Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. - Jaewoon Jung; Chigusa Kobayashi; Toshiyuki Imamura; Yuji Sugita (Comput. Phys. Commun., 2016)

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. - Chigusa Kobayashi; Jaewoon Jung; Yasuhiro Matsunaga; Takaharu Mori; Tadashi Ando; Koichi Tamura; Motoshi Kamiya; Yuji Sugita (J. Comput. Chem., 2017)

Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. - Osamu Miyashita; Chigusa Kobayashi; Takaharu Mori; Yuji Sugita; Florence Tama (J. Comput. Chem., 2017)

Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations. - Jaewoon Jung; Wataru Nishima; Marcus Daniels; Gavin Bascom; Chigusa Kobayashi; Adetokunbo Adedoyin; Michael E. Wall; Anna Lappala; Dominic Phillips; William Fischer 001; Chang-Shung Tung; Tamar Schlick; et al. (J. Comput. Chem., 2019)

New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. - Jaewoon Jung; Chigusa Kobayashi; Kento Kasahara; Cheng Tan 004; Akiyoshi Kuroda; Kazuo Minami; Shigeru Ishiduki; Tatsuo Nishiki; Hikaru Inoue; Yutaka Ishikawa; Michael Feig; Yuji Sugita (J. Comput. Chem., 2021)

Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. - Ai Shinobu; Chigusa Kobayashi; Yasuhiro Matsunaga; Yuji Sugita (J. Chem. Inf. Model., 2021)

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. - Cheng Tan 004; Jaewoon Jung; Chigusa Kobayashi; Diego Ugarte La Torre; Shoji Takada; Yuji Sugita (PLoS Comput. Biol., 2022)

Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. - Jaewoon Jung; Chigusa Kobayashi; Yuji Sugita (J. Comput. Chem., 2023)