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[[Vol. 21]Supercomputing in materials science_ First-principles simulations of large molecules_ WPI-MANA.pdf](https://mdr.nims.go.jp/filesets/0ad1fee4-67f9-4b4c-b257-5046c6c65d1a/download)

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International Center for Materials Nanoarchitectonics (WPI-MANA)

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[[Research Highlights Vol.21] Supercomputing in materials science: First-principles simulations of large molecules](https://mdr.nims.go.jp/datasets/120eb35f-7a1c-4780-910c-e376bd8601e4)

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2022/04/04 10:19 Supercomputing in materials science: First-principles simulations of large molecules| MANAhttps://www.nims.go.jp/mana/research/highlights/vol21.html 1/3Previous  Index  NextResearch Highlights[Vol. 21]Supercomputing in materials science: First-principles simulations of largemolecules27 Mar, 2015Large-scale calculation capable of handling material systems containing 100to 1,000 times more atoms than conventional methods.Figure 1: Calculation time of O(N) first-principles calculation program run by the“K computer” (1 CPU = 8 cores). The calculations were performed on siliconsystems. The horizontal axis shows the number of atoms, indicating that first-principles calculation of million atom systems is possible. The O(N) methodcombined with ideal parallel performance of the program (twice the number ofCPUs achieving twice the amount of calculation) can calculate systems containingtwice the number of atoms in the same time by doubling the number of CPUs.Calculation time by “K computer” Elapsed time (sec/step) Number of atoms 16atoms/core 8 atoms/core 4 atoms/core Million atomshttps://www.nims.go.jp/mana/research/highlights/vol20.htmlhttps://www.nims.go.jp/mana/research/highlights/index.htmlhttps://www.nims.go.jp/mana/research/highlights/vol22.html2022/04/04 10:19 Supercomputing in materials science: First-principles simulations of large molecules| MANAhttps://www.nims.go.jp/mana/research/highlights/vol21.html 2/3Figure 2: Snapshot structure from first-principles simulation of DNA in watermedium using the calculation method developed by the research. The forcesbetween atoms are calculated by first-principles calculation (joint research withRIKEN).Matter is composed of atoms, and its physical properties are determined by the complexinteractions between atoms and electrons. Theoreticians use quantum mechanics to calculate theforces between atoms, and the behaviour of electrons in materials. Specifically, first-principlessimulations are based on quantum mechanics, and are a powerful technique widely used toelucidate diverse properties of matter and materials at the atomic scale.However, the size of the systems modelled with conventional first-principles methods is limited toonly a few hundred atoms (in most cases) because the complexity and time required forsimulations increases as the cube of the number of atoms being modelled.Now, a research team led by David Bowler, NIMS MANA and UCL London Centre forNanotechnology, and Tsuyoshi Miyazaki at NIMS, has successfully developed a highly efficient,large-scale first-principles simulation method for simulating the dynamics of very large systems,containing 100-1,000 times more atoms than conventional methods (up to millions of atoms).This method provides the means of performing atomic and electronic structure simulations ofbiological molecules and complex matter, including nanostructured materials, for whichconventional methods cannot be used.The research team has been pursuing the development of a calculation method capable ofperforming highly efficient large-scale simulations of dynamics. Here, by introducing a newtechnique where the time required increases linearly with the number of atoms and utilizingsupercomputers, namely the “K computer” and FX10 installed at RIKEN and the University ofTokyo, respectively, the team successfully performed first-principles dynamical simulations ofsystems comprising more than 30,000 atoms, which is 100 times larger than is usual withconventional methods. Their success will pave the way for simulation of very large systemsincluding up to millions of atoms.2022/04/04 10:19 Supercomputing in materials science: First-principles simulations of large molecules| MANAhttps://www.nims.go.jp/mana/research/highlights/vol21.html 3/3Reference"Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10,000+ atoms"Michiaki Arita, David R. Bowler, and Tsuyoshi MiyazakiJournal : Journal of Chemical Theory and Computation 10 , 5419 (2014).DOI : 10.1021/ct500847yAffiliationsInternational Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for MaterialsScience (NIMS), Namiki 1-1, Tsukuba, Ibaraki 305-0044, JapanContact informationInternational Center for Materials Nanoarchitectonics(WPI-MANA)National Institute for Materials Science1-1 Namiki, Tsukuba, Ibaraki 305-0044 JapanPhone: +81-29-860-4710E-mail: mana-pr[AT]ml.nims.go.jphttps://samurai.nims.go.jp/profiles/miyazaki_tsuyoshi?locale=enhttps://pubs.acs.org/doi/10.1021/ct500847y