Kyushu University Academic Staff Educational and Research Activities Database
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Hiroshi Watanabe Last modified date:2023.05.31

Graduate School
Undergraduate School

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 Reseacher Profiling Tool Kyushu University Pure
Academic Degree
Doctor of Science
Country of degree conferring institution (Overseas)
Field of Specialization
Quantum Chemistry, Molecular Science, Biophysics, Quantum Computing
ORCID(Open Researcher and Contributor ID)
Total Priod of education and research career in the foreign country
Research Interests
  • Development of variational quantum algorithm based on the circuit structure optimization
    keyword : Quantum computing, variational quantum algorithm, variational quantum eigensolver, circuit structure optimization
  • Incorporation of the quantum chemical effect of solvation into molecular dynamics simulation
    keyword : Molecular dynamics, quantum chemical calculation, solvation effect
Academic Activities
1. Kaito Wada, Rudy Raymond, Yuki Sato, Hiroshi C. Watanabe, Full optimization of a single-qubit gate on the generalized sequential quantum optimizer, arXiv, 10.48550/arXiv.2209.08535, arXiv:2209.08535, 2022.09.
2. Hiroshi C. Watanabe*, Masayuki Yamada, Yohichi Suzuki, Proton transfer in bulk water using the full adaptive QM/MM method: Integration of solute- and solvent-adaptive approaches, Physical Chemistry Chemical Physics, 10.1039/D1CP00116G , 23, 8344-8360, 2021.04, [URL].
3. Hiroshi C. Watanabe*, Qiang Cui, Quantitative analysis of QM/MM boundary artifacts and the correction in adaptive QM/MM methods, Journal of Chemical Theory and Computation, 10.1021/acs.jctc.9b00180, 15, 7, 3917-3928, 2019.05.
4. Hiroshi C. Watanabe, Tomas Kubar, Marcus Elstner, Size-Consistent Multipartitioning QM/MM: A Stable and Efficient Adaptive QM/MM Method, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10.1021/ct5005593, 10, 10, 4242-4252, 2014.10, We propose a new adaptive QM/MM method, the size-consistent multipartitioning (SCMP) QM/MM scheme, which enables stable and computationally efficient QM/MM simulations. A number of partitionings with identical size of the QM and the MM regions are considered with a new adaptive scheme in order to (1) realize smooth QM/MM switching, (2) introduce a conserved quantity (total energy, Hamiltonian), (3) avoid spurious artificial forces on the QM/MM border, and (4) allow for an efficient parallel implementation. Benchmark simulations performed for "QM water in MM water" show that energy conservation can be significantly improved and the computational efficiency allows treating also larger QM regions, for which previous methods had to face an intractable increase in computer time..
5. Hiroshi C. Watanabe, Kai Welke, Daniel J. Sindhikara, Peter Hegemann, Marcus Elstner, Towards an Understanding of Channelrhodopsin Function: Simulations Lead to Novel Insights of the Channel Mechanism, JOURNAL OF MOLECULAR BIOLOGY, 10.1016/j.jmb.2013.01.033, 425, 10, 1795-1814, 2013.05, Channelrhodopsins (ChRs) are light-gated cation channels that mediate ion transport across membranes in microalgae (vectorial catalysis). ChRs gain increasing attention as useful tools for the analysis of neural networks in tissues and living animals (optogenetics). In fact, various mutagenesis approaches have realized practical applications with high reliability by enhancement of the expression level, channel kinetics control, and color tuning. Furthermore, the recently published x-ray structure has provided valuable information for further atomistic studies and engineering ChRs for a wider application. The present study is a computational attempt to describe the functional mechanism at the atomic level based on the x-ray structure. We present several structural characteristics that are highly involved in ion channel gating and ion transport, including (1) water distribution, (2) cation binding sites, (3) intrahelical hydrogen bond, (4) DC gate, and (5) active site. (C) 2013 Elsevier Ltd. All rights reserved..
6. Hiroshi C. Watanabe, Kai Welke, Franziska Schneider, Satoshi Tsunoda, Feng Zhang, Karl Deisseroth, Peter Hegemann, Marcus Elstner, Structural Model of Channelrhodopsin, JOURNAL OF BIOLOGICAL CHEMISTRY, 10.1074/jbc.M111.320309, 287, 10, 7456-7466, 2012.03, Channelrhodopsins (ChRs) are light-gated cation channels that mediate ion transport across membranes in microalgae (vectorial catalysis). ChRs are now widely used for the analysis of neural networks in tissues and living animals with light (optogenetics). For elucidation of functional mechanisms at the atomic level, as well as for further engineering and application, a detailed structure is urgently needed. In the absence of an experimental structure, here we develop a structural ChR model based on several molecular computational approaches, capitalizing on characteristic patterns in amino acid sequences of ChR1, ChR2, Volvox ChRs, Mesostigma ChR, and the recently identified ChR of the halophilic alga Dunaliella salina. In the present model, we identify remarkable structural motifs that may explain fundamental electrophysiological properties of ChR2, ChR1, and their mutants, and in a crucial validation of the model, we successfully reproduce the excitation energy predicted by absorption spectra..
Works, Software and Database
1. .
Membership in Academic Society
  • Best Poster Presentation Award
  • Best Presentation Award
  • Invitated Presentation Award
  • Best Presentation Award
  • Young Scientist Award