2024/02/02 更新

写真a

スミ トモナリ
墨 智成
SUMI Tomonari
所属
異分野基礎科学研究所 准教授
職名
准教授

学位

  • 博士 (工学) ( 1999年3月   九州大学 )

研究キーワード

  • 海馬

  • 統計力学

  • 液体論

  • 化学物理

  • 生物物理

  • ソフトマター物理

  • 密度汎関数理論

  • 確率的モデリング

  • 分子モーター

  • 溶媒効果

  • タンパク質

  • フォールディング

  • シナプス可塑性

  • 炭素代謝

  • 代謝進化

  • 最終普遍共通祖先LUCA

  • 独立栄養生物

  • 宿主内持続感染

  • 新型コロナ後遺症

  • 免疫応答

  • SARS-CoV-2

  • 数理モデル

  • アルツハイマー病

  • ムスカリン受容体

研究分野

  • ライフサイエンス / 生物物理学

  • ナノテク・材料 / 基礎物理化学

  • 自然科学一般 / 生物物理、化学物理、ソフトマターの物理

  • 情報通信 / 生命、健康、医療情報学

学歴

  • 九州大学    

    1994年4月 - 1999年3月

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    国名: 日本国

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  • 山口大学   Faculty of Science  

    1990年4月 - 1994年3月

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    国名: 日本国

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経歴

  • 岡山大学   異分野基礎科学研究所   准教授

    2016年4月 - 現在

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  • 岡山大学   大学院自然科学研究科   准教授

    2013年4月 - 2016年3月

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  • 豊橋技術科学大学   助教

    2007年4月 - 2013年3月

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  • 豊橋技術科学大学   助手

    2002年4月 - 2007年3月

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  • 日本学術振興会特別研究員(PD)

    1999年 - 2002年

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所属学協会

委員歴

  • 分子シミュレーション学会   第35回分子シミュレーション討論会実行委員  

    2021年11月 - 2021年12月   

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    団体区分:学協会

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  • 日本生物物理学会   第56回日本生物物理学会実行委員  

    2018年9月   

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    団体区分:学協会

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  • 日本化学会   第42回国際化学オリンピック準備問題翻訳担当  

    2012年2月   

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    団体区分:学協会

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  • 日本化学会   第41回国際化学オリンピック準備問題翻訳担当  

    2011年2月   

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    団体区分:学協会

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  • 日本化学会   第40回国際化学オリンピック準備問題翻訳担当  

    2010年2月   

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    団体区分:学協会

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  • 日本物理学会   領域12化学物理分野運営委員  

    2008年5月 - 2009年4月   

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    団体区分:学協会

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  • 量子化学データーベースQCLDB収集  

    2006年10月 - 2011年3月   

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▼全件表示

 

論文

  • Solvation free energies of alcohols in water: temperature and pressure dependences 査読 国際誌

    Aoi Taira, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga

    Physical Chemistry Chemical Physics   25 ( 45 )   31107 - 31117   2023年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    The three important contributions to the solvation free energy of alcohols in water are quantified as functions of temperature and pressure based the perturbation combining method and other step-wise methods.

    DOI: 10.1039/d3cp03799a

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  • Molecular mechanism of the common and opposing co-solvent effects of fluorinated alcohol and urea on a coiled coil protein 査読 国際誌

    Noa Nakata, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga, Takeshi Morita, Hiroshi Imamura

    Protein Science   32 ( 10 )   e4763-1 - e4763-15   2023年8月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Protein Society  

    Abstract

    Alcohols and urea are widely used as effective protein denaturants. Among monohydric alcohols, 2,2,2‐trifluoroethanol (TFE) has large cosolvent effects as a helix stabilizer in proteins. In contrast, urea efficiently denatures ordered native structures, including helices, into coils. These opposing cosolvent effects of TFE and urea are well known, even though both preferentially bind to proteins; however, the underlying molecular mechanism remains controversial. Cosolvent‐dependent relative stability between native and denatured states is rigorously related to the difference in preferential binding parameters (PBPs) between these states. In this study, GCN4‐p1 with two‐stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2 M TFE and urea. As 2 M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization of helix by TFE and that of coil by urea. The former was caused by electrostatic interactions between TFE and side chains of the helices, while the latter was attributed to both electrostatic and dispersion interactions between urea and the main chains. Unexpectedly, reverse‐micelle‐like orientations of TFE molecules strengthened the electrostatic interactions between TFE and the side chains, resulting in strengthening of TFE solvation.

    DOI: 10.1002/pro.4763

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  • How do water-mediated interactions and osmotic second virial coefficients vary with particle size? 査読 国際誌

    Hidefumi Naito, Tomonari Sumi, Kenichiro Koga

    Faraday Discussions   2023年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    We examine quantitatively the solute-size dependences of the effective interactions between nonpolar solutes in water and in a simple liquid. The potential w(r) of mean force and the osmotic second...

    DOI: 10.1039/d3fd00104k

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  • Muscarinic acetylcholine receptor-dependent and NMDA receptor-dependent LTP and LTD share the common AMPAR trafficking pathway 査読

    Tomonari Sumi, Kouji Harada

    iScience   26 ( 3 )   106133 - 106133   2023年3月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.isci.2023.106133

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  • Immune response to SARS-CoV-2 in severe disease and long COVID-19 査読

    Tomonari Sumi, Kouji Harada

    iScience   25 ( 8 )   104723 - 104723   2022年8月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.isci.2022.104723

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  • Osmotic second virial coefficients for hydrophobic interactions as a function of solute size 国際誌

    Hidefumi Naito, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga

    The Journal of Chemical Physics   156 ( 22 )   221104 - 221104   2022年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AIP Publishing  

    To gain quantitative insight into how the overall strength of the hydrophobic interaction varies with the molecular size, we calculate osmotic second virial coefficients B for hydrophobic spherical molecules of different diameters σ in water based on molecular simulation with corrections to the finite-size and finite-concentration effects. It is shown that B (<0) changes by two orders of magnitude greater as σ increases twofold and its solute-size dependence is best fit by a power law B ∝ σ α with the exponent α ≃ 6, which contrasts with the cubic power law that the second virial coefficients of gases obey. It is also found that values of B for the solutes in a nonpolar solvent are positive but they obey the same power law as in water. A thermodynamic identity for B derived earlier [K. Koga, V. Holten, and B. Widom, J. Phys. Chem. B 119, 13391 (2015)] indicates that if B is asymptotically proportional to a power of σ, the exponent α must be equal to or greater than 6.

    DOI: 10.1063/5.0097547

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  • Improvement of Protein Solubility in Macromolecular Crowding during Myoglobin Evolution 査読 国際誌

    Yasuhiro Isogai, Hiroshi Imamura, Tomonari Sumi, Tsuyoshi Shirai

    Biochemistry   61 ( 15 )   1543 - 1547   2022年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.biochem.2c00166

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  • Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea 査読 国際誌

    Tomonari Sumi, Kouji Harada

    Communications Chemistry   4 ( 1 )   149-1 - 149-9   2021年12月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    <title>Abstract</title>The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood–Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic <italic>Thermosulfidibacter takaii</italic>, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.

