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Jaewoon Jung · SciRah

Researcher profile · Semantic Scholar

Jaewoon Jung

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Jaewoon Jung — researcher profile on SciRah

h-index: 22
Works: 81
Citations: 1,655

Most-cited papers

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
I. Yu, Takaharu Mori, T. Ando, R. Harada +3 more
2016eLife237 citations Open access
Semantic Scholar
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
Jaewoon Jung, Takaharu Mori, C. Kobayashi, Y. Matsunaga +3 more
2015Wiley Interdisciplinary Reviews. Computational Molecular Science221 citations Open access
Semantic Scholar
GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
C. Kobayashi, Jaewoon Jung, Y. Matsunaga, Takaharu Mori +4 more
2017Journal of Computational Chemistry170 citations Open access
Semantic Scholar
Scaling Molecular Dynamics Beyond 100,000 Processor Cores for Large-Scale Biophysical Simulations
Jaewoon Jung, W. Nishima, M. Daniels, Gavin D. Bascom +10 more
2019Journal of Computational Chemistry107 citations Open access
Semantic Scholar
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
Cheng Tan, Jaewoon Jung, C. Kobayashi, Diego Ugarte La Torre +2 more
2021bioRxiv76 citations Open access
Semantic Scholar
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems
Jaewoon Jung, C. Kobayashi, Kento Kasahara, Cheng Tan +8 more
2020Journal of Computational Chemistry66 citations Open access
Semantic Scholar
Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
Takaharu Mori, Jaewoon Jung, C. Kobayashi, H. Dokainish +2 more
2021Biophysical Journal58 citations Open access
Semantic Scholar
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
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima +7 more
2024Journal of Physical Chemistry B47 citations Open access
Semantic Scholar
Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.
Takaharu Mori, Jaewoon Jung, Y. Sugita
2013Journal of Chemical Theory and Computation43 citations
Semantic Scholar
The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein
H. Dokainish, Suyong Re, Takaharu Mori, C. Kobayashi +2 more
2021bioRxiv41 citations Open access
Semantic Scholar
Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems.
Jaewoon Jung, Kento Kasahara, C. Kobayashi, Hiraku Oshima +2 more
2021Journal of Chemical Theory and Computation41 citations Open access
Semantic Scholar
Assessment of free energy expressions in RISM integral equation theory: theoretical prediction of partition coefficients revisited
S. Ten-no, Jaewoon Jung, H. Chuman, Y. Kawashima
201041 citations
Semantic Scholar
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems
Jaewoon Jung, Cheng Tan, Y. Sugita
2023bioRxiv36 citations Open access
Semantic Scholar
Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation
Y. Matsunaga, M. Kamiya, Hiraku Oshima, Jaewoon Jung +2 more
2022Biophysical Reviews32 citations Open access
Semantic Scholar
Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations
Jaewoon Jung, C. Kobayashi, Toshiyuki Imamura, Y. Sugita
2016Computer Physics Communications31 citations
Semantic Scholar
Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein.
Y. Matsunaga, Yasuaki Komuro, C. Kobayashi, Jaewoon Jung +2 more
2016Journal of Physical Chemistry Letters29 citations
Semantic Scholar
Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step.
Jaewoon Jung, C. Kobayashi, Y. Sugita
2018Journal of Chemical Theory and Computation28 citations Open access
Semantic Scholar
Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation.
Jaewoon Jung, C. Kobayashi, Y. Sugita
2018Journal of Chemical Physics27 citations
Semantic Scholar
New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals
Jaewoon Jung, C. Choi, Y. Sugita, S. Ten-no
200726 citations
Semantic Scholar
Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations.
Jaewoon Jung, Akira Naurse, C. Kobayashi, Y. Sugita
2016Journal of Chemical Theory and Computation25 citations
Semantic Scholar
Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations
Jaewoon Jung, Takaharu Mori, Y. Sugita
2014Journal of Computational Chemistry24 citations
Semantic Scholar
Topological determinants of protein unfolding rates
Jaewoon Jung, Jooyoung Lee, H. Moon
2004Proteins: Structure, Function, and Bioinformatics22 citations
Semantic Scholar
Efficient lookup table using a linear function of inverse distance squared
Jaewoon Jung, Takaharu Mori, Y. Sugita
2013Journal of Computational Chemistry21 citations
Semantic Scholar
One-pot synthesis of hybrid TiO2-polyaniline nanoparticles by self-catalyzed hydroamination and oxidative polymerization from TiO2-methacrylic acid nanoparticles.
W. Bae, A. Davis, Jaewoon Jung, W. Jo +2 more
2011Chemical Communications21 citations
Semantic Scholar
Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step.
Jaewoon Jung, Y. Sugita
2020Journal of Chemical Physics19 citations Open access
Semantic Scholar
Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase
C. Kobayashi, Y. Matsunaga, Jaewoon Jung, Y. Sugita
2021Proceedings of the National Academy of Sciences of the United States of America17 citations Open access
Semantic Scholar
Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning.
Takaharu Mori, M. Kulik, O. Miyashita, Jaewoon Jung +2 more
2019Structure17 citations Open access
