論文
公開件数:62件
No. 種別 査読の有無 標題 単著・共著区分 著者 誌名 巻号頁 出版日 ISSN DOI URL
1 一般論文

CUDA offloading for energy‐efficient and high‐frame‐rate simulations using tablets
共著
Edgar Josafat Martinez‐Noriega, Syunji Yazaki, Tetsu Narumi
Concurrency and Computation: Practice and Experience
33/ 2, e5488-
2019/08/23

10.1002/cpe.5488

2 一般論文

Structural determinants in the bulk heterojunction
共著
Angela Acocella, Siegfried Hofinger, Ernst Haunschmid, Sergiu C. Pop, Tetsu Narumi, Kenji Yasuoka, Masato Yasui and Francesco Zerbetto
Physical Chemistry Chemical Physics
20, 5708-5720
2018/01/30

10.1039/c7cp08435h

3 一般論文

Acceleration of the Fast Multipole Method on FPGA devices
共著
Hitoshi UKAWA and Tetsu NARUMI
IEICE TRANS. INF. & SYST.
E98-D/ 2, 309-312
2015/02/01
1745-1361


4 一般論文

Application of isotropic periodic sum method for 4-pentyl-4'-cyanobiphenyl liquid crystal
共著
Nozawa, T., Takahashi, K. Z., Kameoka, S., Narumi, T. and Yasuoka, K.
Molecular Simulation
41, 927-935
2015/01/22

10.1080/08927022.2014.998210

5 一般論文

1,024GPUを使用したレプリカ交換分子動力学シミュレーションの並列化
共著
老川 稔,野村 昴太郎,泰岡 顕治,成見 哲
情報処理学会ACS論文誌
7/ 4, 1-14
2014/12



6 一般論文

Petascale molecular dynamics simulation using the fast multipole method on K computer
共著
Yousuke Ohno, Rio Yokota, Hiroshi Koyama, Gentaro Morimoto, Aki Hasegawa, Gen Masumoto, Noriaki Okimoto, Yoshinori Hirano, Huda Ibeid, Tetsu Narumi, Makoto Taiji
Computer Physics Communications
185/ 10, 2575-2585
2014/10

10.1016/j.cpc.2014.06.004

7 一般論文

GPU-Accelerated Replica Exchange Molecular Simulation on Solid-Liquid Phase Transition Study of Lennard-Jones Fluids
共著
Nomura K., Oikawa M., Kawai A., Narumi T. and Yasuoka K.
Molecular Simulation
41, 874-880
2014/09/17

DOI : 10.1080/08927022.2014.954572

8 一般論文

Petascale Turbulence Simulation Using a Highly Parallel Fast Multipole Method

Yokota, R., Barba, L. A., Narumi, T. and Yasuoka, K.
Comput. Phys. Comm.
184, 445-455
2013



9 一般論文

Common Force Field Thermodynamics of Cholesterol

Francesco Giangreco, Eiji Yamamoto, Yoshinori Hirano, Milan Hodoscek, Volker Knecht, Matteo di Giosia, Matteo Calvaresi, Francesco Zerbetto, Kenji Yasuoka, Tetsu Narumi, Masato Yasui, and Siegfried Hoefinger
The Scientific World Journal
2013, 1-7
2013/11



10 一般論文

An improved isotropic periodic sum method that uses linear combinations of basis potentials

Takahashi, K. Z., Narumi, T., Suh, D. and Yasuoka, K.
J. Chem. Theory Comput.
8, 4503-4516
2012



11 一般論文

GPU-Accelerated Computation of Electron
Transfer

SIEGFRIED HOEFINGER, ANGELA ACOCELLA,
SERGIU C. POP, TETSU NARUMI,
KENJI YASUOKA, TITUS BEU,
FRANCESCO ZERBETTO
Journal of Computational Chemistry
33, 2351-2356
2012



12 一般論文

Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes

Siegfried Hoefinger, Eiji Yamamoto, Yoshinori Hirano, Francesco Zerbetto, Tetsu Narumi, Kenji Yasuoka, and Masato Yasui
BBA-Biomembranes
1818, 2234-2243
2012



