Faculty Profiles - KIMURA, Akihiro

Papers - KIMURA, Akihiro

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Experimental and Theoretical Mutation of Exciton States on the Smallest Type-I Photosynthetic Reaction Center Complex of a Green Sulfur Bacterium Chlorobaclum tepidum Reviewed

Akihiro Kimura, Hirotaka Kitoh-Nishioka, Toru Kondo, Hirozo Oh-oka, Shigeru Itoh, Chihiro Azai

The Journal of Physical Chemistry B Vol. 128 ( 3 ) page： 731 - 743 2024.1

Polarizable Molecular Block Model: Toward the Development of an Induced Dipole Force Field for DNA Reviewed

Setsuko Nakagawa, Akihiro Kimura, Yuko Okamoto

The Journal of Physical Chemistry B Vol. 126 ( 50 ) page： 10646 - 10661 2022.12

Theoretical Model of the Far-Red-Light-Adapted Photosystem I Reaction Center of Cyanobacterium Acaryochloris marina Using Chlorophyll d and the Effect of Chlorophyll Exchange Reviewed

Akihiro Kimura, Hirotaka Kitoh-Nishioka, Toshimichi Aota, Tasuku Hamaguchi, Koji Yonekura, Keisuke Kawakami, Kyoko Shinzawa-Itoh, Natsuko Inoue-Kashino, Kentaro Ifuku, Eiki Yamashita, Yasuhiro Kashino, Shigeru Itoh

The Journal of Physical Chemistry B Vol. 126 ( 22 ) page： 4009 - 4021 2022.6

Comparison between the Light-Harvesting Mechanisms of Type-I Photosynthetic Reaction Centers of Heliobacteria and Photosystem I: Pigment Site Energy Distribution and Exciton State Reviewed International journal

Akihiro Kimura, Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh

The Journal of Physical Chemistry B Vol. 125 ( 15 ) page： 3727 - 3738 2021.4

Authorship：Lead author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

The photosynthetic pigment system on the anoxygenic type-I reaction center of heliobacteria (hRC), which has a symmetrical structure, was analyzed. The excitonic coupling among all of the bacteriochlorophyll g (BChl-g) molecules and chlorophyll a (Chl-a) molecules and the site energy for each pigment were calculated using Poisson-TrESP and the charge density coupling (CDC) methods. The obtained theoretical model reproduced the optical absorption and circular dichroism spectra. It also interpreted the decay-associated spectra upon the photoselective laser excitation, which represent the ultrafast excitation energy migration process, better than the simpler hRC models that assumed constant pigment site energy shifts. Spatial movements of excitation energy on pigments on hRC upon the laser excitation were visualized. The energy dissipation by carotenoid molecules in hRC was also predicted. The hRC model was compared with the model of the reaction center of cyanobacterial photosystem I (PSI), which carries 95 Chl-a on the analogous type-I structure with significantly different amino-acid sequences, pigment species, and output redox powers. It is shown that the locations and site energy values of pigments in hRC resemble those in the core of PSI, except for the red-Chl-a sites, suggesting common functional mechanisms implicated in their evolution.

DOI： 10.1021/acs.jpcb.0c09400

Web of Science

PubMed

Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem I Reviewed

Hirotaka Kitoh-Nishioka, Yasuteru Shigeta, Shigeru Itoh, Akihiro Kimura

The Journal of Physical Chemistry B Vol. 124 ( 2 ) page： 389 - 403 2020.1

Theoretical Model of Exciton States and Ultrafast Energy Transfer in Heliobacterial Type I Homodimeric Reaction Center Reviewed

Akihiro Kimura, Shigeru Itoh

The Journal of Physical Chemistry B Vol. 122 ( 50 ) page： 11852 - 11859 2018.12

Time-dependent renormalized Redfield theory II for off-diagonal transition in reduced density matrix Reviewed

Akihiro Kimura

Chemical Physics Letters Vol. 661 page： 70 2016.8

Time-dependent renormalized Redfield theory Reviewed

Akihiro Kimura

Chemical Physics Letters Vol. 645 page： 123 2015.12

Assignment of Exciton Domain in Light Harvesting Systems Based on the Variational Polaron Approach Reviewed

Yuta Fujihashi, and Akihiro Kimura

The Journal of Physical Chemistry B Vol. 119 page： 8349-8356 2015.6

Quantitative correction of the rate constant in the improved variational master equation for excitation energy transfer Reviewed

Akihiro Kimura, Yuta Fujihashi

The Journal of Chemical Physics Vol. 141 page： 194110 2014.11

Improved Variational Master Equation Theory for the Excitation Energy Transfer Reviewed

