Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations

Abstract In this work, we present the bond order redefinition needed to reduce the inherent noise in order to enhance the accuracy of molecular dynamics simulations. We propose defining the bond order as a fraction of energy distribution. It happens due to the character of the material in nature, wh...

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Autores principales:	Ibnu Syuhada, Nikodemus Umbu Janga Hauwali, Ahmad Rosikhin, Euis Sustini, Fatimah Arofiati Noor, Toto Winata
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ef4b0430231c4cb79ad1a8e2eb3688d7
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spelling	oai:doaj.org-article:ef4b0430231c4cb79ad1a8e2eb3688d72021-12-02T14:26:47ZBond order redefinition needed to reduce inherent noise in molecular dynamics simulations10.1038/s41598-020-80217-02045-2322https://doaj.org/article/ef4b0430231c4cb79ad1a8e2eb3688d72021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80217-0https://doaj.org/toc/2045-2322Abstract In this work, we present the bond order redefinition needed to reduce the inherent noise in order to enhance the accuracy of molecular dynamics simulations. We propose defining the bond order as a fraction of energy distribution. It happens due to the character of the material in nature, which tries to maintain its environment. To show the necessity, we developed a factory empirical interatomic potential (FEIP) for carbon that implements the redefinition with a short-range interaction approach. FEIP has been shown to enhance the accuracy of the calculation of lattice constants, cohesive energy, elastic properties, and phonons compared to experimental data, and can even be compared to other potentials with the long-range interaction approach. The enhancements due to FEIP can reduce the inherent noise, then provide a better prediction of the energy based on the behaviour of the atomic environment. FEIP can also transform simple two-body interactions into many-body interactions, which is useful for enhancing accuracy. Due to implementing the bond order redefinition, FEIP offers faster calculations than other complex interatomic potentials.Ibnu SyuhadaNikodemus Umbu Janga HauwaliAhmad RosikhinEuis SustiniFatimah Arofiati NoorToto WinataNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ibnu Syuhada Nikodemus Umbu Janga Hauwali Ahmad Rosikhin Euis Sustini Fatimah Arofiati Noor Toto Winata Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
description	Abstract In this work, we present the bond order redefinition needed to reduce the inherent noise in order to enhance the accuracy of molecular dynamics simulations. We propose defining the bond order as a fraction of energy distribution. It happens due to the character of the material in nature, which tries to maintain its environment. To show the necessity, we developed a factory empirical interatomic potential (FEIP) for carbon that implements the redefinition with a short-range interaction approach. FEIP has been shown to enhance the accuracy of the calculation of lattice constants, cohesive energy, elastic properties, and phonons compared to experimental data, and can even be compared to other potentials with the long-range interaction approach. The enhancements due to FEIP can reduce the inherent noise, then provide a better prediction of the energy based on the behaviour of the atomic environment. FEIP can also transform simple two-body interactions into many-body interactions, which is useful for enhancing accuracy. Due to implementing the bond order redefinition, FEIP offers faster calculations than other complex interatomic potentials.
format	article
author	Ibnu Syuhada Nikodemus Umbu Janga Hauwali Ahmad Rosikhin Euis Sustini Fatimah Arofiati Noor Toto Winata
author_facet	Ibnu Syuhada Nikodemus Umbu Janga Hauwali Ahmad Rosikhin Euis Sustini Fatimah Arofiati Noor Toto Winata
author_sort	Ibnu Syuhada
title	Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
title_short	Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
title_full	Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
title_fullStr	Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
title_full_unstemmed	Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
title_sort	bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ef4b0430231c4cb79ad1a8e2eb3688d7
work_keys_str_mv	AT ibnusyuhada bondorderredefinitionneededtoreduceinherentnoiseinmoleculardynamicssimulations AT nikodemusumbujangahauwali bondorderredefinitionneededtoreduceinherentnoiseinmoleculardynamicssimulations AT ahmadrosikhin bondorderredefinitionneededtoreduceinherentnoiseinmoleculardynamicssimulations AT euissustini bondorderredefinitionneededtoreduceinherentnoiseinmoleculardynamicssimulations AT fatimaharofiatinoor bondorderredefinitionneededtoreduceinherentnoiseinmoleculardynamicssimulations AT totowinata bondorderredefinitionneededtoreduceinherentnoiseinmoleculardynamicssimulations
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Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations

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