13 一般論文

Cutoff radius effect of the isotropic periodic sum method for polar molecules in a bulk water system

Takahashi, K., Narumi, T., and Yasuoka, K.
Molec. Simul.
38, 397-
2012



14 一般論文

A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics

Takahashi, K. Z., Narumi, T., and Yasuoka, K.
J. Chem. Phys.
135, 174108-
2011



15 一般論文

Cutoff radius effect of the isotropic periodic sum and Wolf method in liquid-vapor interfaces of water

Takahashi, K. Z., Narumi, T., and Yasuoka, K.
J. Chem. Phys.
134, 174112-
2011



16 一般論文

Thermodynamic Properties of Methane/Water Interface Predicted by Molecular Dynamics Simulations

Sakamaki, R., Sum, A. K., Narumi, T., Ohmura, R., and Yasuoka, K.
J. Chem. Phys.
134, 144702-
2011



17 一般論文

Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models

Sakamaki, R., Sum, A. K., Narumi, T., and Yasuoka, K.
J. Chem. Phys.
134, 124708-
2011



18 一般論文

Fast quasi double-precision method with single-precision hardware to accelerate scientific applications

Narumi, T., Hamada, T., Nitadori, K., Sakamaki, R., and Yasuoka, K.
Int. J. Comput. Meth.
8/ 3, 561-581
2011



19 一般論文

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Francesco
Zerbetto and Siegfried Hoefinger
The Computer Journal
54/ 7, 1181-1187
2011



20 一般論文

Accelerating molecular dynamics simulation using graphics processing unit

Hun Joo Myung, Ryuji Sakamaki, Kwang Jin Oh, Tetsu Narumi, Kenji Yasuoka, and Sik Lee
Bulletin of the Korean Chemical Society
31, 3639-
2010



21 一般論文

Cutoff radius effect of the isotropic periodic sum method in homogeneous system. II. Water

Takahashi K, Narumi T, Yasuoka K.
Journal of Chemical Physics
133/ 1, 014109-
2010/07



22 一般論文

Fast Multipole Methods on a Cluster of GPUs for the Meshless Simulation of Turbulence

Yokota, R., _Narumi, T._, Sakamaki, R., Kameoka, S., Obi, S., and Yasuoka, K.
COMPUTER PHYSICS COMMUNICATIONS
180/ 11, 2066-2078
2009



23 一般論文

JINR CICC in Computational Chemistry and Nanotechnology Problems: DL_POLY Performance for Different Communication Architectures

E. Dushanov, Kh. Kholmurodov, G. Aru, V. Korenkov, W. Smith, Y. Ohno, T. Narumi, G. Morimoto, M. Taiji, and K. Yasuoka
Physics of Particles and Nuclei Letters
6/ 3, 251-
2009



24 一般論文

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji
PLoS Computational Biology
5/ 10, e1000528-
2009



25 一般論文

Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Hofinger
Journal of Computational Chemistry
30/ 14, 2351-2357
2009



26 一般論文

グラフィックカードを用いた水表面張力の高速分子動力学シミュレーション

坂牧隆司, 成見哲, 泰岡顕治
情報処理学会ACS論文誌
2/ 2, 89-97
2009



27 一般論文

Accelerating Molecular Dynamics Simulations on PLAYSTATION 3 Platform Using Vertual-GRAPE Programming Model

Tetsu Narumi, Shun Kameoka, Makoto Taiji, Kenji Yasuoka
SIAM Journal on Scientific Computing
30/ 6, 3108-3125
2008



28 一般論文

Cell Size Dependence of Orientational Order of Uniaxial Liquid

Toshiki Mima, Tetsu Narumi, Shun Mameoka, Kenji Yasuoka
Molecular Simulation
34, 761-773
2008



