Jaewoon Jung

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 19

Top Topics

Endoplasmic Reticulum

Herpes Simplex Virus

Molecular Dynamics

Top Venues

The journal of physical chemistry. B

Nature communications

The Journal of chemical physics

Journal of computational chemistry

This page only lists publications with an associated author ORCID identifier.

Publications

Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The journal of physical chemistry. B 128 (25) (2024)
Jaewoon Jung, Cheng Tan, Yuji Sugita
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nature communications 15 (1) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The journal of physical chemistry. B (2024)
Jaewoon Jung, Cheng Tan, Yuji Sugita
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nature communications 15 (1) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The journal of physical chemistry. B 128 (25) (2024)
Jaewoon Jung, Cheng Tan, Yuji Sugita
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nature communications 15 (1) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The journal of physical chemistry. B 128 (25) (2024)
Jaewoon Jung, Cheng Tan, Yuji Sugita
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nature communications 15 (1) (2024)
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. Journal of computational chemistry (2023)
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 computational biology 18 (4) (2022)
Hisham M Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, Yuji Sugita
The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein. eLife 11 (2022)
Chigusa Kobayashi, Yasuhiro Matsunaga, Jaewoon Jung, Yuji Sugita
Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase. Proceedings of the National Academy of Sciences of the United States of America 118 (40) (2021)
Jaewoon Jung, Kento Kasahara, Chigusa Kobayashi, Hiraku Oshima, Takaharu Mori, Yuji Sugita
Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems. Journal of chemical theory and computation 17 (8) (2021)
Jaewoon Jung, Yuji Sugita
Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step. The Journal of chemical physics 153 (23) (2021)
Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. The Journal of chemical physics 153 (4) (2021)
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. Journal of computational chemistry 42 (4) (2020)
Jaewoon Jung, Wataru Nishima, Marcus Daniels, Gavin Bascom, Chigusa Kobayashi, Adetokunbo Adedoyin, Michael 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. Journal of computational chemistry 40 (21) (2019)
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. The Journal of chemical physics 148 (16) (2018)
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. Journal of chemical theory and computation 15 (1) (2018)