Liquid Water and Interfacial, Cubic, and Hexagonal Ice Classification through Eclipsed and Staggered Conformation Template Matching

Golnaz Roudsari; Farshad G. Veshki; Bernhard Reischl; Olli H. Pakarinen

doi:10.1021/acs.jpcb.1c01926

Liquid Water and Interfacial, Cubic, and Hexagonal Ice Classification through Eclipsed and Staggered Conformation Template Matching

Golnaz Roudsari^*
, Farshad G. Veshki
, Bernhard Reischl
, Olli H. Pakarinen

^*Tämän työn vastaava kirjoittaja

Sergiy Vorobyov Group

University of Helsinki

Tutkimustuotos: Lehtiartikkeli › Article › Scientific › vertaisarvioitu

8 Sitaatiot (Scopus)

54 Lataukset (Pure)

Abstrakti

We propose a novel method based on template matching for the recognition of liquid water, cubic ice (ice Ic), hexagonal ice (ice Ih), clathrate hydrates, and different interfacial structures in atomistic and coarse-grained simulations of water and ice. The two template matrices represent staggered and eclipsed conformations, which are the building blocks of hexagonal and cubic ice and clathrate crystals. The algorithm is rotationally invariant and highly robust against imperfections in the ice structure, and its sensitivity for recognizing ice-like structures can be tuned for different applications. Unlike most other algorithms, it can discriminate between cubic, hexagonal, clathrate, mixed, and other interfacial ice types and is therefore well suited to study complex systems and heterogeneous ice nucleation.

Alkuperäiskieli	Englanti
Sivut	3909-3917
Sivumäärä	9
Julkaisu	Journal of Physical Chemistry B
Vuosikerta	125
Numero	15
DOI - pysyväislinkit	https://doi.org/10.1021/acs.jpcb.1c01926
Tila	Julkaistu - 22 huhtik. 2021
OKM-julkaisutyyppi	A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä

Rahoitus

This work was supported by the ERC Grant 692891-DAMOCLES, the Academy of Finland Flagship funding (grant no. 337549), the University of Helsinki, Faculty of Science ATMATH project, and the National Center of Meteorology (NCM), Abu Dhabi, UAE, under the UAE Research Program for Rain Enhancement Science. Supercomputing resources were provided by CSC–IT Center for Science, Ltd., Finland. B.R. is grateful to Dr. Stephen Ingram for his advice on setting up the antifreeze protein simulations. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Center of Meteorology, Abu Dhabi, UAE, funder of the research.

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10.1021/acs.jpcb.1c01926

ICEAccepted author manuscript, 12,9 MB

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title = "Liquid Water and Interfacial, Cubic, and Hexagonal Ice Classification through Eclipsed and Staggered Conformation Template Matching",

abstract = "We propose a novel method based on template matching for the recognition of liquid water, cubic ice (ice Ic), hexagonal ice (ice Ih), clathrate hydrates, and different interfacial structures in atomistic and coarse-grained simulations of water and ice. The two template matrices represent staggered and eclipsed conformations, which are the building blocks of hexagonal and cubic ice and clathrate crystals. The algorithm is rotationally invariant and highly robust against imperfections in the ice structure, and its sensitivity for recognizing ice-like structures can be tuned for different applications. Unlike most other algorithms, it can discriminate between cubic, hexagonal, clathrate, mixed, and other interfacial ice types and is therefore well suited to study complex systems and heterogeneous ice nucleation. ",

author = "Golnaz Roudsari and Veshki, \{Farshad G.\} and Bernhard Reischl and Pakarinen, \{Olli H.\}",

note = "Funding Information: This work was supported by the ERC Grant 692891-DAMOCLES, the Academy of Finland Flagship funding (grant no. 337549), the University of Helsinki, Faculty of Science ATMATH project, and the National Center of Meteorology (NCM), Abu Dhabi, UAE, under the UAE Research Program for Rain Enhancement Science. Supercomputing resources were provided by CSC–IT Center for Science, Ltd., Finland. B.R. is grateful to Dr. Stephen Ingram for his advice on setting up the antifreeze protein simulations. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Center of Meteorology, Abu Dhabi, UAE, funder of the research. Publisher Copyright: {\textcopyright} 2021 American Chemical Society. All rights reserved. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

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doi = "10.1021/acs.jpcb.1c01926",

language = "English",

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Liquid Water and Interfacial, Cubic, and Hexagonal Ice Classification through Eclipsed and Staggered Conformation Template Matching. / Roudsari, Golnaz; Veshki, Farshad G.; Reischl, Bernhard et al.
julkaisussa: Journal of Physical Chemistry B, Vuosikerta 125, Nro 15, 22.04.2021, s. 3909-3917.

Tutkimustuotos: Lehtiartikkeli › Article › Scientific › vertaisarvioitu

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AU - Roudsari, Golnaz

AU - Veshki, Farshad G.

AU - Reischl, Bernhard

AU - Pakarinen, Olli H.

N1 - Funding Information: This work was supported by the ERC Grant 692891-DAMOCLES, the Academy of Finland Flagship funding (grant no. 337549), the University of Helsinki, Faculty of Science ATMATH project, and the National Center of Meteorology (NCM), Abu Dhabi, UAE, under the UAE Research Program for Rain Enhancement Science. Supercomputing resources were provided by CSC–IT Center for Science, Ltd., Finland. B.R. is grateful to Dr. Stephen Ingram for his advice on setting up the antifreeze protein simulations. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Center of Meteorology, Abu Dhabi, UAE, funder of the research. Publisher Copyright: © 2021 American Chemical Society. All rights reserved. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/4/22

Y1 - 2021/4/22

N2 - We propose a novel method based on template matching for the recognition of liquid water, cubic ice (ice Ic), hexagonal ice (ice Ih), clathrate hydrates, and different interfacial structures in atomistic and coarse-grained simulations of water and ice. The two template matrices represent staggered and eclipsed conformations, which are the building blocks of hexagonal and cubic ice and clathrate crystals. The algorithm is rotationally invariant and highly robust against imperfections in the ice structure, and its sensitivity for recognizing ice-like structures can be tuned for different applications. Unlike most other algorithms, it can discriminate between cubic, hexagonal, clathrate, mixed, and other interfacial ice types and is therefore well suited to study complex systems and heterogeneous ice nucleation.

AB - We propose a novel method based on template matching for the recognition of liquid water, cubic ice (ice Ic), hexagonal ice (ice Ih), clathrate hydrates, and different interfacial structures in atomistic and coarse-grained simulations of water and ice. The two template matrices represent staggered and eclipsed conformations, which are the building blocks of hexagonal and cubic ice and clathrate crystals. The algorithm is rotationally invariant and highly robust against imperfections in the ice structure, and its sensitivity for recognizing ice-like structures can be tuned for different applications. Unlike most other algorithms, it can discriminate between cubic, hexagonal, clathrate, mixed, and other interfacial ice types and is therefore well suited to study complex systems and heterogeneous ice nucleation.

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JF - Journal of Physical Chemistry B

IS - 15

ER -

Liquid Water and Interfacial, Cubic, and Hexagonal Ice Classification through Eclipsed and Staggered Conformation Template Matching

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