Jaewoon Jung

发表

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

Y. Sugita, T. Ando, M. Feig, 2016, eLife.

Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning.

Y. Sugita, F. Tama, O. Miyashita, 2019, Structure.

Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.

Yuji Sugita, Jaewoon Jung, Takaharu Mori, 2013, Journal of chemical theory and computation.

A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase

Y. Sugita, S. Ten-no, Jaewoon Jung, 2009 .

Møller-Plesset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method.

Y. Sugita, S. Ten-no, Jaewoon Jung, 2010, The Journal of chemical physics.

Simple avoidance of Pauli repulsion errors in the generalized hybrid orbital (GHO) method

S. Ten-no, Jaewoon Jung, 2010 .

Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein

Y. Sugita, Takaharu Mori, Jaewoon Jung, 2021, Biophysical Journal.

A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations.

Y. Sugita, Jaewoon Jung, Cheng Tan, 2020, The Journal of chemical physics.

Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation

Y. Sugita, Jaewoon Jung, Hiraku Oshima, 2022, Biophysical Reviews.

QM/MM calculation of protein magnetic shielding tensors with generalized hybrid-orbital method: a GIAO approach.

S. Ten-no, Jaewoon Jung, Yoshinobu Akinaga, 2011, Physical chemistry chemical physics : PCCP.

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

Y. Sugita, S. Takada, Jaewoon Jung, 2021, bioRxiv.

Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations.

Yuji Sugita, Jaewoon Jung, Chigusa Kobayashi, 2016, Journal of chemical theory and computation.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Yasuhiro Matsunaga, Yuji Sugita, Jaewoon Jung, 2015, Wiley interdisciplinary reviews. Computational molecular science.

GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

Yasuhiro Matsunaga, Yuji Sugita, Jaewoon Jung, 2017, J. Comput. Chem..

Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations

Tamar Schlick, Yuji Sugita, Jaewoon Jung, 2019, J. Comput. Chem..

1 1 Implementation of residue-level coarse-grained models in GENESIS for 2 large-scale molecular dynamics simulations 3

Y. Sugita, S. Takada, Jaewoon Jung, 2021 .

The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein

Y. Sugita, Takaharu Mori, Jaewoon Jung, 2021, bioRxiv.

Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein.

Yasuhiro Matsunaga, Yuji Sugita, Jaewoon Jung, 2016, The journal of physical chemistry letters.

One-pot synthesis of hybrid TiO2-polyaniline nanoparticles by self-catalyzed hydroamination and oxidative polymerization from TiO2-methacrylic acid nanoparticles.

Jaewoon Jung, K. Carter, W. Jo, 2011, Chemical communications.

Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation

Yuji Sugita, Seiichiro Ten-no, Suyong Re, 2011, J. Comput. Chem..

Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase

Y. Sugita, Jaewoon Jung, Y. Matsunaga, 2021, Proceedings of the National Academy of Sciences.

A QM/MM-MD study on protein electronic properties: Circular dichroism spectra of oxytocin and insulin

S. Ten-no, Jaewoon Jung, Y. Kawashima, 2012 .

A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals: implementation for electronic excited states.

S. Ten-no, Jaewoon Jung, H. Nakano, 2011, Physical chemistry chemical physics : PCCP.

New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems

Cheng Tan, Yutaka Ishikawa, Yuji Sugita, 2020, J. Comput. Chem..

Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations.

Yuji Sugita, Seiichiro Ten-no, Jaewoon Jung, 2013, The Journal of chemical physics.

Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation.

Yuji Sugita, Jaewoon Jung, Chigusa Kobayashi, 2018, The Journal of chemical physics.

Assessment of free energy expressions in RISM integral equation theory: theoretical prediction of partition coefficients revisited

S. Ten-no, H. Chuman, Jaewoon Jung, 2010 .

Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer

Y. Sugita, Jaewoon Jung, C. Kobayashi, 2023, J. Comput. Chem..

Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

Toshiyuki Imamura, Yuji Sugita, Jaewoon Jung, 2016, Comput. Phys. Commun..

Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations

Yuji Sugita, Jaewoon Jung, Takaharu Mori, 2014, J. Comput. Chem..

GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems

Y. Sugita, Jaewoon Jung, Cheng Tan, 2023, bioRxiv.

Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step.

Yuji Sugita, Jaewoon Jung, Chigusa Kobayashi, 2018, Journal of chemical theory and computation.

New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals

Yuji Sugita, Seiichiro Ten-no, Jaewoon Jung, 2007 .

Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems.

Y. Sugita, Takaharu Mori, Jaewoon Jung, 2021, Journal of chemical theory and computation.

Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems

Yuji Sugita, Jaewoon Jung, Y. Sugita, 2017, J. Comput. Chem..

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

I. Yu, Takaharu Mori, Jaewoon Jung, 2024, The journal of physical chemistry. B.