as well as Prof. Toshihiro Shimada (Hokkaido University) for their long-standing support with computational modeling of ceramics and semiconductors. He thanks for the visiting scholar opportunities, offered by the Institute of Scientific and Industrial Research, Osaka University. DC gratefully acknowledge support from the European Union within the programme “The European Funds for Śląsk (Silesia) 2021-2027” Our simulations used resources provided by the CSC-IT Centre for Science, Finland, which we gratefully acknowledge. RN expresses appreciation to Prof. Koichi Niihara (Nagaoka University of Technology), Prof. Tohru Sekino (Osaka University), as well as Prof. Toshihiro Shimada (Hokkaido University) for their long-standing support with computational modeling of ceramics and semiconductors. He thanks for the visiting scholar opportunities, offered by the Institute of Scientific and Industrial Research, Osaka University. DC gratefully acknowledge support from the European Union within the programme “The European Funds for Śląsk (Silesia) 2021-2027”.

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title = "Atom{\textquoteright}s Dynamics and Crystal Structure: An Ordinal Pattern Method",

abstract = "The ubiquitous nature of thermal fluctuations poses a limitation on the identification of crystal structures. However, the trajectory of an atom carries a fingerprint of its surroundings. This rationalizes the search for a method that can determine the local atomic configuration via the analysis of the movement of an individual atom. Here, we report, while using molecular modeling, how a statistical analysis of a single-atom speed trajectory, represented by ordinal patterns, distinguishes between actual crystal structures. Using the Shannon entropy of ordinal patterns enabled discernment of the studied high-pressure silicon phases. Identification of the atoms occupying the 2(c) and 6(f) Wyckoff positions of the r8 crystal revealed an increase in the developed method{\textquoteright}s accuracy with trajectory length. The proposed concept of studying the structure of crystals offers new opportunities in solid-solid phase transformation studies.",

author = "Rafa{\l} Abram and Roman Nowak and Dariusz Chrobak",

note = "Our simulations used resources provided by the CSC-IT Centre for Science, Finland, which we gratefully acknowledge. RN expresses appreciation to Prof. Koichi Niihara (Nagaoka University of Technology), Prof. Tohru Sekino (Osaka University), as well as Prof. Toshihiro Shimada (Hokkaido University) for their long-standing support with computational modeling of ceramics and semiconductors. He thanks for the visiting scholar opportunities, offered by the Institute of Scientific and Industrial Research, Osaka University. DC gratefully acknowledge support from the European Union within the programme “The European Funds for {\'S}l{\c a}sk (Silesia) 2021-2027”.",

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AU - Abram, Rafał

AU - Nowak, Roman

AU - Chrobak, Dariusz

N1 - Our simulations used resources provided by the CSC-IT Centre for Science, Finland, which we gratefully acknowledge. RN expresses appreciation to Prof. Koichi Niihara (Nagaoka University of Technology), Prof. Tohru Sekino (Osaka University), as well as Prof. Toshihiro Shimada (Hokkaido University) for their long-standing support with computational modeling of ceramics and semiconductors. He thanks for the visiting scholar opportunities, offered by the Institute of Scientific and Industrial Research, Osaka University. DC gratefully acknowledge support from the European Union within the programme “The European Funds for Śląsk (Silesia) 2021-2027”.

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N2 - The ubiquitous nature of thermal fluctuations poses a limitation on the identification of crystal structures. However, the trajectory of an atom carries a fingerprint of its surroundings. This rationalizes the search for a method that can determine the local atomic configuration via the analysis of the movement of an individual atom. Here, we report, while using molecular modeling, how a statistical analysis of a single-atom speed trajectory, represented by ordinal patterns, distinguishes between actual crystal structures. Using the Shannon entropy of ordinal patterns enabled discernment of the studied high-pressure silicon phases. Identification of the atoms occupying the 2(c) and 6(f) Wyckoff positions of the r8 crystal revealed an increase in the developed method’s accuracy with trajectory length. The proposed concept of studying the structure of crystals offers new opportunities in solid-solid phase transformation studies.

AB - The ubiquitous nature of thermal fluctuations poses a limitation on the identification of crystal structures. However, the trajectory of an atom carries a fingerprint of its surroundings. This rationalizes the search for a method that can determine the local atomic configuration via the analysis of the movement of an individual atom. Here, we report, while using molecular modeling, how a statistical analysis of a single-atom speed trajectory, represented by ordinal patterns, distinguishes between actual crystal structures. Using the Shannon entropy of ordinal patterns enabled discernment of the studied high-pressure silicon phases. Identification of the atoms occupying the 2(c) and 6(f) Wyckoff positions of the r8 crystal revealed an increase in the developed method’s accuracy with trajectory length. The proposed concept of studying the structure of crystals offers new opportunities in solid-solid phase transformation studies.

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SP - 1136

EP - 1142

JO - Journal of Physical Chemistry A

JF - Journal of Physical Chemistry A

IS - 4

ER -

Atom’s Dynamics and Crystal Structure: An Ordinal Pattern Method

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