    DOI: 10.1038/s42004-021-00585-0

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    その他リンク: https://www.nature.com/articles/s42004-021-00585-0

  • Water‐mediated interactions destabilize proteins 査読 国際誌

    Tomonari Sumi, Hiroshi Imamura

    Protein Science   30 ( 10 )   2132 - 2143   2021年8月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/pro.4168

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    その他リンク: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/pro.4168

  • Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals 査読 国際誌

    Yasuhiro Isogai, Hiroshi Imamura, Setsu Nakae, Tomonari Sumi, Ken-ichi Takahashi, Tsuyoshi Shirai

    iScience   24 ( 8 )   102920 - 102920   2021年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    Myoglobin (Mb) is highly concentrated in the myocytes of diving mammals such as whales and seals, in comparison with land animals, and its molecular evolution has played a crucial role in their deep-sea adaptation. We previously resurrected ancestral whale Mbs and demonstrated the evolutional strategies for higher solubility under macromolecular crowding conditions. Pinnipeds, such as seals and sea lions, are also expert diving mammals with Mb-rich muscles. In the present study, we resurrected ancestral pinniped Mbs and investigated their biochemical and structural properties. Comparisons between pinniped and whale Mbs revealed the common and distinctive strategies for the deep-sea adaptation. The overall evolution processes, gaining precipitant tolerance and improving thermodynamic stability, were commonly observed. However, the strategies for improving the folding stability differed, and the pinniped Mbs exploited the shielding of hydrophobic surfaces more effectively than the whale Mbs.

    DOI: 10.1016/j.isci.2021.102920

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  • Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions 査読 国際誌

    Hiroyuki Katsuto, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga

    The Journal of Physical Chemistry B   125 ( 23 )   6296 - 6305   2021年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.1c03388

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  • A mathematical study on the effects of a combination of an immune checkpoint inhibitor and a mutagen for anti-HIV-1 therapy 招待 査読 国際誌

    Kouji Harada, Tomonari Sumi

    Artificial Life and Robotics   26 ( 2 )   210 - 215   2021年5月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    DOI: 10.1007/s10015-020-00664-w

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    その他リンク: https://link.springer.com/article/10.1007/s10015-020-00664-w/fulltext.html

  • Unveiling the Interaction Potential Surface between Drug-Entrapped Polymeric Micelles Clarifying the High Drug Nanocarrier Efficiency 査読 国際誌

    Takeshi Morita, Sayaka Mukaide, Ziqiao Chen, Kenjirou Higashi, Hiroshi Imamura, Kunikazu Moribe, Tomonari Sumi

    Nano Letters   21 ( 3 )   1303 - 1310   2021年2月

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    担当区分:最終著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.nanolett.0c03978

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  • Two different regimes in alcohol-induced coil–helix transition: effects of 2,2,2-trifluoroethanol on proteins being either independent of or enhanced by solvent structural fluctuations 査読 国際共著 国際誌

    Hiroyo Ohgi, Hiroshi Imamura, Tomonari Sumi, Keiko Nishikawa, Yoshikata Koga, Peter Westh, Takeshi Morita

    Physical Chemistry Chemical Physics   23 ( 10 )   5760 - 5772   2021年

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    担当区分:責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    <p>Solvent fluctuation (<italic>G</italic>TFE-TFE) of 2,2,2-trifluoroethanol (TFE)–H2O mixture was determined by small-angle X-ray scattering investigation. Protein’s coil–helix transition can be induced by preferential binding of TFE (Δ<italic>Γ</italic>23) without aggregation of TFE.</p>

    DOI: 10.1039/d0cp05103a

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  • Mechanism underlying hippocampal long-term potentiation and depression based on competition between endocytosis and exocytosis of AMPA receptors 査読 国際誌

    Tomonari Sumi, Kouji Harada

    Scientific Reports   10 ( 14711 )   14711-1 - 14711-14   2020年12月

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    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    <title>Abstract</title>N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP) and long-term depression (LTD) of signal transmission form neural circuits and thus are thought to underlie learning and memory. These mechanisms are mediated by AMPA receptor (AMPAR) trafficking in postsynaptic neurons. However, the regulatory mechanism of bidirectional plasticity at excitatory synapses remains unclear. We present a network model of AMPAR trafficking for adult hippocampal pyramidal neurons, which reproduces both LTP and LTD. We show that the induction of both LTP and LTD is regulated by the competition between exocytosis and endocytosis of AMPARs, which are mediated by the calcium-sensors synaptotagmin 1/7 (Syt1/7) and protein interacting with C-kinase 1 (PICK1), respectively. Our result indicates that recycling endosomes containing AMPAR are always ready for Syt1/7-dependent exocytosis of AMPAR at peri-synaptic/synaptic membranes. This is because molecular motor myosin Vb constitutively transports the recycling endosome toward the membrane in a Ca2+-independent manner.

    DOI: 10.1038/s41598-020-71528-3

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    その他リンク: https://www.nature.com/articles/s41598-020-71528-3

  • An Improved Model-potential-free Analysis of the Structure Factor Obtained from a Small-angle Scattering: Acquisitions of the Pair Distribution Function and the Pair Potential 査読 国際誌

    Ken-ichi Amano, Ryosuke Sawazumi, Hiroshi Imamura, Tomonari Sumi, Kota Hashimoto, Kazuhiro Fukami, Haru Kitaoka, Naoya Nishi, Tetsuo Sakka

    Chemistry Letters   49 ( 9 )   1017 - 1021   2020年9月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:The Chemical Society of Japan  

    Small-angle X-ray and neutron scatterings can measure the structure factor of dispersed particles (macromolecules or colloidal particles), which can estimate the pair distribution function and the pair potential between the particles. However, the assumption of a model pair potential is usually necessary in the estimations. Especially when the system condition is complicated, one cannot prepare a plausible model pair potential. Hence, we propose a model-potential-free method. The new method does not require the assumptions of rigid particle surface and random phase approximation unlike the conventional model-potential-free method.

    DOI: 10.1246/cl.200292

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  • Is F1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip 国際共著

    Tomonari Sumi, Stefan Klumpp

    Nano Letters   19 ( 5 )   3370 - 3378   2019年5月

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    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.nanolett.9b01181

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  • Interaction potential surface between Raman scattering enhancing nanoparticles conjugated with a functional copolymer 査読 国際誌

    Takeshi Morita, Yuki Ogawa, Hiroshi Imamura, Kouki Ookubo, Nobuo Uehara, Tomonari Sumi

    Phys. Chem. Chem. Phys.   21 ( 31 )   16889 - 16894   2019年5月

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    担当区分:最終著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1039/C9CP01946D

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  • Theoretical analysis on thermodynamic stability of chignolin 査読 国際誌

    Tomonari Sumi, Kenichiro Koga

    Sci. Rept.   9   5186-1 - 5186-9   2019年3月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/s41598-019-41518-1

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  • Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy 査読 国際誌

    Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenji Mochizuki, Kenichiro Koga

    JOURNAL OF COMPUTATIONAL CHEMISTRY   39 ( 4 )   202 - 216   2018年2月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY  

    Recently, we proposed a reference-modified density functional theory (RMDFT) to calculate solvation free energy (SFE), in which a hard-sphere fluid was introduced as the reference system instead of an ideal molecular gas. Through the RMDFT, using an optimal diameter for the hard-sphere reference system, the values of the SFE calculated at room temperature and normal pressure were in good agreement with those for more than 500 small organic molecules in water as determined by experiments. In this study, we present an application of the RMDFT for calculating the temperature and pressure dependences of the SFE for solute molecules in water. We demonstrate that the RMDFT has high predictive ability for the temperature and pressure dependences of the SFE for small solute molecules in water when the optimal reference hard-sphere diameter determined for each thermodynamic condition is used. We also apply the RMDFT to investigate the temperature and pressure dependences of the thermodynamic stability of an artificial small protein, chignolin, and discuss the mechanism of high-temperature and high-pressure unfolding of the protein. (c) 2017 Wiley Periodicals, Inc.

