List of Research Output | FY 2021

Papers, peer-reviewed conference proceedings etc.

【Computer Science Research and Development Office】

＜Research papers＞

Onodera Naoyuki, Idomura Yasuhiro, Hasegawa Yuta, Nakayama Hiromasa, Shimokawabe Takashi, Aoki Takayuki,

"Real-time tracer dispersion simulations in Oklahoma City using the locally mesh-refined lattice Boltzmann method",

Boundary-Layer Meteorology, Vol.179, No.2, pp.187-208 (2021).

Matsuoka Seikichi, Sugama Hideo, Idomura Yasuhiro,

"Neoclassical transport simulations with an improved model collision operator",

Physics of Plasmas, Vol.28, No.6, pp.064501_1-064501_5 (2021).

Koyamada Koji, Yu Long, Kawamura Takuma, Konishi Katsumi,

"Data-driven derivation of partial differential equations using neural network model",

International Journal of Modeling, Simulation, and Scientific Computing, Vol.12, No.2, pp.2140001_1-2140001_19 (2021).

Hasegawa Yuta, Aoki Takayuki, Kobayashi Hiromichi, Idomura Yasuhiro, Onodera Naoyuki,

"Tree cutting approach for domain partitioning on forest-of-octrees-based block-structured static adaptive mesh refinement with lattice Boltzmann method",

Parallel Computing, Vol.108, pp.102851_1-102851_12 (2021).

Watanabe Tsutomu, Takagi Marie, Shimoyama Ko, Kawashima Masayuki, Onodera Naoyuki, Inagaki Atsushi,

"Coherent eddies transporting passive scalars through the plant canopy revealed by Large-Eddy simulations using the lattice Boltzmann method",

Boundary-Layer Meteorology, Vol.181, No.1, pp.39-71 (2021).

Asahi Yuichi, Fujii Keisuke, Heim Dennis Manuel, Maeyama Shinya, Garbet Xavier, Grandgirard Vinginie, Sarazin Yanick, Dif-Pradalier Guilhem, Idomura Yasuhiro, Yagi Masatoshi,

"Compressing the time series of five dimensional distribution function data from gyrokinetic simulation using principal component analysis",

Physics of Plasmas, Vol.28, No.1, pp.012304_1-012304_21 (2021).

＜Peer-reviewed conference proceedings＞

Asahi Yuichi, Hatayama Sora, Shimokawabe Takashi, Onodera Naoyuki, Hasegawa Yuta, Idomura Yasuhiro,

"AMR-Net: Convolutional neural networks for multi-resolution steady flow prediction",

Proceedings of 2021 IEEE International Conference on Cluster Computing (IEEE Cluster 2021) (Internet), "2021 IEEE International Conference on Cluster Computing (IEEE Cluster 2021); 2nd Workshop on Artificial Intelligence and Machine Learning for Scientific Applications (AI4S)", pp.686-691 (2021).

Ina Takuya, Idomura Yasuhiro, Imamura Toshiyuki, Yamashita Susumu, Onodera Naoyuki,

"Iterative methods with mixed-precision preconditioning for ill-conditioned linear systems in multiphase CFD simulations",

Proceedings of 12th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems ScalA21) (Internet) , "International Conference for High Performance Computing, Networking, Storage, and Analysis (SC 2021); 12th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (ScalA21)", pp.8 (2021).

Asahi Yuichi, Latu Guillaume, Bigot Julien, Grandgirard Virginie,

"Optimization strategy for a performance portable Vlasov code",

Proceedings of 2021 International Workshop on Performance, Portability, and Productivity in HPC (P3HPC) (Internet), "International Conference for High Performance Computing, Networking, Storage, and Analysis (SC 2021); 2021 International Workshop on Performance, Portability, and Productivity in HPC (P3HPC)", pp.79-91 (2021).

【Simulation Technology Research and Development Office】

＜Research papers＞

Thomsen Bo, Shiga Motoyuki,

"Nuclear quantum effects on autoionization of water isotopologs studied by ab initio path integral molecular dynamics",

Journal of Chemical Physics, Vol.154, No.8, pp.084117_1-084117_10 (2021).

