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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. Weight Averaged Anharmonic Vibrational Calculations: Applications to Polypeptide, Lipid Bilayers, and Polymer Materials.

    Kiyoshi Yagi, Hiroki Otaki, Pai‐Chi Li, Bo Thomsen, Yuji Sugita
    Molecular Spectroscopy: A Quantum Chemistry Approach, Volume 1, DOI: 10.1002/9783527814596.ch5 (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).

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