    DOI: 10.1002/jcc.25101

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  • Tracing whale myoglobin evolution by resurrecting ancient proteins 査読 国際誌

    Yasuhiro Isogai, Hiroshi Imamura, Setsu Nakae, Tomonari Sumi, Ken-ichi Takahashi, Taro Nakagawa, Antonio Tsuneshige, Tsuyoshi Shirai

    Sci. Rept.   8 ( 1 )   16883-1 - 16883-14   2018年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/s41598-018-34984-6

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  • Numerical calculation on a two-step subdiffusion behavior of lateral protein movement in plasma membranes 査読 国際誌

    Tomonari Sumi, Atsushi Okumoto, Hitoshi Goto, Hideo Sekino

    PHYSICAL REVIEW E   96 ( 4 )   042410-1 - 042410-10   2017年10月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER PHYSICAL SOC  

    A two-step subdiffusion behavior of lateral movement of transmembrane proteins in plasma membranes has been observed by using single-molecule experiments. A nested double-compartment model where large compartments are divided into several smaller ones has been proposed in order to explain this observation. These compartments are considered to be delimited by membrane-skeleton "fences" and membrane-protein "pickets" bound to the fences. We perform numerical simulations of a master equation using a simple two-dimensional lattice model to investigate the heterogeneous diffusion dynamics behavior of transmembrane proteins within plasma membranes. We show that the experimentally observed two-step subdiffusion process can be described using fence and picket models combined with decreased local diffusivity of transmembrane proteins in the vicinity of the pickets. This allows us to explain the two-step subdiffusion behavior without explicitly introducing nested double compartments.

    DOI: 10.1103/PhysRevE.96.042410

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  • Myosin V: Chemomechanical-coupling ratchet with load-induced mechanical slip 査読 国際誌

    Tomonari Sumi

    SCIENTIFIC REPORTS   7   13489-1 - 13489-12   2017年10月

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    担当区分:筆頭著者, 最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    A chemomechanical-network model for myosin V is presented on the basis of both the nucleotide-dependent binding affinity of the head to an actin filament (AF) and asymmetries and similarity relations among the chemical transitions due to an intramolecular strain of the leading and trailing heads. The model allows for branched chemomechanical cycles and takes into account not only two different force-generating mechanical transitions between states wherein the leading head is strongly bound and the trailing head is weakly bound to the AF but also load-induced mechanical-slip transitions between states in which both heads are strongly bound. The latter is supported by the fact that ATP-independent high-speed backward stepping has been observed for myosin V, although such motility has never been for kinesin. The network model appears as follows: (1) the high chemomechanical-coupling ratio between forward step and ATP hydrolysis is achieved even at low ATP concentrations by the dual mechanical transitions; (2) the forward stepping at high ATP concentrations is explained by the front head-gating mechanism wherein the power stroke is triggered by the inorganic-phosphate (Pi) release from the leading head; (3) the ATP-binding or hydrolyzed ADP.Pi-binding leading head produces a stable binding to the AF, especially against backward loading.

    DOI: 10.1038/s41598-017-13661-0

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  • Influence of co-non-solvency on hydrophobic molecules driven by excluded volume effect 査読 国際誌

    Kenji Mochizuki, Tomonari Sumi, Kenichiro Koga

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   19 ( 35 )   23915 - 23918   2017年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    We demonstrate by molecular dynamics simulation that co-nonsolvency manifests itself in the solvent-induced interaction between three hydrophobes, methane, propane and neopentane, inmethanol-water mixtures. Decomposition of the potential of mean force, based on the potential distribution theorem, clearly shows that the solute-solvent entropic change is responsible for stabilizing the aggregation of these hydrophobic molecules. Furthermore, we show that the entropic change pertains to the excluded volume effect.

    DOI: 10.1039/c7cp04152g

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  • Design principles governing chemomechanical coupling of kinesin 査読 国際誌

    Tomonari Sumi

    SCIENTIFIC REPORTS   7   1163-1 - 1163-13   2017年4月

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    担当区分:筆頭著者, 最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

    A systematic chemomechanical network model for the molecular motor kinesin is presented in this report. The network model is based on the nucleotide-dependent binding affinity of the heads to an microtubule (MT) and the asymmetries and similarities between the chemical transitions caused by the intramolecular strain between the front and rear heads. The network model allows for multiple chemomechanical cycles and takes into account all possible mechanical transitions between states in which one head is strongly bound and the other head is weakly bound to an MT. The results obtained from the model show the ATP-concentration dependence of the dominant forward stepping cycle and support a gated rear head mechanism in which the forward step is controlled by ATP hydrolysis and the resulting ADP-bound state of the rear head when the ATP level is saturated. When the ATP level is saturated, the energy from ATP hydrolysis is used to concentrate the chemical transition flux to a force-generating state that can produce the power stroke. In contrast, when the ATP level is low, the hydrolysis energy is consumed to avoid states in which the leading head is weakly bound to an MT and to inhibit frequent backward steps upon loading.

    DOI: 10.1038/s41598-017-01328-9

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  • Hydrophobic Polymer Chain in Water That Undergoes a Coil-to-Globule Transition Near Room Temperature 査読 国際誌

    I. Hatano, K. Mochizuki, T. Sumi, K. Koga

    JOURNAL OF PHYSICAL CHEMISTRY B   120 ( 47 )   12127 - 12134   2016年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER CHEMICAL SOC  

    A simple model of a hydrophobic polymer in water is studied. The model polymer, a chain of Lennard-Jones particles with a fixed bond length, is designed in such a way that it undergoes a coil-to-globule conformational change near room temperature upon heating in liquid water. At low temperatures (less than or similar to 270 K), the polymer chain under vacuum takes a globular conformation, whereas in water, it adopts an extended form. At higher temperatures (greater than or similar to 320 K), the polymer has a more compact conformation in water than under vacuum. The same polymer chain in a nonpolar solvent is always extended and shows no sign of a coil-to-globule transformation up to 360 K. The heat-induced collapse of the polymer uniquely observed in water is not attributed to the hydrophobic effect on individual monomers, but it is correlated with the temperature dependence of the potential of mean force between two monomers at contact distance.

    DOI: 10.1021/acs.jpcb.6b08347

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  • Interaction Potential between Biological Sensing Nanoparticles Determined by Combining Small-Angle X‑ray Scattering and Model-Potential-Free Liquid Theory 査読 国際誌

    Takeshi Morita, Nobuo Uehara, Kenji Kuwahata, Hiroshi Imamura, Takeshi Shimada, Kouki Ookubo, Maki Fujita, Tomonari Sumi

    J. Phys. Chem. C   120 ( 44 )   25564 - 25571   2016年11月

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    担当区分:最終著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/acs.jpcc.6b06487

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  • A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution 査読 国際誌

    Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenichiro Koga

    JOURNAL OF CHEMICAL PHYSICS   144 ( 22 )   224104-1 - 224104-15   2016年6月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids. Published by AIP Publishing.

