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Research Scientist Jaewoon Jung

EDUCATION

2005 Ph.D. (Physics) Korea Advanced Institute of Science and Techonology, Korea
2000 M.S. (Physics) Korea Advanced Institute of Science and Techonology, Korea
1998 B.S. (Physics) Korea Advanced Institute of Science and Techonology, Korea

RESEARCH AND TEACHING EXPERIENCES

2015-present Technical Scientist, RIKEN Theoretical Molecular Science Laboratory, Japan
2010-present Research Scientist, RIKEN Advanced Institute for Computational Science, Japan
2010 Assistant Professor Extraordinary, Graduate School of System Informatics, Kobe University, Japan
2009 Assistant Professor Extraordinary, Graduate School of Engineering, Kobe University, Japan
2006 Post Doctor, Graduate School of Information Science, Nagoya University, Japan
2005 Post Doctor, Department of Chemistry, Korea Institute of Science and Technology, Korea

PROFESSIONAL AFFILIATIONS

The Biophysical Society of Japan, Japan Society for Molecular Science

RESEARCH PROJECTS

  1. Development of parallel Molecular Dynamics program
  2. Development of QM/MM program and simulations of the enzyme reactions

PUBLICATIONS

  1. New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, and Yuji Sugita
  2. Elucidation of interactions regulating conformational stability and dynamics of SARS-Cov-2 S-protein. Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, and Yuji Sugita
  3. Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time steps. Jaewoon Jung and Yuji Sugita
  4. A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
  5. 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 Wall, Anna Lappala, Dominic Phillips, William Fischer, Chang-Shung Tung, Tamar Schlick, Yuji Sugita, and Karissa Y. Sanbonmatsu
  6. Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
  7. Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
  8. 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, and Yuji Sugita
  9. Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems. Jaewoon Jung and Yuji Sugita
  10. Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations. Jaewoon Jung, Akira Naurse, Chigusa Kobayashi, and Yuji Sugita
  11. Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein. Yasuhiro Matsunaga, Yasuaki Komuro, Chigusa Kobayashi, Jaewoon Jung, Takaharu Mori, and Yuji Sugita
  12. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, and Yuji Sugita
  13. GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations. Jaewoon Jung*, Takaharu Mori*, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, and Yuji Sugita
  14. Midpoint Cell Method for Hybrid (MPI+OpenMP) Parallelization of Molecular Dynamics Simulations. Jaewoon Jung, Takaharu Mori, and Yuji Sugita
  15. Surface-tension replica-exchange molecular dynamics method for enhanced sampling of biological membrane systems. Takaharu Mori, Jaewoon Jung, and Yuji Sugita
  16. Efficient lookup table using a linear function of inverse distance squared. Jaewoon Jung, Takaharu Mori, and Yuji Sugita
  17. Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations. Jaewoon Jung, Suyong Re, Yuji Sugita, and Seiichiro Ten-no
  18. A QM/MM-MD study on protein electronic properties: Circular dichroism spectra of oxytocin and insulin. Yuya Kitagawa, Yoshinobu Akinaga, Yukio Kawashima, Jaewoon Jung, and Seiichiro Ten-no
  19. QM/MM calculation of protein magnetic shielding tensors with generalized hybrid-orbital method: A GIAO approach. Yoshinobu Akinaga, Jaewoon Jung, and Seiichiro Ten-no
  20. A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals: Implementation for electronic excited states. Yukio Kawashima, Haruyuki Nakano, Jaewoon Jung, and Seiichiro Ten-no
  21. Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation. Suyong Re, Takashi Imai, Jaewoon Jung, Seiichiro Ten-no, and Yuji Sugita
  22. Møller-Plesset gradient implementation in the generalized hybrid orbital (GHO) method. Jaewoon Jung, Yuji Sugita, and Seiichiro Ten-no
  23. Topological quantities determining the folding/unfolding rate of two-state folding proteins. Jaewoon Jung, Alan J. Bugals, and Eok-Kyun Lee
  24. Simple avoidance of Pauli repulsion errors in the generalized hybrid orbital (GHO) method. Jaewoon Jung and Seiichiro Ten-no
  25. Assessment of free energy expressions in RISM integral equation theory: Theoretical prediction of partition coefficients revisited.
  26. Seiichiro Ten-no, Jaewoon Jung, Hiroshi Chuman, and Yukio Kawashima
  27. A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase. Suyong Re, Jaewoon Jung, Seiichiro Ten-no, and Yuji Sugita
  28. New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals. Jaewoon Jung, Cheol Ho Choi, Yuji Sugita, and Seiichiro Ten-no
  29. Topological Determinants of protein unfolding rates. Jaewoon Jung, Jooyoung Lee, and Hie-Tae Moon
  30. Identification of the Protein Native Structure by Using a Sequence-Dependent Feature in Contact Maps. Jaewoon Jung, Jooyoung Lee, and Hie-Tae Moon