Detection of Anomalous Dynamics for a Single Water Molecule

Katsufumi Tomobe, Kenji Yasuoka

Research output: Contribution to journalArticle

Abstract

Water dynamics is of predominant importance in life, and it plays a critical role in chemical and biological systems. Many studies have reported nonbulk and anomalous dynamics of water molecules; however, a general method to detect the anomalous dynamics is yet to be established. Here, we develop a detection approach for the anomalous dynamics of a water molecule. Using a time series of the dipole vector of a water molecule, our approach achieves single-molecule detection of the anomalous dynamics for all water molecules in the system. Moreover, our approach quantifies the anomalous dynamics of a water molecule, which enables users to compare between different systems. In addition to the applicability, our approach has computational efficiency because it never calculates interactions with any other molecules. Experiments on five different systems of molecular dynamics simulations illustrate that our approach successfully detects the change points of water-molecule dynamics. These results demonstrate that our approach is a useful tool and provides a better understanding of dynamics of water molecules.

Original languageEnglish
Pages (from-to)1177-1185
Number of pages9
JournalJournal of Chemical Theory and Computation
Volume14
Issue number3
DOIs
Publication statusPublished - 2018 Mar 13

Fingerprint

Molecules
Water
water
molecules
Biological systems
Computational efficiency
Molecular dynamics
Time series
dipoles
molecular dynamics
Computer simulation
simulation
Experiments
interactions

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Detection of Anomalous Dynamics for a Single Water Molecule. / Tomobe, Katsufumi; Yasuoka, Kenji.

In: Journal of Chemical Theory and Computation, Vol. 14, No. 3, 13.03.2018, p. 1177-1185.

Research output: Contribution to journalArticle

@article{ec712bb0578447a98e0bbe910eb84183,
title = "Detection of Anomalous Dynamics for a Single Water Molecule",
abstract = "Water dynamics is of predominant importance in life, and it plays a critical role in chemical and biological systems. Many studies have reported nonbulk and anomalous dynamics of water molecules; however, a general method to detect the anomalous dynamics is yet to be established. Here, we develop a detection approach for the anomalous dynamics of a water molecule. Using a time series of the dipole vector of a water molecule, our approach achieves single-molecule detection of the anomalous dynamics for all water molecules in the system. Moreover, our approach quantifies the anomalous dynamics of a water molecule, which enables users to compare between different systems. In addition to the applicability, our approach has computational efficiency because it never calculates interactions with any other molecules. Experiments on five different systems of molecular dynamics simulations illustrate that our approach successfully detects the change points of water-molecule dynamics. These results demonstrate that our approach is a useful tool and provides a better understanding of dynamics of water molecules.",
author = "Katsufumi Tomobe and Kenji Yasuoka",
year = "2018",
month = "3",
day = "13",
doi = "10.1021/acs.jctc.7b01104",
language = "English",
volume = "14",
pages = "1177--1185",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "American Chemical Society",
number = "3",

}

TY - JOUR

T1 - Detection of Anomalous Dynamics for a Single Water Molecule

AU - Tomobe, Katsufumi

AU - Yasuoka, Kenji

PY - 2018/3/13

Y1 - 2018/3/13

N2 - Water dynamics is of predominant importance in life, and it plays a critical role in chemical and biological systems. Many studies have reported nonbulk and anomalous dynamics of water molecules; however, a general method to detect the anomalous dynamics is yet to be established. Here, we develop a detection approach for the anomalous dynamics of a water molecule. Using a time series of the dipole vector of a water molecule, our approach achieves single-molecule detection of the anomalous dynamics for all water molecules in the system. Moreover, our approach quantifies the anomalous dynamics of a water molecule, which enables users to compare between different systems. In addition to the applicability, our approach has computational efficiency because it never calculates interactions with any other molecules. Experiments on five different systems of molecular dynamics simulations illustrate that our approach successfully detects the change points of water-molecule dynamics. These results demonstrate that our approach is a useful tool and provides a better understanding of dynamics of water molecules.

AB - Water dynamics is of predominant importance in life, and it plays a critical role in chemical and biological systems. Many studies have reported nonbulk and anomalous dynamics of water molecules; however, a general method to detect the anomalous dynamics is yet to be established. Here, we develop a detection approach for the anomalous dynamics of a water molecule. Using a time series of the dipole vector of a water molecule, our approach achieves single-molecule detection of the anomalous dynamics for all water molecules in the system. Moreover, our approach quantifies the anomalous dynamics of a water molecule, which enables users to compare between different systems. In addition to the applicability, our approach has computational efficiency because it never calculates interactions with any other molecules. Experiments on five different systems of molecular dynamics simulations illustrate that our approach successfully detects the change points of water-molecule dynamics. These results demonstrate that our approach is a useful tool and provides a better understanding of dynamics of water molecules.

UR - http://www.scopus.com/inward/record.url?scp=85044001261&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85044001261&partnerID=8YFLogxK

U2 - 10.1021/acs.jctc.7b01104

DO - 10.1021/acs.jctc.7b01104

M3 - Article

VL - 14

SP - 1177

EP - 1185

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 3

ER -