    DOI: 10.1063/1.4953191

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  • Liquid–liquid phase separation of N-isopropylpropionamide aqueous solutions above the lower critical solution temperature 査読 国際誌

    Kenji Mochizuki, Tomonari Sumi, Kenichiro Koga

    Sci. Rept.   6   24657-1 - 24657-10   2016年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/srep24657

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  • Mean-Field Approximation to the Hydrophobic Hydration in the Liquid-Vapor Interface of Water 査読 国際誌

    Kiharu Abe, Tomonari Sumi, Kenichiro Koga

    J. Phys. Chem. B   120 ( 8 )   2012 - 2019   2016年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/acs.jpcb.5b10169

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  • Driving forces for the pressure-induced aggregation of poly(N-isopropylacrylamide) in water 査読 国際誌

    Kenji Mochizuki, Tomonari Sumi, Kenichiro Koga

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   18 ( 6 )   4697 - 4703   2016年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Driving forces for the pressure-induced aggregation of poly(N-isopropylacrylamide) (PNiPA) in water are investigated by performing extensive molecular dynamics simulations. First, we observe that the model short oligomer of PNiPA with a modified OPLS-AA force field in water shrinks with increasing pressure. At varying pressures, the potentials of mean force (PMFs) between a pair of N-isopropylpropionamide (NiPPA) molecules, the repeating unit of PNiPA, are obtained and decomposed into the nonpolar and Coulombic contributions. The nonpolar contribution is the PMF between the hypothetical nonpolar NiPPA molecules in the solvent, which is mainly due to the molecular volume effect. The attractive force between NiPPA molecules is enhanced at higher pressures in agreement with the behavior of PNiPA. This pressure dependence of the PMF is caused by the growing nonpolar contribution at higher pressures. In contrast, the Coulombic contribution to the PMF becomes higher overall, making the mean force less attractive or more repulsive, with increasing pressure. The strength of the aggregation and its pressure dependence of the nonpolar contribution in water are closely reproduced even in nonpolar solvents. The degree of the pressure dependence is explained by the isothermal compressibility or the tightness of the solvation shell around an isolated solute, without regard to the existence and variation of hydrogen bond networks in a solvent. The role of hydrogen bonds in the aggregation of NiPPA and PNiPA molecules is also discussed.

    DOI: 10.1039/c5cp07674a

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  • Investigation of a virtual nested two-dimensional lattice model for representing the diffusive motion of a transmembrane protein in cell membrane 査読

    Atsushi OKUMOTO, Tomonari SUMI, Hideo SEKINO, Hitoshi GOTO

    Journal of Computer Chemistry, Japan   15 ( 6 )   229 - 231   2016年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:日本コンピュータ化学会  

    <p>As a refinement of the fluid mosaic model for explaining cell membrane functions, membrane-skeleton fence model and anchored membrane protein picket model have been proposed according to the tracing experiment of a single molecule in plasma membrane. In addition, the experimental observation that the diffusive motion of a transmembrane protein in plasma membrane leads to a normal diffusion through two-step relaxation has suggested that there are two types of nested compartments, large and small. In this paper, we propose a virtual nested two-dimensional lattice model that can express a nested compartment structure of plasma membrane using three parameters in order to represent such a single molecule diffusion movement. Using this 2D lattice model, various diffusive motion simulations of one particle random walks were performed and their trajectories were analyzed by Detrended fluctuation analysis. As a result, we have confirmed that both plasma membrane models, "fence" and "picket," can be represented by our virtual nested 2D lattice model.</p>

    DOI: 10.2477/jccj.2016-0069

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  • Erratum: “A solvation-Free-Energy Functional: A Reference-Modified Density Functional Formulation" [J. Comput. Chem. 2015, 36, 1359–1369] 査読 国際誌

    Tomonari Sumi, Ayori Mitsutake, Yutaka Maruyama

    J. Comput. Chem.   36 ( 26 )   2009 - 2011   2015年10月

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    担当区分:筆頭著者, 責任著者   記述言語:英語  

    DOI: 10.1002/jcc.24035

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  • A solvation-free-energy functional: A reference-modified density functional formulation 査読 国際誌

    Tomonari Sumi, Ayori Mitsutake, Yutaka Maruyama

    JOURNAL OF COMPUTATIONAL CHEMISTRY   36 ( 18 )   1359 - 1369   2015年7月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    The three-dimensional reference interaction site model (3D-RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation-free-energy (SFE) for large solute molecules in water. To improve the free-energy density functional for the SFE of solute molecules, we propose a reference-modified density functional theory (RMDFT) that is a general theoretical approach to construct the free-energy density functional systematically. In the RMDFT formulation, hard-sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction-site-model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side-chain analogues as well as for 504 small organic molecules. (c) 2015 Wiley Periodicals, Inc.

    DOI: 10.1002/jcc.23942

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  • A model-free method for extracting interaction potential between protein molecules using small-angle X-ray scattering 査読 国際誌

    Tomonari Sumi, Hiroshi Imamura, Takeshi Morita, Keiko Nishikawa

    JOURNAL OF MOLECULAR LIQUIDS   200   42 - 46   2014年12月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    A small-angle X-ray scattering has been used to probe protein-protein interaction in solution. Conventional methods need to input modeled potentials with variable/invariable parameters to reproduce the experimental structure factor. In the present study, a model-free method for extracting the excess part of effective interaction potential between protein molecules in solutions over an introduced hard-sphere potential by using experimental data of small-angle X-ray scattering is presented on the basis of liquid-state integral equation theory. The reliability of the model-free method is tested by the application to experimentally derived structure factors for dense lysozyme solutions with different solution conditions [Javid et al., Phys. Rev. Lett. 99, 028101 (2007), Schroer et al., Phys. Rev. Lett. 106, 178102 (2011)]. The structure factors calculated from the model-free method agree well with the experimental ones. The model-free method provides the following picture of the lysozyme solution: these are the stabilization of contact-pair configurations, large activation barrier against their formations, and screened Coulomb repulsion between the charged proteins. In addition, the model-free method will be useful to verify whether or not a model for colloidal system is acceptable to describing protein-protein interaction. (C) 2014 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.molliq.2014.03.014

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  • Temperature dependence of local solubility of hydrophobic molecules in the liquid-vapor interface of water 招待 査読 国際誌

    Kiharu Abe, Tomonari Sumi, Kenichiro Koga

    JOURNAL OF CHEMICAL PHYSICS   141 ( 18 )   18C516-1 - 18C516-8   2014年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    One important aspect of the hydrophobic effect is that solubility of small, nonpolar molecules in liquid water decreases with increasing temperature. We investigate here how the characteristic temperature dependence in liquid water persists or changes in the vicinity of the liquid-vapor interface. From the molecular dynamics simulation and the test-particle insertion method, the local solubility Sigma of methane in the liquid-vapor interface of water as well as Sigma of nonpolar solutes in the interface of simple liquids are calculated as a function of the distance z from the interface. We then examine the temperature dependence of Sigma under two conditions: variation of Sigma at fixed position z and that at fixed local solvent density around the solute molecule. It is found that the temperature dependence of Sigma at fixed z depends on the position z and the system, whereas Sigma at fixed local density decreases with increasing temperature for all the model solutions at any fixed density between vapor and liquid phases. The monotonic decrease of Sigma under the fixed-density condition in the liquid-vapor interface is in accord with what we know for the solubility of nonpolar molecules in bulk liquid water under the fixed-volume condition but it is much robust since the solvent density to be fixed can be anything between the coexisting vapor and liquid phases. A unique feature found in the water interface is that there is a minimum in the local solubility profile Sigma(z) on the liquid side of the interface. We find that with decreasing temperature the minimum of Sigma grows and at the same time the first peak in the oscillatory density profile of water develops. It is likely that the minimum of Sigma is due to the layering structure of the free interface of water. (C) 2014 AIP Publishing LLC.

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  • Model-potential-free analysis of small angle scattering of proteins in solution: insights into solvent effects on protein–protein interaction 査読 国際誌

    Tomonari Sumi, Hiroshi Imamura, Takeshi Morita, Keiko Nishikawa, K. Nishikawa

    Phys. Chem. Chem. Phys.   16 ( 46 )   25492 - 25497   2014年

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1039/c4cp03606a

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  • Time series data analysis using DFA 査読 国際誌

    A. Okumoto, T. Akiyama, H. Sekino, T. Sumi

    IRAGO CONFERENCE 2013   1585   175 - 180   2014年

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    記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:AMER INST PHYSICS  

    Detrended fluctuation analysis (DFA) was originally developed for the evaluation of DNA sequence and interval for heart rate variability (HRV), but it is now used to obtain various biological information. In this study we perform DFA on artificially generated data where we already know the relationship between signal and the physical event causing the signal. We generate artificial data using molecular dynamics. The Brownian motion of a polymer under an external force is investigated. In order to generate artificial fluctuation in the physical properties, we introduce obstacle pillars fixed to nanostructures. Using different conditions such as presence or absence of obstacles, external field, and the polymer length, we perform DFA on energies and positions of the polymer.

