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Senior Research Scientist Kiyoshi Yagi

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EDUCATION

2004 Ph. D. (Engineer) University of Tokyo, Japan.
2001 M. A. (Applied Chem.) University of Tokyo, Japan.
1999 B. S. (Applied Chem.) University of Tokyo, Japan.）

RESEARCH AND TEACHING EXPERIENCES

2015-present Senior Research Scientist, RIKEN Theoretical Molecular Science Laboratory, Japan.
2012-2015 Research Scientist, RIKEN Advanced Science Institute, Japan.
2011-2012 Research Assistant Professor, University of Illinois at Urbana-Champaign, USA.
2009-2011 Lecturer, University of Yamanashi, Japan.
2008 Visiting Scholar, Aarhus University, Denmark.
2005 Visiting Scholar, University of Florida, USA.
2005-2009 Assistant Professor, University of Tokyo, Japan.
2004-2005 JSPS Postdoctoral fellowship, University of Tokyo, Japan.）

AWARDS AND GRANTS

2015 Japan Society for Molecular Science, Young Scientists Award）

PROFESSIONAL AFFILIATIONS

Chemical Society of Japan, Japan Society for Molecular Science, The Spectroscopical Society of Japan, Theoretical Chemistry Society, Protein Science Society of Japan

RESEARCH PROJECTS

  1. Vibrational structure theory for complex systems
  2. Development of QM/MM method
  3. Anharmonic vibrational analysis of biomolecules
  4. Reaction mechanism of enzymatic reactions

PUBLICATIONS

  1. Amide A band is a fingerprint for water dynamics in reverse osmosis polyamide membranes.
    Donatas Surblys, Taro Yamada, Bo Thomsen, Tomonori Kawakami, Isamu Shigemoto, Jun Okabe, Takafumi Ogawa, Masahiro Kimura, Yuji Sugita, Kiyoshi Yagi J. Memb. Sci., DOI:10.1016/j.memsci.2019.117705 (2019).
  2. Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations.
    Kiyoshi Yagi, Kenta Yamada, Chigusa Kobayashi, and Yuji Sugita J. Chem. Theory Comput., 15, 1924-1938 (2019).
  3. Fundamental peak disappears upon binding of a noble gas: a case of the vibrational spectrum of PtCO in an argon matrix
    Yuriko Ono, Kiyoshi Yagi, Toshiyuki Takayanagi and Tetsuya Taketsugu
    Phys. Chem. Chem. Phys., 20, 3296-3302 (2018).
  4. Infrared Spectra of Protonated Water Clusters, H+(H2O)4, in Eigen and Zundel Forms Studied by Vibrational Quasi-Degenerate Perturbation Theory.
    Kiyoshi Yagi and Bo Thomsen.
    J. Phys. Chem. A, 121, 2386-2398 (2017).
  5. Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations.
    Hiroki Otaki, Kiyoshi Yagi, Shun-ichi Ishiuchi, Masaaki Fujii, and Yuji Sugita.
    J. Phys. Chem. B, 120, 10199-10213 (2016).
  6. Detection of Sphingomyelin Clusters by Raman Spectroscopy.
    Koichiro Shirota, Kiyoshi Yagi, Takehiko Inaba, Pai-Chi Li, Michio Murata, Yuji Sugita, and Toshihide Kobayashi.
    Biophys. J., 111, 999-1007 (2016).
  7. A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer.
    K. Yagi, P. -C. Li, K. Shirota, T. Kobayashi and Y. Sugita,
    Phys. Chem. Chem. Phys., 17, 29113-29123 (2015).
  8. A simple state-average procedure determining optimal coordinates for anharmonic vibrational calculations.
    B. Thomsen, K. Yagi and O. Christiansen,
    Chem. Phys. Lett., 610-611, 288-297 (2014).
  9. Optimized coordinates in vibrational coupled cluster calculations.
    B. Thomsen, K. Yagi and O. Christiansen,
    J. Chem. Phys., 140, 154102 (2014).
  10. Vibrational quasi-degenerate perturbation theory with optimized coordinates: Applications to ethylene and trans-1,3-butadiene.
    K. Yagi and H. Otaki,
    J. Chem. Phys., 140, 084113 (2014).