29 一般論文

Knoppix for CUDA-CD-ROM起動可能なGPGPUトレーニング環境-

濱田剛, 小栗清, 柴田裕一郎, 成見哲, 泰岡顕治, 小西史一, 泰地真弘人
可視化情報学会誌
28/ Suppl. 1, 249-254
2008/07



30 一般論文

Cutoff Radius Effect of Isotropic Periodic Sum Method for Transport Coefficients of Lennard-Jones Liquid

Kazuaki Takahashi, Kenji Yasuoka, Tetsu Narumi
Journal of Chemical Physics
127, 114511-
2007



31 一般論文

Folding Dynamics of 10-Residue Beta-Hairpin Peptide Chignolin

Atsushi Suenaga, Tetsu Narumi, Noriyuki Futatsugi, Ryoko Yanai, Yousuke Ohno, Noriaki Okimoto, Makoto Taiji
Chemistry - An Asian Journal
2/ 5, 591-598
2007



32 一般論文

Structre and Dynamics of RNA Polymerase II Elongation Complex

Atsushi Suenaga, Noriaki Okimoto, Noriyuki Futatsugi, Yoshinori Hirano, Tetsu Narumi, Yosuke Ohno, Ryoko Yanai, Takatsugu Hirokawa, Toshikazu Ebisuzaki, Akihiko Konagaya and Makoto Taiji
Biochemical and Biophysical Research Communications
343, 90-98
2006



33 一般論文

Novel Mechanism of Interaction of p85 Subunit of Phosphatidylinositol 3-Kinase and ErbB3 Receptor-derived Phosphotyrosyl Peptides

Atsushi Suenaga, Naoki Takada, Mariko Hatakeyama, Mio Ichikawa, Xiaomei Yu, Kentaro Tomii, Noriaki Okimoto, Noriyuki Futatsugi, Tetsu Narumi, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya and Makoto Taiji
Journal of Biological Chemistry
280, 1321-1326
2005



34 一般論文

Nanoscale Hydrophobic Interaction and Nanobubble Nucleation

Takahiro Koishi, S. Yoo, Kenji Yasuoka, X. C. Zeng, Tetsu Narumi, Ryutaro Susukita, Atsushi Kawai, Hideaki Furusawa, Atsushi Suenaga, Noriaki Okimoto, Noriyuki Futatsugi, and Toshikazu Ebisuzaki
Physical Review Letters
93, 185701-1-4-
2004



35 一般論文

Tyr-317 Phosphorylation Increases Shc Structural Rigidity and Reduces Coupling of Domain Motions Remote from the Phosphorylation Site as Revealed by Molecular Dynamics Simulations

Atsushi Suenaga, Anotoly B. Kiyatkin, Mariko Hatakeyama, Noriyuki Futatsugi, Noriaki Okimoto, Yoshinori Hirano, Tetsu Narumi, Atsushi Kawai, Ryutaro Susukita, Takahiro Koishi, Hideaki Furusawa, Kenji Yasuoka, Naoki Takada, Yousuke Ohno, Makoto Taiji, Toshikazu Ebisuzaki, Jan B. Hoek, Akihiko Konagaya, and Boris N. Kholodenko
Journal of Biological Chemistry
279, 4657-4662
2004



36 一般論文

Simulations of Magnetic Materials with MDGRAPE-2

Bruce G. Elemegreen, Roger H. Koch, Manfred E. Schabes, Tiffany Crawford, Toshikazu Ebisuzaki, Hideaki Furusawa, Tetsu Narumi, Ryutaro Susukita, and Kenji Yasuoka
IBM Journal of Research and Development
48, 199-208
2004



37 一般論文

Hardware Accelerator for Molecular Dynamics: MDGRAPE-2

Ryutaro Susukita, Toshikazu Ebisuzaki, Bruce G. Elmegreen, Hideaki Furusawa, Kenya Kato, Atsushi Kawai, Yoshinao Kobayashi, Takahiro Koishi, Geoffrey D. McNiven, Tetsu Narumi, and Kenji Yasuoka
Computer Physics Communications
155, 115-131
2003



38 一般論文

Molecular Dymamics, Free Energy and SPR Analyses of the Interactions between the SH2 Domain of Grb2 and ErbB Phosphotyrosyl Peptides

