Chigusa Kobayashi

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 15

Top Topics

Molecular Dynamics

Top Venues

The journal of physical chemistry. B

Journal of computational chemistry

Journal of chemical theory and computation

PLoS computational biology

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, 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, 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, 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, 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)
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)
Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita
Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. Journal of chemical information and modeling 61 (5) (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)
Kiyoshi Yagi, Kenta Yamada, Chigusa Kobayashi, Yuji Sugita
Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. Journal of chemical theory and computation 15 (3) (2019)
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
Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. Journal of chemical theory and computation 15 (1) (2018)
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. Journal of computational chemistry 38 (25) (2017)