2023/02/05 更新

写真a

オノ ジュンイチ
小野 純一
Scopus 論文情報  
論文数: 0  Citation: 0  h-index: 7

Citation Countは当該年に発表した論文の被引用数

所属
理工学術院 理工学術院総合研究所
職名
次席研究員(研究院講師)
メールアドレス
メールアドレス

学位

  • 京都大学   博士(理学)

 

研究分野

  • 基礎物理化学   理論・計算分子科学

  • 生物物理学   理論生物物理学

論文

  • Hybrid in Silico Drug Discovery Study toward the Development of Oral Antivirals for COVID-19

    Uika KOSHIMIZU, Junichi ONO, Yoshifum FUKUNISHI, Hiromi NAKAI

    Journal of Computer Chemistry, Japan   21 ( 2 ) 48 - 51  2022年11月  [査読有り]

    DOI

  • Hydroxide Ion Mechanism for Long‐Range Proton Pumping in the Third Proton Transfer of Bacteriorhodopsin

    Junichi Ono, Chika Okada, Hiromi Nakai

    ChemPhysChem   23   e202200109  2022年07月  [査読有り]

    担当区分:筆頭著者

    DOI

    Scopus

    1
    被引用数
    (Scopus)
  • Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations

    Junichi Ono, Uika Koshimizu, Yoshifumi Fukunishi, Hiromi Nakai

    Chemical Physics Letters   794   139489 - 139489  2022年05月  [査読有り]

    担当区分:筆頭著者

    DOI

    Scopus

    2
    被引用数
    (Scopus)
  • Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models

    Hiromi Nakai, Toshiaki Takemura, Junichi Ono, Yoshifumi Nishimura

    The Journal of Physical Chemistry B   125 ( 39 ) 10947 - 10963  2021年10月  [査読有り]

    DOI

    Scopus

    7
    被引用数
    (Scopus)
  • Hydroxide Ion Carrier for Proton Pumps in Bacteriorhodopsin: Primary Proton Transfer

    Junichi Ono, Minori Imai, Yoshifumi Nishimura, Hiromi Nakai

    The Journal of Physical Chemistry B   124 ( 39 ) 8524 - 8539  2020年10月  [査読有り]

    担当区分:筆頭著者

    DOI

    Scopus

    10
    被引用数
    (Scopus)
  • Weighted histogram analysis method for multiple short-time metadynamics simulations

    Junichi Ono, Hiromi Nakai

    Chemical Physics Letters   751   137384 - 137384  2020年07月  [査読有り]

    担当区分:筆頭著者

    DOI

    Scopus

    7
    被引用数
    (Scopus)
  • Reversible Sodium Metal Electrodes: Is Fluorine an Essential Interphasial Component?

    Kyosuke Doi, Yuki Yamada, Masaki Okoshi, Junichi Ono, Chien‐Pin Chou, Hiromi Nakai, Atsuo Yamada

    Angewandte Chemie   131 ( 24 ) 8108 - 8112  2019年06月

    DOI

  • Reversible Sodium Metal Electrodes: Is Fluorine an Essential Interphasial Component?

    Kyosuke Doi, Yuki Yamada, Masaki Okoshi, Junichi Ono, Chien-Pin Chou, Hiromi Nakai, Atsuo Yamada

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   58 ( 24 ) 8024 - 8028  2019年06月

     概要を見る

    Alkaline metals are an ideal negative electrode for rechargeable batteries. Forming a fluorine-rich interphase by a fluorinated electrolyte is recognized as key to utilizing lithium metal electrodes, and the same strategy is being applied to sodium metal electrodes. However, their reversible plating/stripping reactions have yet to be achieved. Herein, we report a contrary concept of fluorine-free electrolytes for sodium metal batteries. A sodium tetraphenylborate/monoglyme electrolyte enables reversible sodium plating/stripping at an average Coulombic efficiency of 99.85 % over 300 cycles. Importantly, the interphase is composed mainly of carbon, oxygen, and sodium elements with a negligible presence of fluorine, but it has both high stability and extremely low resistance. This work suggests a new direction for stabilizing sodium metal electrodes via fluorine-free interphases.