    DOI: 10.1063/1.4866638

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  • Modulation of the intermolecular interaction of myoglobin by removal of the heme 査読 国際誌

    Hiroshi Imamura, Takeshi Morita, Tomonari Sumi, Yasuhiro Isogai, Minoru Kato, Keiko Nishikawa

    JOURNAL OF SYNCHROTRON RADIATION   20   919 - 922   2013年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Toward understanding intermolecular interactions governing self-association of proteins, the present study investigated a model protein, myoglobin, using a small-angle X-ray scattering technique. It has been known that removal of the heme makes myoglobin aggregation-prone. The interparticle interferences of the holomyoglobin and the apomyoglobin were compared in terms of the structure factor. Analysis of the structure factor using a model potential of Derjaguin-Laudau-Verwey-Overbeek (DLVO) suggests that the intermolecular interaction potential of apomyoglobin is more attractive than that of holomyoglobin at short range from the protein molecule.

    DOI: 10.1107/S0909049513022772

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  • Effects of hydrophobic hydration on polymer chains immersed in supercooled water 査読 国際誌

    Tomonari Sumi, Hideo Sekino

    RSC Advances   3 ( 31 )   12743 - 12750   2013年8月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    A multiscale simulation of a hydrophobic polymer chain immersed in water including the supercooled region is presented. Solvent effects on the polymer conformation were taken into account via liquid-state density functional theory in which a free-energy functional model was constructed using a density response function of bulk water, determined from a molecular dynamics (MD) simulation. This approach overcomes sampling problems in simulations of high-viscosity polymer solutions in the deeply supercooled region. Isobars determined from the MD simulations of 4000 water molecules suggest a liquid-liquid transition in the deeply supercooled region. The multiscale simulation reveals that a hydrophobic polymer chain exhibits swelling upon cooling along isobars below a hypothesized second critical pressure
    no remarkable swelling is observed at higher pressures. These observations agree with the behavior of a polymer chain in a Jagla solvent model that qualitatively reproduces the thermodynamics and dynamics of liquid water. A theoretical analysis of the results obtained from the multiscale simulation show that a decrease in entropy due to the swelling arises from the formation of a tetrahedral hydrogen bond network in the hydration shell. © The Royal Society of Chemistry 2013.

    DOI: 10.1039/c3ra41320a

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  • Generality of anomalous expansion of polymer chains in supercritical fluids 査読 国際共著 国際誌

    Tadanori Koga, P. Gin, H. Yamaguchi, M. K. Endoh, M. Asada, L. Sendogdular, M. Kobayashi, A. Takahara, B. Akgun, S. K. Satija, T. Sumi

    POLYMER   52 ( 19 )   4331 - 4336   2011年9月

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    担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCI LTD  

    By using in-situ neutron reflectivity, we have investigated swelling isotherms of solvophilic and solvophobic end-grafted/non-grafted polymer chains on solid substrates in supercritical carbon dioxide and supercritical ethane. It was found that anomalous expansion of the polymer chains associated with excess absorption of the fluid molecules occurs in the large compressible regions of both supercritical fluids (SCFs) regardless of the polymer-fluid interactions. In addition, we found that the excess expansion of the solvophobic polymer chains in both SCFs collapse onto one master curve under the same magnitude of density fluctuations in the fluids. A simple thermodynamic two-state model along with the experimental results proposes that polymer chains are expanded independently of the polymer fluid interactions to further change solvent density fluctuations around the polymer chains, thereby lowering the free energy of the polymer/SCF systems. (C) 2011 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.polymer.2011.07.039

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  • Possible mechanism underlying high-pressure unfolding of proteins: formation of a short-period high-density hydration shell 査読 国際誌

    Tomonari Sumi, Hideo Sekino

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   13 ( 35 )   15829 - 15832   2011年

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

    Hydration effects on high-pressure unfolding of a hydrophobic polymer chain are investigated through a multiscale simulation based on density-functional theory. The results strongly suggest the following: a thermodynamic origin for high-pressure denaturation, i.e., the decrease in volume due to the unfolding can be explained by the formation of a short-period high-density hydration shell.

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  • Dewetting-induced globule-coil transitions of model polymers and possible implications high-temperature and low-pressure unfolding of proteins 査読 国際誌

    Tomonari Sumi, Nobuyuki Imazaki, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   132 ( 16 )   165101   2010年4月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    A thermodynamic analysis of high-temperature and low-pressure unfolding of proteins using a coarse-grained multiscale simulation combined with a liquid-state density-functional theory is presented. In this study, a hydrophobic polymer chain is employed as a probe molecule for investigating qualitative changes in a hydration free energy surface acting on proteins with changes in temperature and pressure. When water is heated so that its vapor pressure is equal to the atmospheric pressure, it boils. Long-ranged dewetting or drying caused by a hydrophobic planar wall and a large hydrophobic solute surface is significantly enhanced as it approaches the liquid-vapor coexistence curve of water. In this study, we demonstrate that high-temperature and low-pressure unfolding of the polymer chain is interpreted as dewetting-induced unfolding that occurs as it approaches the liquid-vapor coexistence. The unfolding of proteins due to high-temperature and low-pressure denaturation enhances the long-ranged dewetting or drying around them. The long-ranged dewetting phenomenon is considered to be originating from positive changes in both volume and entropy due to the high-temperature and low-pressure denaturation of the proteins. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3394864]

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  • “Erratum: “Dewetting-induced globule-coil transitions of model polymers and possible implications high-temperature and low-pressure unfolding of proteins” [J. Chem. Phys. 132, 165101 (2010)]” 査読 国際誌

    Tomonari Sumi, Nobuyuki Imazaki, Hideo Sekino

    J. Chem. Phys.   132 ( 16 )   229901-1 - 229901-1   2010年4月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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  • Hydrophobic effects on multivalent-salt-induced self-condensation of DNA 査読 国際誌

    Tomonari Sumi, Chiaki Suzuki, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   131 ( 16 )   161103   2009年10月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    Hydrophobic effects on multivalent-salt-induced self-condensation of a single polyelectrolyte chain such as DNA are investigated through a multiscale coarse-grained simulation based on density functional theory. We show that the water-mediated hydrophobic effect that was enhanced by hydration of multivalent salts plays an essential role in self-condensation of DNA. The self-condensation is interpreted as an entropy-driven compaction due to the hydration entropy gain. (C) 2009 American Institute of Physics. [doi:10.1063/1.3256982]

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  • Critical Casimir effect in a polymer chain in supercritical solvents 査読 国際誌

    Tomonari Sumi, Nobuyuki Imazaki, Hideo Sekino

    PHYSICAL REVIEW E   79 ( 3 )   030801   2009年3月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER PHYSICAL SOC  

    Density fluctuation effects on the conformation of a polymer chain in a supercritical solvent were investigated by performing a multiscale simulation based on the density-functional theory. We found (a) a universal swelling of the polymer chain near the critical point, irrespective of whether the polymer chain is solvophilic or solvophobic, and (b) a characteristic collapse of the polymer chain having a strong solvophilicity at a temperature slightly higher than the critical point, where the isothermal compressibility becomes less than the ideal one.

