Published papers
Number of published data : 62
No. Classification Refereed paper Title Authorship Author Journal Volume/issue/page Publication date ISSN DOI URL
1 Paper
Yes
CUDA offloading for energy‐efficient and high‐frame‐rate simulations using tablets
Joint
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 Paper
Yes
Structural determinants in the bulk heterojunction
Joint
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 Paper
Yes
Acceleration of the Fast Multipole Method on FPGA devices
Joint
Hitoshi UKAWA and Tetsu NARUMI
IEICE TRANS. INF. & SYST.
E98-D/ 2, 309-312
2015/02/01
1745-1361


4 Paper
Yes
Application of isotropic periodic sum method for 4-pentyl-4'-cyanobiphenyl liquid crystal
Joint
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 Paper
Yes
Parallel Molecular Dynamics Simulation with Replica-Exchange Method using 1,024 GPUs
Joint
Minoru Oikawa,Kentaro Nomura,Kenji Yasuoka,Tetsu Narumi
IPSJ Trans. ACS
7/ 4, 1-14
2014/12



6 Paper
Yes
Petascale molecular dynamics simulation using the fast multipole method on K computer
Joint
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 Paper
Yes
GPU-Accelerated Replica Exchange Molecular Simulation on Solid-Liquid Phase Transition Study of Lennard-Jones Fluids
Joint
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
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 Paper
Yes
Cell Size Dependence of Orientational Order of Uniaxial Liquid

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



29 Paper
No
Knoppix for CUDA-a CD-bootable GPGPU training environment-

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



45 International conference proceedings, etc.
Yes
An FPGA-based tiled display system for a wearable display
Only
Tetsu Narumi
The Fifth International Conference on Informatics and Applications (ICIA2016)
12-17
2016/11/14


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



47 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
No
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 International conference proceedings, etc.
Yes
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 Tutorial
No
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 Tutorial
No
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 Tutorial
No
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 Tutorial
No
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