Semantic Scholar
Rational Design Principles for De Novo α-Helical Peptide Barrels with Dynamic Conductive Channels.
Ai Niitsu, A. R. Thomson, Alistair J. Scott, Jason T. Sengel +7 more
2025Journal of the American Chemical Society12 citations Open access
Semantic Scholar
A QM/MM-MD study on protein electronic properties: Circular dichroism spectra of oxytocin and insulin
Y. Kitagawa, Yoshinobu Akinaga, Y. Kawashima, Jaewoon Jung +1 more
201210 citations
Semantic Scholar
Møller-Plesset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method.
Jaewoon Jung, Y. Sugita, S. Ten-no
2010Journal of Chemical Physics10 citations Open access
Semantic Scholar
Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems
Jaewoon Jung, Y. Sugita
2017Journal of Computational Chemistry9 citations
Semantic Scholar
Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations.
Jaewoon Jung, Suyong Re, Y. Sugita, S. Ten-no
2013Journal of Chemical Physics9 citations Open access
Semantic Scholar
A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals: implementation for electronic excited states.
Y. Kawashima, H. Nakano, Jaewoon Jung, S. Ten-no
2011Physical Chemistry, Chemical Physics - PCCP9 citations
Semantic Scholar
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation
Suyong Re, T. Imai, Jaewoon Jung, S. Ten-no +1 more
2011Journal of Computational Chemistry9 citations
Semantic Scholar
Topological Quantities Determining the Folding/Unfolding Rate of Two-state Folding Proteins
Jaewoon Jung, A. Buglass, E. Lee
20109 citations
Semantic Scholar
A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase
Suyong Re, Jaewoon Jung, S. Ten-no, Y. Sugita
20099 citations
Semantic Scholar
A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations.
Cheng Tan, Jaewoon Jung, C. Kobayashi, Y. Sugita
2020Journal of Chemical Physics8 citations
Semantic Scholar
In silico nanoscope to study the interplay of genome organization and transcription regulation
Soundhararajan Gopi, Giovani B. Brandani, Cheng Tan, Jaewoon Jung +5 more
2024bioRxiv7 citations Open access
Semantic Scholar
Simple avoidance of Pauli repulsion errors in the generalized hybrid orbital (GHO) method
Jaewoon Jung, S. Ten-no
20107 citations
Semantic Scholar
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer
Jaewoon Jung, C. Kobayashi, Y. Sugita
2023Journal of Computational Chemistry5 citations
Semantic Scholar
Optimized Build Orientation and Laser Scanning Strategies for Reducing Thermal Residual Stress in Topology-Optimized Automotive Components
Jeongho Yang, Y. Jung, Jaewoon Jung, J. Ock +4 more
2024Metals4 citations Open access
Semantic Scholar
The distortion–push mechanism for the γ subunit rotation in F1-ATPase
M. Motohashi, Mao Oide, C. Kobayashi, Jaewoon Jung +2 more
2025bioRxiv3 citations Open access
Semantic Scholar
Structural dynamics of a designed peptide pore under an external electric field.
Ai Niitsu, Jaewoon Jung, Yuji Sugita
2024Biophysical Chemistry3 citations Open access
Semantic Scholar
ColBuilder: Flexible structure generation of crosslinked collagen fibrils
Debora Monego, Matthias Brosz, Johanna Buck, Vsevolod Viliuga +5 more
2024bioRxiv3 citations Open access
Semantic Scholar
QM/MM calculation of protein magnetic shielding tensors with generalized hybrid-orbital method: a GIAO approach.
Yoshinobu Akinaga, Jaewoon Jung, S. Ten-no
2011Physical Chemistry, Chemical Physics - PCCP3 citations
Semantic Scholar
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
2025International Conference on High Performance Computing in Asia-Pacific Region2 citations Open access
Semantic Scholar
Coarse-grained Martini 3 model for collagen fibrils
Matthias Brosz, Johanna Buck, F. Grünewald, Debora Monego +4 more
2025Biophysical Journal2 citations Open access
Semantic Scholar
Langevin integration for isothermal-isobaric condition with a large time step.
Jaewoon Jung, Yuji Sugita
2025Journal of Chemical Physics2 citations Open access
Semantic Scholar
Surface-Tension Replica-Exchange Molecular Dynamics Method for Efficient Conformational Sampling of Biological Membrane Systems
Takaharu Mori, Jaewoon Jung, Y. Sugita
20142 citations Open access
Semantic Scholar
Statistical evaluation of nitrogenous oxygen demand as a dominant driver of oxygen dynamics in wastewater treatment plant effluent-impacted watershed
Yuri Kim, Sooho Park, Jaewoon Jung, Dong-Ho Choi +3 more
2026Environmental Technology & Innovation1 citations Open access
Semantic Scholar

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Y. Sugita×31
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Y. Sugita — researcher profile on SciRah
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C. Kobayashi — researcher profile on SciRah
Takaharu Mori×13
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Takaharu Mori — researcher profile on SciRah
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Yuji Sugita — researcher profile on SciRah

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Y. Matsunaga×5

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Suyong Re — researcher profile on SciRah

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Y. Kawashima×3

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Y. Kawashima — researcher profile on SciRah

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