    DOI: 10.1103/PhysRevE.79.030801

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  • A self-consistent density-functional approach for homogeneous and inhomogeneous classical fluids 査読 国際誌

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   77 ( 3 )   034605-1 - 034605-8   2008年3月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:PHYSICAL SOC JAPAN  

    A self-consistent density-functional theory (DFT) for homogeneous and inhomogeneous classical fluids is presented using the density-functional Taylor expansion of an effective density that is introduced to describe the intrinsic excess free-energy functional. The first-order density expansion of the effective density around the uniform bulk density provides the same intrinsic excess chemical potential as the weighted density-functional approach proposed by Patra and Ghosh [J. Chem. Phys. 116 (2002) 8509]. The density-expansion coefficient is determined in a self-consistent manner by using Percus' relation between the pair correlation function and the density distribution function. The pair correlation functions for hard-sphere (HS) and Lennard-Jones (U) fluids as well as one-component plasma obtained from the self-consistent DFT are compared with the simulation results. The DFr with the self-consistent expansion coefficient is applied to calculate density distribution functions for the inhomogeneous fluids, interacting via the HS and LJ potentials, under external fields such as confinement in several geometries.

    DOI: 10.1143/JPSJ.77.034605

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  • Metal-nonmetal transition in dense fluid hydrogen 査読 国際誌

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   128 ( 4 )   044712   2008年1月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    The density dependence of the fluid structure and electrical resistivity of dense fluid hydrogen are studied along an isotherm of T=10(4) K using a density-functional theory for an electron-proton binary mixture. A metal-nonmetal (M-NM) transition is estimated to occur around the dimensionless density value of r(s)=2.19. The electrical resistivity rapidly increases around this value with a decrease in the hydrogen density. Simultaneously, the density dependence of the fluid structure reveals a significant jump near the M-NM transition. The character of the effective interaction potential between protons is qualitatively changed after the M-NM transition. The pressure variation suggests that the M-NM transition is a discontinuous phase transition under coexistence conditions with regard to the phase equilibrium between the metal and the nonmetal phases. (C) 2008 American Institute of Physics.

    DOI: 10.1063/1.2824930

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  • Behavior of a polymer chain immersed in a binary mixture of solvents 査読

    Tomonari Sumi, Kazuhiko Kobayashi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   127 ( 16 )   164904   2007年10月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    The behavior of a polymer chain immersed in a binary solvent mixture is investigated via a single-polymer simulation using an effective Hamiltonian, where the solvent effects are taken into account through a density-functional theory for polymer-solvent admixtures. The liquid-liquid phase separation of the binary solvent mixture is modeled as that of a Lennard-Jones binary fluid mixture with weakly attractive interactions between the different components. Two types of energetic preferences of the polymer chain for the better solvent - (A) no preferential solvophilicity and (B) strong preferential solvophilicity - are employed as polymer-solvent interaction models. The radius of gyration and the polymer-solvent radial distribution functions are determined from the simulations of various molar fractions along an isotherm slightly above the critical temperature of the liquid-liquid phase separation. These quantities near the critical point conspicuously depend on the strength of the preferential solvophilicity. In the case where the polymer exhibits a strong preferential solvophilicity, a remarkable expansion of the polymer chain is observed near the critical point. On the other hand, in the case where the polymer has no preferential solvophilicity, no characteristic variation of the polymer conformation is observed even near the critical point. These results indicate that the expansion of a polymer chain enhances the local phase separation around it, acting as a nucleus of demixing in the vicinity of the critical point. This phenomenon in binary solvents near the liquid-liquid critical point is similar to the expansion of the polymer chain in one-component supercritical solvents near the liquid-vapor critical point, which we have reported. (C) 2007 American Institute of Physics.

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  • Integral equation study of hydrophobic interaction: A comparison between the simple point charge model for water and a Lennard-Jones model for solvent 査読 国際誌

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   126 ( 14 )   144508-1 - 144508-7   2007年4月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    The hydrophobic interaction that is characterized by a potential of mean force (PMF) between spherical apolar solutes immersed in the simple point charge (SPCE) model for water was studied using an interaction site model integral equation based on a density-functional theory for molecular fluids. For comparison with the PMFs for various size solutes in the SPCE model, the PMFs in a Lennard-Jones (LJ) model for a solvent whose diameter is same as the SPCE model were also studied using a hypernetted chain integral equation. It is noted in the LJ model that the hydrogen bond and its network structure are completely ignored, but the translational entropy is taken into account. Both PMFs obtained from the SPCE model and from the LJ model have a large first minimum at a contact distance of solutes. In the case that the solute size is about three times larger than water, these PMFs also have a large maximum at a longer distance than the contact position. The strong attraction is attributed to the translational entropy of the solvent, and that the large activation barrier is arising from the weak attraction between the solute and the solvent. The comparison between the SPCE model and the LJ solvent model suggests that the qualitative description of the hydrophobic interaction is possible by using the LJ solvent model. On the other hand, the dewetting tendency on the surface of the apolar solute in a room condition is observed only on the SPCE model. These results indicate that the characteristics of water such as the hydrogen bond affect rather the hydrophobic hydration than the hydrophobic interaction. (c) 2007 American Institute of Physics.

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  • A crossover from metal to plasma in dense fluid hydrogen 査読 国際誌

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   125 ( 19 )   194526-1 - 194526-10   2006年11月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    Thermodynamic properties in dense fluid hydrogen are studied by using a density-functional theory for electron-proton binary mixtures that is called quantal hypernetted-chain (QHNC) integral equation. A nonlocal approximation for the exchange-correlation potential in a finite-temperature Kohn-Sham equation is presented. Results obtained from the QHNC with the nonlocal approximation are compared with those obtained from the QHNC with a local density approximation. Temperature variation of thermodynamic quantities between 10(4) and 10(6) K are investigated along an isochor specified by a dimensionless density parameter of r(s)=0.5. These quantities obtained from the QHNCs show that a crossover from metal to plasma occurs around a temperature of T=1.78x10(5) K. Electrical resistivity R-e of the dense fluid hydrogen evaluated from a Ziman formula [The Properties of Liquid Metals, edited by S. Takenohi (Wiley, New York, 1973)] extended to finite temperature is about 0.7 mu Omega cm at T=10(4) K. The dense fluid hydrogen at the temperature can be considered as a metallic fluid, because the value is smaller than typical values of R-e in alkali metals at room temperature. The R-e slightly increases with the temperature increase, and the temperature valuation of R-e is monotonic. We clearly show that the contribution from the electronic excited states plays an important role for the sharp crossover from the metal to the plasma, and that the crossover is interpreted as a crossover from degenerate electron gas to nondegenerate electron gas. (c) 2006 American Institute of Physics.

    DOI: 10.1063/1.2390704

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  • An interaction site model integral equation study of molecular fluids explicitly considering the molecular orientation 査読 国際誌

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   125 ( 3 )   034509-1 - 034509-9   2006年7月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    We implemented an interaction site model integral equation for rigid molecules based on a density-functional theory where the molecular orientation is explicitly considered. In this implementation of the integral equation, multiple integral of the degree of freedom of the molecular orientation is performed using efficient quadrature methods, so that the site-site pair correlation functions are evaluated exactly in the limit of low density. We apply this method to Cl-2, HCl, and H2O molecular fluids that have been investigated by several integral equation studies using various models. The site-site pair correlation functions obtained from the integral equation are in good agreement with the one from a simulation of these molecules. Rotational invariant coefficients, which characterize the microscopic structure of molecular fluids, are determined from the integral equation and the simulation in order to investigate the accuracy of the integral equation.

