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Research Scientist Jaewoon Jung

EDUCATION

RESEARCH AND TEACHING EXPERIENCES

PROFESSIONAL AFFILIATIONS

RESEARCH PROJECTS

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

PUBLICATIONS

1. Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
   J. Compute. Chem. 44, 1740-1749 (2023).
2. Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation. Yasuhiro Matsunaga, Motoshi Kamiya, Hiraku Oshima, Jaewoon Jung, Shingo Ito and Yuji Sugita
   Biophys. rev. 14, 1503-1512 (2022).
3. Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. Cheng Tan, Jaewoon Jung, Chigusa Kobayashi,  Diego Ugarte La Torre, Shoji Takada and Yuji Sugita
   PLOS Comput. Biol. 18, e1009578 (2022).
4. The inhderent flexibility of receptor binding domains in SARS-CoV-2 spike protein. Hisham M Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung and Yuji Sugita
   eLife 11, e75720 (2022).
5. Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase. Chigusa Kobayashi, Yasuhiro Matsunaga, Jaewoon Jung and Yuji Sugita
   Proc. Natl. Acad. Sci. USA 118, e2105507118 (2021).
6. Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems. Jaewoon Jung, Kento Kasahara, Chigusa Kobayashi, Hiraku Oshima, Takaharu Mori and Yuji Sugita
   J. Chem. Theory Comput. 17, 5312-5321 (2021).
7. 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
   J. Comput. Chem., 42, 231-241 (2021)
8. 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
   Biophysical J., 120, 1060-1071 (2021)
9. Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time steps. Jaewoon Jung and Yuji Sugita
   J. Chem. Phys., 153, 234115 (2020).
10. A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
    J. Chem. Phys., 153, 044110 (2020).
11. 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
    J. Comput. Chem., 40, 1919-1930 (2019).
12. Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
    J. Chem. Theory Comput., 15, 84-94 (2019).
13. Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation. Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita
    J. Chem. Phys., 148, 164109 (2018).
14. 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
    J. Comput. Chem., 38, 2193-2203 (2017). (*equally contributed)
15. Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems. Jaewoon Jung and Yuji Sugita
    J. Comput. Chem., 38, 1410-1418 (2017).
16. Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations. Jaewoon Jung, Akira Naurse, Chigusa Kobayashi, and Yuji Sugita
    J. Chem. Theory Comput., 12, 4947–4958 (2016).
17. 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
    J. Phys. Chem. Lett., 7, 1446-1451 (2016).
18. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. Jaewoon Jung, Chigusa Kobayashi, Toshiyuki Imamura, and Yuji Sugita
    Comp. Phys. Comm., 200, 57-65 (2016).
19. 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
    WIREs Comput. Mol. Sci., 5, 310–323 (2015). (* equally contributed)
20. Midpoint Cell Method for Hybrid (MPI+OpenMP) Parallelization of Molecular Dynamics Simulations. Jaewoon Jung, Takaharu Mori, and Yuji Sugita
    J. Comp. Chem. 35, 1064-1072 (2014).
21. Surface-tension replica-exchange molecular dynamics method for enhanced sampling of biological membrane systems. Takaharu Mori, Jaewoon Jung, and Yuji Sugita
    J. Chem. Theory Comput. 9, 5629-5640 (2013).
22. Efficient lookup table using a linear function of inverse distance squared. Jaewoon Jung, Takaharu Mori, and Yuji Sugita
    J. Comput. Chem. 34, 2412-2420 (2013).
23. 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
    J. Chem. Phys. 138, 044106 (2013).
24. 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
    Chem. Phys. strong>401, 95-102 (2012).
25. QM/MM calculation of protein magnetic shielding tensors with generalized hybrid-orbital method: A GIAO approach. Yoshinobu Akinaga, Jaewoon Jung, and Seiichiro Ten-no
    Phys. Chem. Chem. Phys. 13, 14490-14499 (2011).
26. 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
    Phys. Chem. Chem. Phys. 13, 11731-11738 (2011).
27. 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
    J. Comput. Chem. 32, 260-270 (2011).
28. Møller-Plesset gradient implementation in the generalized hybrid orbital (GHO) method. Jaewoon Jung, Yuji Sugita, and Seiichiro Ten-no
    J. Chem. Phys. 132, 084106 (2010).
29. Topological quantities determining the folding/unfolding rate of two-state folding proteins. Jaewoon Jung, Alan J. Bugals, and Eok-Kyun Lee
    J. Sol. Chem. 39, 943-958 (2010).
30. Simple avoidance of Pauli repulsion errors in the generalized hybrid orbital (GHO) method. Jaewoon Jung and Seiichiro Ten-no
    Chem. Phys. Lett. 484, 344-348 (2010).
31. Assessment of free energy expressions in RISM integral equation theory: Theoretical prediction of partition coefficients revisited.Seiichiro Ten-no, Jaewoon Jung, Hiroshi Chuman, and Yukio Kawashima
    Mol. Phys. 108, 327-332 (2010).
32. A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase. Suyong Re, Jaewoon Jung, Seiichiro Ten-no, and Yuji Sugita
    Chem. Phys. Lett. 480, 284-288 (2009).
33. 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
    J. Chem. Phys. 127, 204102 (2007).
34. Topological Determinants of protein unfolding rates. Jaewoon Jung, Jooyoung Lee, and Hie-Tae Moon
    Proteins:Structure, Function, and Bioinformatics 58, 389-395 (2005).
35. Identification of the Protein Native Structure by Using a Sequence-Dependent Feature in Contact Maps. Jaewoon Jung, Jooyoung Lee, and Hie-Tae Moon
    J. Korean Phys. Soc. 46, 625-630 (2005).