Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation. - Suyong Re; Takashi Imai; Jaewoon Jung; Seiichiro Ten-no; Yuji Sugita (J. Comput. Chem., 2011)

Efficient lookup table using a linear function of inverse distance squared. - Jaewoon Jung; Takaharu Mori; Yuji Sugita (J. Comput. Chem., 2013)

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations. - Jaewoon Jung; Takaharu Mori; Yuji Sugita (J. Comput. Chem., 2014)

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)

Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems. - Jaewoon Jung; Yuji Sugita (J. Comput. Chem., 2017)

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)

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)

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)

Scaling molecular dynamics for large-scale simulation of biological systems on AMD CPU/GPU supercomputers: Lessons from LUMI: Optimizing GENESIS for maximizing the computational efficiency of CPU and GPU kernels on the LUMI supercomputer. - Diego Ugarte La Torre; Jaewoon Jung; Yuji Sugita (HPC Asia, 2025)