    DOI: 10.1063/1.2215603

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  • Entropy- or enthalpy-driven collapse of strongly charged polymer chains in a one-component charged fluid of counterions or coions 査読 国際誌

    T Sumi, C Suzuki, H Sekino

    JOURNAL OF CHEMICAL PHYSICS   123 ( 20 )   204907-1 - 204907-6   2005年11月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    We applied a simulation method [T. Sumi and H. Sekino, J. Chem. Phys. 122, 194910 (2005)] to an infinitely dilute polyelectrolyte immersed in one-component charged fluids in order to investigate salt effects on its collapse. In this model system, the degree of freedom of the counterion (or the coion) is considered using a density-functional theory for polymer-solvent admixtures, while the oppositely charged ions are treated as a structureless background having the opposite charge. Results obtained by these simulations show that not only the counterion but also the coion makes the polymer chain collapsed. The effects by the coion are stronger than that by the counterion. Temperature variation of the gyration radius of the polymer chain immersed in the counterion is opposite to that in the coion: while the radius of gyration decreases as the temperature decreases in the case of the counterion, it decreases as the temperature increases in the case of the coion. From these results we conclude that the former is interpreted as an enthalpy-driven collapse caused by the screening effects of the counterion, whereas the latter is interpreted as an entropy-driven one due to the translational entropy of the coion.

    DOI: 10.1063/1.2110007

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  • A cooperative phenomenon between polymer chain and supercritical solvent: Remarkable expansions of solvophobic and solvophilic polymers 査読 国際誌

    T Sumi, H Sekino

    JOURNAL OF CHEMICAL PHYSICS   122 ( 19 )   194910-1 - 194910-11   2005年5月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    We propose a simulation method for infinitely dilute polymer solutions. In this method, an effective Hamiltonian of the solvated polymer chain is introduced to eliminate the degree of freedom of the solvent particle. The effective Hamiltonian is coupled with the density-functional theory (DFT) that we have developed for a polymer-solvent pair correlation function. All the equations proposed in this paper are derived from the first principle. This simulation method was applied to polymer chains in supercritical solvents. We observed anomalous behaviors of polymer chains near the liquid-vapor critical point: both solvophilic and solvophobic polymers expand significantly near the critical point; this is in contrast to the behavior of polymer chains in vacuum. This expansion can be interpreted as a cooperative phenomenon, which enhances the large long-wavelength density fluctuation of the solvent. (c) 2005 American Institute of Physics.

    DOI: 10.1063/1.1900728

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  • A remarkable increase of positron annihilation rate in supercritical fluid xenon 査読 国際誌

    T Sumi, H Sekino

    CHEMICAL PHYSICS LETTERS   407 ( 4-6 )   294 - 297   2005年5月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    An anomalous increase of positron annihilation rare caused by a decrease of the temperature has been observed in supercritical fluid He-4 along isochors by an experiment. By using a molecular simulation, we demonstrate the similar increase in supercritical fluid xenon at the temperature that is far away from the liquid-vapor phase transition. The phenomenon can be interpreted as a sudden clustering of xenon atom that is induced by a self-trapping of the positron. (c) 2005 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.cplett.2005.03.106

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  • Anomalous behavior of a polymer chain in supercritical solvents: A remarkable expansion of solvophobic polymer 査読 国際誌

    T Sumi, H Sekino

    CHEMICAL PHYSICS LETTERS   407 ( 4-6 )   322 - 326   2005年5月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    Conformational change of a solvophobic polymer along an isotherm slightly above critical temperature of solvent is studied by using a simulation with an effective Hamiltonian of the solvated polymer chain, where solvent effects are taken into account. We observe an expansion of the solvophobic polymer in the vicinity of the critical density. The anomalous behavior can be understood only through the large fluctuation of solvent density near the critical point. (c) 2005 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.cplett.2005.03.094

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  • A density-functional study for the liquid-vapor coexistence curve of nitrogen fluid 査読 国際誌

    T Sumi, H Shirahama, H Sekino

    JOURNAL OF CHEMICAL PHYSICS   121 ( 2 )   1014 - 1019   2004年7月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    We have used a density-functional theory based on the interaction site model to predict the liquid-vapor coexistence curve of nitrogen fluid. The pressure and chemical potential were calculated from thermodynamic integrations. The different paths of thermodynamic integration provide slightly different predictions for the liquid-vapor coexistence curve. However, these critical points and coexistence curves evaluated by the theory are in qualitative agreement with the experimental data. The theoretical coexistence curves scaled to critical constants agree with the experimental data quantitatively. (C) 2004 American Institute of Physics.

    DOI: 10.1063/1.1759618

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  • A path integral influence functional for excess electron in fluids: Density-functional formulation 国際誌

    T Sumi, H Sekino

    JOURNAL OF CHEMICAL PHYSICS   120 ( 17 )   8157 - 8165   2004年5月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    In paper, we propose a path integral influence functional from a solvent to determine a self-correlation function of a quantum particle in classical simple fluid. It is shown that the influence functional is related to a grand potential functional of the pure solvent under a three-dimensional external field arising from a classical isomorphic polymer, on which the quantum particle is mapped. The influence functional can be calculated from the self-correlation function, the solute-solvent and the solvent-solvent pair correlation function. The obtained equation of the self-correlation function is applied to an excess electron problem in fluid helium. The Fourier path-integral Monte Carlo method is employed to perform the path integral of the electron. The solute-solvent pair correlation function is estimated from a reference interaction site model integral equation. These results obtained form our proposed influence functional and from that proposed by Chandler, Singh, and Richardson are compared with those provided by a path integral Monte Carlo simulation with the explicit helium solvent. (C) 2004 American Institute of Physics.

    DOI: 10.1063/1.1695324

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  • A density-functional theory for polymer liquids based on the interaction site model 査読 国際誌

    T Sumi, F Hirata

    JOURNAL OF CHEMICAL PHYSICS   118 ( 5 )   2431 - 2442   2003年2月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    The density-functional theory (DFT) for molecular fluids [J. Chem. Phys. 115, 6653 (2001)] is extended to the case of polymer liquids. A system consisting of the ideal chains is employed as a reference system for the DFT, where many-body effects are considered as an effective field that acts on each site of the ideal chains. We derived a relation between the site-site pair distribution functions and the site-density distribution functions under a mean field arising from a single polymer molecule. An integral equation for the site-site pair distribution functions is obtained by the DFT, where the external field is taken to be the mean field. We propose an approximate expression of the intramolecular correlation functions for isolated single-polymer chains to take account for the excluded volume effects inside a polymer chain. The intramolecular correlation function considering the excluded volume effects was in qualitative agreement with those obtained from a simulation for liquid consisting of freely jointed tangent-soft-core chains. The site-density integral equation under the mean field, using the intramolecular correlation function, reproduces the simulation results for site-site pair distribution functions of the system of freely jointed tangent-soft-core chains. (C) 2003 American Institute of Physics.

    DOI: 10.1063/1.1533784

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  • Integral equations for molecular fluids based on the interaction site model: Density-functional formulation 査読 国際誌

    T Sumi, T Imai, F Hirata

    JOURNAL OF CHEMICAL PHYSICS   115 ( 14 )   6653 - 6662   2001年10月

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    担当区分:筆頭著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER INST PHYSICS  

    An integral equation for rigid-body molecules with respect to site-density distribution function under arbitrary external fields is derived by the density-functional theory. Using a grand canonical partition function of molecular systems, we extend original Percus' idea to molecular fluids. The extended Percus' idea provides a relation between the site-site pair distribution function and site-density distribution function under an external field composed of the site-site interaction potentials of a molecule fixed at the origin. The site-density integral equation combined with the extended Percus' relation to molecular fluids gives a closure relation of reference interaction site model equation. The site-site pair distribution functions of homonuclear diatomic Lennard-Jones fluids obtained by the integral equation agree well with those of Monte Carlo simulation. (C) 2001 American Institute of Physics.