    DOI

    Scopus

    54
    被引用数
    (Scopus)
  • Development of Large-Scale Excited-State Calculations Based on the Divide-and-Conquer Time-Dependent Density Functional Tight-Binding Method

    Nana Komoto, Takeshi Yoshikawa, Junichi Ono, Yoshifumi Nishimura, Hiromi Nakai

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION   15 ( 3 ) 1719 - 1727  2019年03月

     概要を見る

    In this study, the divide-and-conquer (DC) method was extended to time-dependent density functional tight-binding (TDDFTB) theory to enable excited-state calculations of large systems and is denoted by DC-TDDFTB. The efficient diagonalization algorithms of TDDFTB and DC-TDDFTB methods were implemented into our in-house program. Test calculations of polyethylene aldehyde and p-coumaric acid, a pigment in photoactive yellow protein, in water demonstrate the high accuracy and efficiency of the developed DC-TDDFTB method. Furthermore, the (TD)-DFTB metadynamics simulations of acridinium in the ground and excited states give reasonable pK(a) values compared with the corresponding experimental values.

    DOI

    Scopus

    10
    被引用数
    (Scopus)
  • Development of the Divide-and-Conquer Time-Dependent Density Functional Tight-Binding Method for Photoreceptor Protein

    Nana Komoto, Takeshi Yoshikawa, Junichi Ono, Hiromi Nakai

    JOURNAL OF COMPUTER CHEMISTRY-JAPAN   17 ( 3 ) 127 - 129  2018年

     概要を見る

    The divide-and-conquer (DC) method was extended to time-dependent density functional tight-binding (TDDFTB) theory to enable excited-state calculations of large systems, as denoted by DC-TDDFTB. In this article, the implementation of TDDFTB and DC-TDDFTB methods into our in-house program, DC-DFTB-K, is explained. Dependence of CPU time on system-size for the DC-TDDFTB calculations indicates significant reduction of computational cost by adopting the DC method. Owing to the feature, excited-state calculations for whole photoactive yellow protein (PYP) surrounded by 4684 water molecules could be carried out in order to examine the hydrogen bond between p-coumaric acid and Glu46 in PYP.

    DOI

  • Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

    Junichi Ono, Shoji Takada, Shinji Saito

    JOURNAL OF CHEMICAL PHYSICS   142 ( 21 )  2015年06月

     概要を見る

    An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchical conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Forster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function. (C) 2015 AIP Publishing LLC.

    DOI

    Scopus

    14
    被引用数
    (Scopus)
  • Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using spherical gaussian wave packets

    Junichi Ono, Kim Hyeon-Deuk, Koji Ando

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   113 ( 3 ) 356 - 365  2013年02月

     概要を見る

    A semiquantal (SQ) molecular dynamics (MD) simulation method using spherical Gaussian wave packets (WPs) is applied to a microscopic analysis of hydrogen-bond (H-bond) exchange dynamics in liquid water. We focus on the molecular jump mechanism of H-bond reorientation dynamics proposed from a classical MD simulation by Laage and Hynes (Science 2006, 311, 832). As a notable quantum effect, broadenings of both the oxygen and hydrogen WPs of jumping water are observed associated with the H-bond switching events. Nonetheless, quantum effects on averaged trajectories of structural parameters measured with respect to the WP centers are rather minor. A 1/f fluctuation of local H-bond number is observed in both SQ and classical simulations. This is obtained straightforwardly from the real-time trajectories, in contrast with the originally found 1/f fluctuation (Sasai et al., J. Chem. Phys. 1992, 96, 3045) of the total potential energies collected at quenched inherent structures. The quantum effects are found to accelerate the relaxation of H-bond number fluctuation, which is reflected in the region near the lower bound of the 1/f behavior in the power spectra. New developments in the implementation of SQMD simulations including all atoms are also described. (c) 2012 Wiley Periodicals, Inc.

    DOI

    Scopus

    7
    被引用数
    (Scopus)
  • Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets

    Junichi Ono, Koji Ando

    JOURNAL OF CHEMICAL PHYSICS   137 ( 17 )  2012年11月

     概要を見る

    A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed Gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many-body molecular systems in which the local anisotropic fluctuations of nuclear WPs play an essential role. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4762840]

    DOI

    Scopus

    9
    被引用数
    (Scopus)
  • Note: Inverted time-ordering in two-dimensional-Raman-terahertz spectroscopy of water

    Peter Hamm, Janne Savolainen, Junichi Ono, Yoshitaka Tanimura

    JOURNAL OF CHEMICAL PHYSICS   136 ( 23 )  2012年06月

    DOI

    Scopus

    24
    被引用数
    (Scopus)
  • Ultrafast energy relaxation and anisotropy decay of the librational motion in liquid water: A molecular dynamics study