Kondo Tomomi, Sasaki Takehiko, Ruiz-Barragan Sergei, Ribas-Ariño Jordi, Shiga Motoyuki,

"Refined metadynamics through canonical sampling using time-invariant bias potential; A Study of polyalcohol dehydration in hot acidic solutions",

Journal of Computational Chemistry, Vol.42, No.3, pp.156-165 (2021).

Noguchi Yoshifumi, Hiyama Miyabi, Shiga Motoyuki, Akiyama Hidefumi, Sugino Osamu,

"Quantum-mechanical hydration plays critical role in the stability of firefly oxyluciferin isomers; State-of-the-art calculations of the excited states",

Journal of Chemical Physics, Vol.153, No.20, pp.201103_1-201103_6 (2020).

Suno Hiroya, Machida Masahiko, Dohi Terumi, Omura Yoshihito,

"Quantum chemical calculation studies toward microscopic understanding of retention mechanism of Cs radioisotopes and other alkali metals in lichens",

Scientific Reports (Internet), Vol.11, No.1, pp.8228_1-8228_13 (2021).

Suzudo Tomoaki,

"Computational study of solute effects in tungsten under irradiation",

Materials Science Forum, Vol.1024, pp.87-94 (2021).

Yamaguchi Masatake, Itakura Mitsuhiro, Tsuru Tomohito, Ebihara Kenichi,

"Hydrogen-trapping energy in screw and edge dislocations in aluminum; First-principles calculations",

Materials Transactions, Vol.62, No.5, pp.582-589 (2021).

Nagai Yuki,

"N-independent localized Krylov-Bogoliubov-de Gennes Method; Ultra-fast numerical approach to large-scale inhomogeneous superconductors",

Journal of the Physical Society of Japan, Vol.89, No.7, pp.074703_1-074703_6 (2020).

Suzudo Tomoaki, Tsuru Tomohito,

"Inclination of self-interstitial dumbbells in molybdenum and tungsten; A First-principles study",

AIP Advances (Internet), Vol.11, No.6, pp.065012_1-065012_7 (2021).

Terayama Satoshi, Iwase Yuki, Hayakawa Sho, Okita Taira, Itakura Mitsuhiro, Suzuki Katsuyuki,

"Molecular dynamic simulations evaluating the effect of the stacking fault energy on defect formations in face-centered cubic metals subjected to high-energy particle irradiation",

Computational Materials Science, Vol.195, pp.110479_1-110479_12 (2021).

Zhao Can, Suzudo Tomoaki, Toyama Takeshi, Nishitani Shigeto, Inoue Koji, Nagai Yasuyoshi,

"Investigation of Cu diffusivity in Fe by a combination of atom probe experiments and kinetic Monte Carlo simulation",

Materials Transactions, Vol.62, No.7, pp.929-934 (2021).

Kobayashi Keita, Nagai Yuki, Itakura Mitsuhiro, Shiga Motoyuki,

"Self-learning hybrid Monte Carlo method for isothermal-isobaric ensemble; Application to liquid silica",

Journal of Chemical Physics, Vol.155, No.3, pp.034106_1-034106_9 (2021).

Yamaguchi Akiko, Kobayashi Keita, Takahashi Yoshio, Machida Masahiko, Okumura Masahiko,

"Hydration structures of barium ions; Ab initio molecular dynamics simulations using the SCAN meta-GGA density functional and EXAFS spectroscopy studies",

Chemical Physics Letters, Vol.780, pp.138945_1-138945_5 (2021).

Konagaya Rimi, Kawamura Naomi, Yamaguchi Akiko, Takahashi Yoshio,

"Highly-sensitive analysis of fluorescence XANES at Europium (Eu) LIII-edge for the determination of oxidation state for trace amount of Eu in natural samples by bragg-type crystal analyzer system",

Chemistry Letters, Vol.50, No.8, pp.1570-1572 (2021).

Okita Taira, Terayama Satoshi, Tsugawa Kiyoto, Kobayashi Keita, Okumura Masahiko, Itakura Mitsuhiro, Suzuki Katsuyuki,

"Construction of machine-learning Zr interatomic potentials for identifying the formation process of c-type dislocation loops",

Computational Materials Science, Vol.202, pp.110865_1-110865_9 (2022).

