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Journal Articles
- 2023
[j8]Jaewoon Jung
, Chigusa Kobayashi, Yuji Sugita:
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. J. Comput. Chem. 44(20): 1740-1749 (2023)- 2022
- [j7]Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita:
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. PLoS Comput. Biol. 18(4) (2022) - 2021
- [j6]Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita:
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. J. Comput. Chem. 42(4): 231-241 (2021) - [j5]Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita:
Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. J. Chem. Inf. Model. 61(5): 2427-2443 (2021) - 2019
- [j4]Jaewoon Jung, Wataru Nishima, Marcus Daniels, Gavin Bascom, Chigusa Kobayashi, Adetokunbo Adedoyin, Michael E. Wall, Anna Lappala, Dominic Phillips, William Fischer, Chang-Shung Tung, Tamar Schlick, Yuji Sugita, Karissa Y. Sanbonmatsu:
Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations. J. Comput. Chem. 40(21): 1919-1930 (2019) - 2017
- [j3]Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama:
Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. J. Comput. Chem. 38(16): 1447-1461 (2017) - [j2]Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, Yuji Sugita:
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. J. Comput. Chem. 38(25): 2193-2206 (2017) - 2016
- [j1]Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, Yuji Sugita:
Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. Comput. Phys. Commun. 200: 57-65 (2016)
Coauthor Index
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