    Takuma Yagasaki, Junichi Ono, Shinji Saito

    JOURNAL OF CHEMICAL PHYSICS   131 ( 16 )  2009年10月

     概要を見る

    We theoretically investigate intermolecular motions in liquid water in terms of third-order infrared (IR) spectroscopy. We calculate two-dimensional (2D) IR spectra, pump-probe signals, and three-pulse stimulated photon echo signals from the combination of equilibrium and nonequilibrium molecular dynamics simulations. The 2D IR spectra and the three-pulse photon echo peak shift exhibit that the frequency correlation of the librational motion decays with a time scale of 100 fs. The two-color 2D IR spectra and the pump-probe signals reveal that the energy transfer from the librational motion at 700 cm(-1) to the low frequency motion below 300 cm(-1) occurs with a time scale of 60 fs and the subsequent relaxation to the hot ground state takes place on a 500 fs time scale. The time scale of the anisotropy decay of the librational motion is found to be similar to 115 fs. The energy dissipation processes are investigated in detail by using the nonequilibrium molecular dynamics simulation, in which an electric field pulse is applied. We show that the fast energy transfer from the librational motion to the low frequency motion is mainly due to the librational-librational energy transfer. We also show that the fast anisotropy decay mainly arises from the rapid intermolecular energy transfer. (C) 2009 American Institute of Physics. [doi:10.1063/1.3254518]

    DOI

    Scopus

    35
    被引用数
    (Scopus)

▼全件表示

Misc

  • バクテリオロドプシンの分子動画に基づく大規模量子分子動力学法によるプロトン移動反応の解析

    小野 純一, 今井 みの莉, 西村 好史, 中井 浩巳

    分子シミュレーション研究会会誌アンサンブル   23 ( 3 ) 171 - 175  2021年07月

    記事・総説・解説・論説等(学術雑誌)  

    DOI

共同研究・競争的資金等の研究課題

  • 高速分子動画と大規模励起状態分子動力学の共創が拓く光生命化学現象の解明

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)

    研究期間:

    2022年04月
    -
    2024年03月
     

    小野 純一

  • 新型コロナ標的タンパク質の共有結合阻害に向けた酵素反応分子動力学シミュレーション

    日本学術振興会  科学研究費助成事業 基盤研究(C)

    研究期間:

    2021年04月
    -
    2024年03月
     

    小野 純一

  • 光受容タンパク質の量子的分子動力学シミュレーションによる遍在プロトンの機能解明

    日本学術振興会  科学研究費助成事業 基盤研究(S)

    研究期間:

    2018年06月
    -
    2023年03月
     

    中井 浩巳, 高野 光則, 吉川 武司, 小野 純一

     概要を見る

    本研究課題では、理論およびプログラム開発に関する基礎テーマ(T1), (T2)、基底状態が関与する応用テーマ(G1), (G2), (G3)ならびに励起状態が関与する応用テーマ(E1), (E2)を計画した。このうち、当初計画において2019年度には、(T1) GPUアクセラレータによる長時間シミュレーション手法の開発、(T2) 大規模励起状態シミュレーション手法の開発、(G1) バクテリオロドプシン(BR)のプロトン移動ダイナミクス、(G2) イオン輸送機能を持つ微生物型ロドプシンにおけるプロトン移動ダイナミクス、(G3) FoF1-ATP合成酵素における機能発現ダイナミクス、(E1) 光活性イエロータンパク質(PYP)における光異性化ダイナミクスに着手する予定であった。
    (T1)では、単精度・倍精度ハイブリッド型の実装により、GPUアクセラレータを用いた密度汎関数強束縛分子動力学(DC-DFTB-MD)法の更なる高速化を実現した。また、自由エネルギー曲面を効率的に求める拡張サンプリング法とDC-DFTB法を組み合わせた階層的並列計算アルゴリズムの開発を行った。(T2)では、GPUアクセラレータを用いて、DC-TDDFTB法の更なる高速化を図った。その結果、マルチGPUアクセラレータにより大幅な高速化に成功した。(G1)では、BRの5段階のプロトン移動のうち、2段階目の結晶構造を対象としたQMD計算を実行した。その結果、放出基近傍の空隙に出現した水分子が形成する水素結合ネットワーク上のプロトンリレーにより反応が進むことを明らかにした。

  • 分子動画に基づく大規模量子分子動力学法による生体内プロトン輸送機構の解明

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)

    研究期間:

    2020年04月
    -
    2022年03月
     

    小野 純一

 

担当経験のある科目(授業)

  • くらしの中の物質

    東京女子大学  

    2022年04月
    -
    継続中
     

  • 情報処理技法(リテラシ)II

    東京女子大学  

    2021年10月
    -
    継続中