Atsushi Suenaga, Mariko Hatakeyama, Mio Ichikawa, Xiaomei Yu, Noriyuki Futatsugi, Tetsu Narumi, Kazuhiko Fukui, Takaho Terada, Makoto Taiji, Mikako Shirouzu, Shigeyuki Yokoyama, and Akihiko Konagaya
Biochemistry
42, 5195-5200
2003



39 一般論文

Molecular Dynamics Simulations of Prion Proteins - Effect of Ala 117→Val Mutation -

Noriaki Okimoto, Kazunori Yamanaka, Atsushi Suenaga, Yoshinori Hirano, Noriyuki Futatsugi, Tetsu Narumi, Kenji Yasuoka, Ryutaro Susukita, Takahiro Koishi, Hideaki Furusawa, Atsushi Kawai, Masayuki Hata, Tyuji Hoshino, and Toshikazu Ebisuzaki
Chem-Bio Informatics Journal
3, 1-11
2003



40 一般論文

Molecular Dynamics Study on Class A β-Lactamase: Hydrogen Bond Network among the Functional Groups of Penicillin G and Side Chains of the Conserved Residues in the Active Site

Yasuyuki Fujii, Noriaki Okimoto, Masayuki Hata, Tetsu Narumi, Kenji Yasuoka, Ryutaro Susukita, Atsushi Suenaga, Noriyuki Futatsugi, Takahiro Koishi, Hideaki Furusawa, Atsushi Kawai, Toshikazu Ebisuzaki, Saburo Neya, and Tyuji Hoshino
Journal of Physical Chemistry B
107, 10274-10283
2003



41 一般論文

Molecular Dynamics Study of the Solidification Process in Alkali Halide Cluster

Takahiro Koishi, Kenji Yasuoka, Tetsu Narumi, Ryutaro Susukita, Hideaki Furusawa, and Toshikazu Ebisuzaki
Journal of Non-Crystalline Solids
312, 332-336
2002



42 一般論文

Numerical Simulations of Magnetic Materials with MD-GRAPE: Curvature Induced Anisotropy

Bruce G. Elemegreen, Roger H. Koch, Kenji Yasuoka, Hideaki Furusawa, Tetsu Narumi, Ryutaro Susukita, and Toshikazu Ebisuzaki
Journal of Magnetism and Magnetic Materials
250, 39-48
2002



43 一般論文

Molecular Dynamics Machine: Special-purpose Computer for Molecular Dynamics Simulations

Tetsu Narumi, Ryutaro Susukita, Toshikazu Ebisuzaki, Geoffrey McNiven, and Bruce Elmegreen
Molecular Simulation
21, 401-415
1999



44 国際会議プロシーディングス等

Estimating Configuration Parameters of Pipelines for accelerating N-Body Simulations with an FPGA using High-level Synthesis
共著
Tetsu Narumi and Akio Muramatsu
9th International Conference on Pervasive and Embedded Computing and Communication Systems
65-64
2019/09/19



45 国際会議プロシーディングス等

An FPGA-based tiled display system for a wearable display
単著
Tetsu Narumi
The Fifth International Conference on Informatics and Applications (ICIA2016)
12-17
2016/11/14


URL
46 国際会議プロシーディングス等

Acceleration of Othello Computer Game using an FPGA Tablet
共著
Tomoya Sato and Tetsu Narumi
6th International Workshop on Advances in Networking and Computing (WANC’15)
WANC2, 1-4
2015/12/10



47 国際会議プロシーディングス等

DS-CUDA: a Middleware to Use Many GPUs in the Cloud Environment

Minoru Oikawa, Atsushi Kawai, Kentaro Nomura, Kazuyuki Yoshikawa, Kenji Yasuoka, Tetsu Narumi
SHPCloud workshop at SC12
10-16
2012/11



48 国際会議プロシーディングス等

Optimization of Molecular Dynamics Core Program on the K computer

Yousuke Ohno, Rio Yokota, Hiroshi Koyama, Gentaro Morimoto, Aki
Hasegawa, Gen Masumoto, Tetsu Narumi, and Makoto Taiji
International Conference on Simulation Technology (JSST2012)
1-2
2012/09



