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RIKEN Baton Zone Program Nakamura Laboratory

Head of Nakamura Laboratory: Shinichiro Nakamura (Ph.D.)

Research Summary

Shinichiro  Nakamura(Ph.D.)

Problems with industrial reality are the subjects of collaborations. Methods mainly consist of computational approaches, such as quantum chemistry, molecular dynamics, band calculations, signal processing, and statistic tools including Bayes statistics as well as category theory.

The mechanism of OEC by Mn cluster is the biggest ever solved problem in natural photosynthesis. The goal of our research is to develop the materials and concepts for energy, health, and environment, learning from natural systems. The focus is on the natural mechanism of OEC in PSII.

Main Research Fields

  • Mathematical & Physical Sciences

Related Research Fields

  • Complex Systems
  • Mathematical & Physical Sciences
  • Chemistry
  • Engineering
  • Biology
  • Agricultural Sciences


  • Quantum Chemistry
  • Molecular Science for industrial problems
  • Electrode and battery related materials
  • Catalyst and Photonics
  • Bayes Statistics, Stochastics, Category Theory

Selected Publications

  • 1. Fujimoto A, Fujinaga N, Nishimura R, Hatano E, Kono L, Nagai A, Sekine A, Hattori Y, Kojima Y, Yasuda N, Morimoto M, Yokojima S, Nakamura S, B L Feringa, Uchida K.:
    "Photoinduced swing of a diarylethene thin broad sword shaped crystal: a study on the detailed mechanism"
    Chem. Sci., 11, 12307-12315 (2020)
  • 2. Koizumi K, Hashizume D, Umeda J, Kimura M, Yokota T, Ito M, Iguchi A, Nakamura S.:
    "A comparison of geometries and electronic structure of plumbogummite (PbAl3P2O14H6), Pb2P4O12 and Pb2P2O7"
    Chemical Physics Letters Vol. 756, P.13780 (2020)
  • 3. Ogata K, Hatakeyama M, Sakamoto Y, Nakamura S.:
    "Investigation of a Pathway for Water Delivery in Photosystem II Protein by Molecular Dynamics Simulation"
    J. Phys. Chem. B, 123, 6444-6452. (2019)
  • 4. Sakamoto Y, Noda Y, Ohno K, Koike K, Fujii K, Suzuki T M, Morikawa T, Nakamura S.:
    "First Principles Calculation of Surface Dependent Electronic Structures: A Study on β-FeOOH and γ-FeOOH"
    Phys. Chem. Chem. Phys., 21, 18486-18494, (2019)
  • 5. Kanie Y, Yamaguchi Y, Hayashi A, Uzawa J, Hatakeyama M, Hidaka Y, Toda N, Nakamura S, Kanie O.:
    "Structural analysis of a novel lipooligosaccharide (LOS) from Rhodobacter azotoformans"
    Carbohydr. Res., 473, 104-114. (2019)
  • 6. Sakamoto Y, Noda Y, Ohno K, Nakamura S.:
    "Chemical Insights from Theoretical Electronic States in nickel Hydroxide and Monolayer Surface Model"
    J. Phys. Chem. C, 121, 24603-24611. (2017)
  • 7. Hatano E, Morimoto M, Imai T, Hyodo K, Fujimoto A, Nishimura R, Sekine A, Yasuda N, Yokojima S, Nakamura S, Uchida K.:
    "Photosalient Phenomena that Mimic Impatiens Are Observed in Hollow Crystals of Diarylethene with a Perfluorocyclohexene Ring"
    Ange. Chem. Int. Ed., 56, 12576-12580. (2017)
  • 8. Nishimura R, Hyodo K, Sawaguchi H, Yamamoto Y, Nonomura Y, Mayama H, Yokojima S, Nakamura S, Uchida K.:
    "Fractional Surfaces of Molecular Crystals Mimicking Lotus Leaf with Phototunable Double Roughness Structures"
    J. Am. Chem. Soc., 138, 10299-1030. (2016)
  • 9. Hatakeyama M, Ogata K, Fujii K, Yachandra V. K, Yano J, Nakamura S.:
    "Structural Changes in the S3 State of the Oxygen Evolving Complex in Photosystem II"
    Chem. Phys. Lett., 651, 243-250. (2016)
  • 10. Ogata K, Yuki T, Hatakeyama M, Uchida W, Nakamura S.:
    "All-Atom Molecular Dynamics Simulation of Photo system ⅡEmbedded in Thylakoid Membrane"
    J. Am. Chem. Soc., 135, 15670-15673. (2013)

Lab Members

Principal investigator

Shinichiro Nakamura
Head of Nakamura Laboratory

Core members

Katsuya Kanda
Research Scientist
Yuki Sakamoto
Postdoctoral Researcher
Yuki Harada
Postdoctoral Researcher
Shigeru Uchiyama
Research Associate
Eiichiro Nishihara
Research Associate
Kunio Tanabe
Senior Visiting Scientist
Hirokazu Hori
Senior Visiting Scientist
Kingo Uchida
Visiting Scientist
Makoto Naruse
Visiting Scientist
Satoshi Yokojima
Visiting Scientist
Koji Ogata
Visiting Scientist
Makoto Hatakeyama
Visiting Scientist
Koji Maruyama
Visiting Scientist
Yuuki Ono
Visiting Scientist

Contact Information

2-1 Hirosawa,
Wako, Saitama
351-0198, Japan
Email: snakamura [at] riken.jp