Toyama Takeshi, Zhao Can, Yoshiie Toshimasa, Yamasaki Shota, Uno Sadanori, Shimodaira Masaki, Miyata Hotaka, Suzudo Tomoaki, Shimizu Yasuo, Yoshida Kenta, Inoue Koji, Nagai Yasuyoshi,

"Radiation-enhanced diffusion of copper in iron studied by three-dimensional atom probe",

Journal of Nuclear Materials, Vol.556, pp.153176_1-153176_7 (2021).

Suno Hiroya, Machida Masahiko,

"Atomistic origin of selective Cs accumulation in mushrooms; DFT analysis for alkali metal cation complexation selectivity of scissors-like pigments",

ACS Food Science & Technology (Internet), Vol.1, No.8, pp.1381-1391 (2021).

Pal Asit, Pal Subhendu, Verma Shivani, Shiga Motoyuki, Nair Nisnanth N.,

"Mean force based temperature accelerated sliced sampling; Efficient reconstruction of high dimensional free energy landscapes",

Journal of Computational Chemistry, Vol.42, No.28, pp.1996-2003 (2021).

Kim Howon, Nagai Yuki, Rózsa Levente, Schreyer Dominik, Wiesendanger Roland,

"Anisotropic non-split zero-energy vortex bound states in a conventional superconductor",

Applied Physics Reviews (Internet), Vol.8, No.3, pp.031417_1-031417_8 (2021).

Kondo Tomomi, Sasaki Takehiko, Shiga Motoyuki,

"The Mechanism of sorbitol dehydration in hot acidic solutions",

Journal of Computational Chemistry, Vol.42, No.25, pp.1783-1791 (2021).

Matsushita Taiki, Nagai Yuki, Fujimoto Satoshi,

"Spectrum collapse of disordered Dirac Landau levels as topological non-Hermitian physics",

Journal of the Physical Society of Japan, Vol.90, No.7, pp.074703_1-074703_7 (2021).

Koshiro Hidehiko, Nagai Yuki,

"Effective Ruderman-Kittel-Kasuya-Yosida-like interaction in diluted double-exchange model; Self-learning Monte Carlo Approach",

Journal of the Physical Society of Japan, Vol.90, No.3, pp.034711_1-034711_8 (2021).

Wang Jing, Hatano Yuji, Toyama Takeshi, Suzudo Tomoaki, Hinoki Tatsuya, Alimov Vladimir Kh., Schwarz-Selinger Thomas,

"Suppression of vacancy formation and hydrogen isotope retention in irradiated tungsten by addition of chromium",

Journal of Nuclear Materials, Vol.559, pp.153449_1-153449_7 (2022).

Akazawa Daisuke, Sasaki Takehiko, Nagasaka Masanari, Shiga Motoyuki,

"X-ray absorption spectra of aqueous cellobiose; Experiment and theory",

Journal of Chemical Physics, Vol.156, No.4, pp.044202_1-044202_7 (2022).

Kimizuka Hajime, Shiga Motoyuki,

"Two distinct non-Arrhenius behaviors of hydrogen diffusivities in fcc aluminum, silver, and copper determined by ab initio path integral simulations",

Physical Review Materials (Internet), Vol.5, No.6, pp.065406_1-065406_9 (2021).

Malins Alex, Lemoine Thom,

"radioactivedecay; A Python package for radioactive decay calculations",

Journal of Open Source Software (Internet), Vol.7, No.71, pp.3318_1-3318_6 (2022).

Talks at international and Japanese conferences

【Computer Science Research and Development Office】

＜Talks＞

Onodera Naoyuki, Hasegawa Yuta, Asahi Yuichi, Idomura Yasuhiro, Shimokawabe Takashi, Aoki Takayuki,

"GPU acceleration of tracer dispersion simulation using the locally mesh-refined lattice Boltzmann method",

ADAC (Accelerated Data Analytics and Computing Institute) Workshop, (online, Jun. 01, 2021).

Idomura Yasuhiro,

"Development of exascale full-f gyrokinetic simulation on Summit and FUGAKU",

The Platform for Advanced Scientific Computing Conference (PASC21), (online, Jul. 01, 2021).