49 国際会議プロシーディングス等

Distributed-Shared CUDA: Virtualization of Large-Scale GPU Systems for Programmability and Reliability

Atsushi Kawai, Kenji Yasuoka, Kazuyuki Yoshikawa, Tetsu Narumi
The Fourth International Conference on Future Computational Technologies and Applications, FUTURE CONPUTING 2012
22-27
2012/07



50 国際会議プロシーディングス等

42 TFlops Hierarchical N-body Simulations on GPUs with Applications in both Astrophysics and Turbulence

Tsuyoshi Hamada, Rio Yokota, Keigo Nitadori, Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Kiyoshi Oguri
Proceedings of the SC2009
USB memory-
2009/11



51 国際会議プロシーディングス等

High-Performance Quasi Double-Precision Method using Single-Precision Hardware for Molecular Dynamics Simulations with GPUs

Tetsu Narumi, Tsuyoshi Hamada, Keigo Nitadori, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka
HPC Asia 2009
160-167
2009/03



52 国際会議プロシーディングス等

Overheads in Accelerating Molecular Dynamics Simulations with GPUs

Tetsu Narumi, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka
9th International Conference on Parallel and Distributed Computing, Applications, and Technologies (PDCAT)
143-150
2008/12



53 国際会議プロシーディングス等

A 281 Tflops Calculation for X-ray Protein Structure Analysis with the Special-Purpose Computer MDGRAPE-3

Yousuke Ohno, Eiji Nishibori, Tetsu Narumi, Takahiro Koishi, Tahir H. Tahirov, Hideo Ago, Masashi Miyano, Ryutaro Himeno, Toshikazu Ebisuzaki, Makoto Sakata, Makoto Taiji
SC2007
USB memory
2007/11



54 国際会議プロシーディングス等

A 55 Tflops Simulation of Amyloid-forming Peptides from Yeast Prion Sup35 with the Special-Purpose Computer System MDGRAPE-3

Tetsu Narumi, Yousuke Ohno, Noriaki Okimoto, Takahiro Koishi, Atsushi Suenaga, Noriyuki Futatsugi, Yoko Yanai, Ryutaro Himeno, Shigenori Fujikawa, Mitsuru Ikei, Makoto Taiji
SC2006
CDROM
2006/11



55 国際会議プロシーディングス等

Prootein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations

Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada, and Akihiko Konagaya
SC2003
CDROM
2003/11



56 国際会議プロシーディングス等

An 8.61 Tflop/s Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM

Tetsu Narumi, Atsushi Kawai, and Takahiro Koishi
SC2001
CDROM
2001/11



57 国際会議プロシーディングス等

1.34 Tflops Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM

Tetsu Narumi, Ryutaro Susukita, Takahiro Koishi, Kenji Yasuoka, Hideaki Furusawa, Atsushi Kawai, and Toshikazu Ebisuzaki
SC2000
CDROM
2000/11



58 国際会議プロシーディングス等

46 Tflops Special-Purpose Computer for Molecular Dynamics Simulations: WINE-2

Tetsu Narumi, Ryutaro Susukita, Hideaki Furusawa, and Toshikazu Ebisuzaki
International Conference on Signal Processing (ICSP) in 16th World Computer Congress (WCC2000)
1, 575-582
2000/08



59 解説

アクセラレータによる粒子法シミュレーションの加速

成見哲,濱田剛,小西史一
情報処理
50/ 2, 129-139
2009/02



60 解説

分子動力学シミュレーション専用計算機MDGRAPE-3

成見哲
化学工学
71/ 4, 7-10
2007/04



61 解説

バイオインフォマティクスのための高性能計算機アーキテクチャ

小長谷明彦, 小西史一, 成見哲
ソフトウェアバイオロジー
1, 73-77
2002



62 解説

100Tflopsの分子動力学シミュレーション専用計算機MDM

成見哲
Bit
11
2000/11