Yuta Fujihashi, and Akihiro Kimura

Journal of the Physical Society of Japan Vol. 83 ( 1 ) page： 014801 2014.1

*General theory of excitation energy transfer in donor-mediator-acceptor systems Reviewed

Akihiro Kimura

The Journal of Chemical Physics Vol. 130 page： 154103 2009.4

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal)

General theory of the excitation energy transfer EET in the case of donor-mediator-acceptor
system was constructed by using generalized master equation GME. In this theory, we consider the
direct and indirect transitions in the EET consistently. Hence, our theory includes the quantum
mechanical interference between the direct and indirect transitions automatically. Memory functions
in the GME were expressed by the overlap integrals among the time-dependent emission spectrum
of the donor, the absorption spectrum of the mediator, the time-dependent emission spectrum of the
mediator, and the absorption spectrum of the acceptor. In the Markov limit of the memory functions,
we obtained the rate of EET which consists of three terms due to the direct transition, the indirect
transition, and the interference between them. We found that the interference works effectively in
the limit of slow thermalization at the intermediate state. The formula of EET rate in this limit was
expressed by the convolution of the EET interaction and optical spectra. The interference effect
strongly depends on the width of the absorption spectrum of mediator molecule and the energy gap
between the donor and the mediator molecules.

*Advanced Theory of Excitation Energy Transfer in Dimers Reviewed

A. Kimura and T. Kakitani

J. Phys. Chem. A Vol. 111 page： 12042 2007.11

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal)

Previously, we developed a unified theory of the excitation energy transfer (EET) in dimers, which is applicable
to all of the cases of excitonic coupling strength (Kimura, A.; Kakitani, T.; Yamato, T. J. Phys. Chem. B
2000, 104, 9276). This theory was formulated only for the forward reaction of the EET. In the present paper,
we advanced this theory so that it might include the backward reaction of the EET as well as the forward
reaction. This new theory is formulated on the basis of the generalized master equation (GME), without
using physically unclear assumptions. Comparing the present result with the previous one, we find that the
excitonic coupling strengths of criteria between exciton and partial exciton and between hot transfer and
hopping (Fo¨rster) mechanisms are reduced by a factor of 2. The critical coherency èc is also reduced
significantly.

Interference, Fluctuation, and Alternation of Electron Tunneling in Protein Media 1. Two Tunneling Routes in Photosynthetic Reaction Center Alternate Due to Thermal Fluctuation of Protein Conformation.

H. Nishioka, A. Kimura, T. Yamato, T. Kawatsu, T. Kakitani

J. Phys. Chem. B Vol. 109 page： 1978 2005

Interference, Fluctuation, and Alternation of Electron Tunneling in Protein Media. 2. Non-Condon Theory for the Energy Gap Dependence of Electron Transfer Rate. Reviewed

H. Nishioka, A. Kimura, T. Yamato, T. Kawatsu T. Kakitani

J. Phys. Chem. B Vol. 109 page： 15621 2005

Fluctuating Hydration Structure around Nanometer-Size Hydrophobic Solutes. I. Caging and Drying around C60 and C60H60 Spheres. Reviewed

T. Hotta, A. Kimura, M. Sasai

J. Phys. Chem. B Vol. 109 page： 18600 2005

液体のダイナミックスと非平衡物理学

吉森明、（記録係：木村明洋、鳥飼正志、後藤振一郎）

Vol. 82 page： 357 2004

Language：Japanese Publishing type：Research paper (bulletin of university, research institution)

本紀要は、2003年9月30日から10月2日の間に、名古屋大学大学院情報科学研究科にて行われた、九州大学理学研究科物理学部門の吉森明による「溶液のダイナミックスと非平衡物理学」というタイトルの集中講義の講義ノートである。

*Theoretical Analysis of the Energy Gap Dependence of the Reconstituted B800 -> B850 Excitation Energy Transfer Rate in Bacterial LH2 Complexes. Reviewed

A. Kimura and T. Kakitani

J. Phys. Chem. B. Vol. 107 page： 7932 2003

*Theory of Excitation Energy Transfer in the Intermediate Coupling Case of Clusters. Reviewed

A. Kimura and T. Kakitani

J. Phys. Chem. B. Vol. 107 page： 14486 2003

Empirical Formula of Exciton Coherent Domain in Oligomers and Application to LH2. Reviewed

T. Kakitani and A. Kimura

J. Phys. Chem. A Vol. 106 page： 2173 2002

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Papers - KIMURA, Akihiro