Idomura Yasuhiro,

"A New synergy effect between neoclassical and turbulent particle transport in ion temperature gradient driven turbulence",

5th Asia-Pacific Conference on Plasma Physics (AAPPS-DPP 2021), (online, Japan, Sep. 01, 2021).

Grandgirard Vinginie, Asahi Yuichi, Bigot Julien, Bourne Emily, Dif-Pradalier Guilhem, Donnel Peter, Garbet Xavier, Ghendrih Phillppe,

"How to prepare the GYSELA-X code to future exascale edge-core simulations",

The Platform for Advanced Scientific Computing Conference (PASC21), (Zürich (online), Switzerland, July 05-09, 2021).

Asahi Yuichi, Fujii Keisuke, Maeyama Shinya, Idomura Yasuhiro,

"Phase-Space Pattern Extraction from 5D gyrokinetic simulation data",

30th International Toki Conference on Plasma and Fusion Research (ITC-30), (Toki (online), Japan, November 16-19, 2021).

Watanabe Tomohiko, Idomura Yasuhiro, Todo Yasushi, Honda Mitsuru,

"Exploration of burning plasma confinement physics using the supercomputer Fugaku",

2nd Fusion HPC Workshop, (online, Dec. 2-3, 2021).

Idomura Yasuhiro,

"Acceleration of full-f gyrokinetic Eulerian code GT5D on Fugaku and Summit",

Joint US-Japan Workshop on Exascale Computing Collaboration and 6th workshop of US-Japan Joint Institute for Fusion Theory (JIFT) program, (online, Jan. 18-19, 2022).

【Simulation Technology Research and Development Office】

＜Talks＞

Itakura Mitsuhiro, Yamaguchi Masatake, Egusa Daisuke, Abe Eiji,

"Density functional theory study of solute cluster growth processes in Mg-Y-Zn LPSO alloys",

12th International Conference on Magnesium Alloys and their Applications (MG 2021), (online, U. S. A., Jun. 01, 2021).

Shiga Motoyuki, Kobayashi Keita, Okumura Masahiko, Nagai Yuki,

"Self-learning hybrid Monte Carlo; A First-principles method",

32nd IUPAP Conference on Computational Physics (CCP 2021), (Coventry (online), U. K., Aug. 01, 2021).

Suzudo Tomoaki, Toyama Takeshi, Hatano Yuji, Wang Jing,

"Solute elements suppress the radiation damage in W alloys; Comparison between first-principles-based modeling and experimental evidence",

20th International conference on fusion reactor materials (ICFRM-20), (Granada (online), Spain, Oct. 24-29, 2021).

Nagai Yuki,

"Localized Krylov Bogoliubov-de Gennes method (LK-BdG); Ultra-fast numerical approach for large-scale inhomogeneous superconductors",

34th International Symposium on Superconductivity (ISS 2021), (online, Japan, November 30-December 2, 2021).

Shiga Motoyuki,

"First-principles simulations with nuclear quantum effects",

1st International Conference on Computational Science & Data Analytics (COMDATA 2021), (Kuala Lumper (online), Malaysia, November 21-24, 2021).

Thomsen Bo, Shiga Motoyuki,

"New insights into nuclear quantum effects of liquid water from first principles calculations",

Materials Research Meeting 2021 (MRM 2021), (Yokohama, Japan, December 13-16, 2021).

Yamaguchi Masatake, Tsuru Tomohito, Ebihara Kenichi, Itakura Mitsuhiro,

"Hydrogen trapping energy at incoherent boundary in aluminum alloy; First-principles calculations",

Materials Research Meeting 2021 (MRM 2021), (Yokohama, Japan, December 13-16, 2021).

Okumura Masahiko, Kobayashi Keita, Nakamura Hiroki, Yamaguchi Akiko, Itakura Mitsuhiro, Machida Masahiko,

"Machine learning potentials for cement and clay minerals",

International Chemical Congress of Pacific Basin Societies 2021 (Pacifichem 2021), (Honolulu, U.S.A. (onlilne), December 16-21, 2021).

Okumura Masahiko,

"Machine learning molecular dynamics simulations of silicate minerals",

American Chemical Society Meetings & Expos (ACS Spring 2022), (San Diego, U.S.A., Mar. 20-24, 2022).