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  • Molecular-dynamics study of liquid mercury in the density region between metal and nonmetal 査読 国際誌

    Tomonari Sumi, Eisaku Miyoshi, Kiyoshi Tanaka

    Phys. Rev. B   59 ( 9 )   6153 - 6158   1999年

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1103/PhysRevB.59.6153

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  • Molecular-orbital and molecular-dynamics study of mercury 査読 国際誌

    Tomonari Sumi, Eisaku Miyoshi, Yoshiko Sakai, Osamu Matsuoka

    Phys. Rev. B   57 ( 2 )   914 - 918   1998年

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1103/PhysRevB.57.914

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  • Ab initio CASSCF and MRSDCI calculations of the (C6H6)(2)(+) radical 査読 国際誌

    E Miyoshi, T Ichikawa, T Sumi, Y Sakai, N Shida

    CHEMICAL PHYSICS LETTERS   275 ( 3-4 )   404 - 408   1997年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    Ab initio complete active space self-consistent field (CASSCF) and multireference singly and doubly excited configuration interaction (MRSDCI) calculations were performed for the (C6H6)(2)(+) radical. The calculations revealed that the global minima of the ground state of(C6H6)(2)(+) are at distorted C-2h geometries. Sandwich (D-6h) and T-shaped (C-2v) structures are higher in energy than the minima by 0.4 and 3.7 kcal/mol, respectively. The calculated binding energy is 15.0 kcal/mol compared with an observed value of 20.6 +/- 1.0 kcal/mol. The excitation energies of low-lying excited states are discussed. (C) 1997 Elsevier Science B.V.

    DOI: 10.1016/S0009-2614(97)00773-2

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  • Molecular-orbital study of Li and LiOH adsorption on a Cu(001) surface. II. Cluster-model calculations with image charges 査読

    Tomonari Sumi, Yoshiko Sakai, Eisaku Miyoshi

    Physical Review B - Condensed Matter and Materials Physics   55 ( 7 )   4755 - 4760   1997年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Hartree-Fock and configuration-interaction calculations were performed for (Formula presented) Li and (Formula presented) LiOH, as models of Li/Cu(001) and LiOH/Cu(001), respectively. To take into account the dielectric-response effect of the metal surface to external point charges, we used cluster models with image charges. For (Formula presented) Li, the calculated vibrational frequency was almost the same as that given by a cluster model without image charges, and both values agreed well with the experimental value. Image charges improved the Li-OH vibrational frequency for (Formula presented) LiOH. On the other hand, simple cluster calculations without image charges gave poor results for work-function changes upon Li and LiOH adsorption
    however, by considering image charges, we obtained excellent results, were comparable to the observed values. © 1997 The American Physical Society.

    DOI: 10.1103/PhysRevB.55.4755

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    墨智成, 今村比呂志

    月刊「アグリバイオ 」4月号 (月刊「細胞」 Vol. 55, 162–165からの転載)   7 ( 4 )   372 - 377   2023年3月

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    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(商業誌、新聞、ウェブメディア)  

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    墨智成, 今村比呂志

    月刊「細胞」3月号   55 ( 2 )   162 - 165   2023年2月

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    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(商業誌、新聞、ウェブメディア)  

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    「BAN」3月号   286   56 - 63   2023年2月

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    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(商業誌、新聞、ウェブメディア)  

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    墨 智成

    化学と工業   75 ( 11 )   803 - 803   2022年11月

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    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(学術雑誌)  

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  • Model-potential-free determination of the interaction potential between biological sensing nanoparticles 招待 査読

    Takeshi Morita, Nobuo Uehara, Hiroshi Imamura, Tomonari Sumi

    Photon Factory Highlights   38 - 39   2016年12月

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    担当区分:最終著者   記述言語:英語   掲載種別:記事・総説・解説・論説等(大学・研究所紀要)   出版者・発行元:High Energy Accelerator Research Organization (KEK)  

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    墨智成

    Colloid and Interface Communication   41   1 - 3   2016年12月

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    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(学術雑誌)   出版者・発行元:日本化学会コロイドおよび界面化学部会  

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  • ポツダム滞在記 招待

    墨智成

    アンサンブル   14 ( 4 )   206 - 210   2012年

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    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(学術雑誌)   出版者・発行元:分子シミュレーション研究会  

    DOI: 10.11436/mssj.14.206

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  • A possible mechanism of high-pressure unfolding of proteins: Formation of high-density hydration shell 招待

    Tomonari Sumi

    物性研究   95 ( 3 )   310 - 313   2010年12月

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    担当区分:筆頭著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(国際会議プロシーディングズ)   出版者・発行元:物性研究刊行会  

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  • 塩による疎水性相互作用とDNAの自己凝縮転移 招待

    墨智成

    アンサンブル   12   22 - 26   2010年12月

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    担当区分:筆頭著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(学術雑誌)  

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  • 28aYH-2 密度汎関数法に基づく相互作用モデルによる分子性液体の積分方程式

    墨 智成, 平田 文男

    日本物理学会講演概要集   56 ( 1 )   712 - 712   2001年3月

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    記述言語:日本語   出版者・発行元:一般社団法人日本物理学会  

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  • 1p-YT-7 低密度化液体水銀の分子動力学計算

    墨 智成, 三好 永作, 酒井 嘉子

    日本物理学会講演概要集   53 ( 1 )   506 - 506   1998年3月

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    記述言語:日本語   出版者・発行元:一般社団法人日本物理学会  

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  • 30p-YJ-2 水銀の2体ポテンシャルと分子動力学計算

    墨 智成, 三好 永作, 酒井 嘉子, 田中 皓

    日本物理学会講演概要集   52 ( 1 )   717 - 717   1997年3月

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    記述言語:日本語   出版者・発行元:一般社団法人日本物理学会  

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▼全件表示

受賞

  • 令和5年度岡山工学振興会科学技術賞(一般研究部門)

    2023年7月  

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  • 岡山大学理学部教育貢献賞

    2022年3月   岡山大学理学部  

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共同研究・競争的資金等の研究

  • 新型コロナ後遺症の原因となる宿主内持続感染の予防法並びに治療法の細胞免疫学的研究

    2023年04月 - 2024年03月

    公益財団法人岡山工学振興会  令和5年度岡山工学振興会(一般研究) 

    墨智成

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    担当区分:研究代表者 

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  • 高分子ナノミセルの相互作用場に立脚した治療薬徐放作用の起源に関する研究

    研究課題/領域番号:22H01888  2022年04月 - 2026年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    森田 剛, 墨 智成, 東 顕二郎, 今村 比呂志

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    担当区分:研究分担者 

    配分額:17550000円 ( 直接経費:13500000円 、 間接経費:4050000円 )

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  • タンパク質構造安定性における疎水性相互作用仮説の検証と共溶媒効果の理論・実験解明

    研究課題/領域番号:20K05431  2020年04月 - 2023年03月

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    墨 智成

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    配分額:4420000円 ( 直接経費:3400000円 、 間接経費:1020000円 )

    (1) Kauzmann疎水性相互作用仮説」(1959年) は生化学や分子生物学の教科書で必ず解説されている学説であり,約60年もの間,タンパク質構造安定性の理論として中心的役割を果たしてきた.本研究では,Kauzmann仮説を理論的に検証すべく,ロイシンジッパーと呼ばれる疎水性相互作用によって安定化する典型的モデルタンパク質,GCN4-p1を採用し,分子動力学シミュレーション(MD)と独自に開発した液体の密度汎関数理論を駆使して,疎水性相互作用の物理化学的起源の解明を試みた.その結果,水はタンパク質のアンフォールディングに伴う非極性基の露出において,むしろ安定化に寄与し,いわゆる「疎水基」は水を嫌っていないことを定量的に示し,天然構造の安定性は,タンパク質内に働く直接分子間相互作用に起因することを示した.
    <BR>
    (2)アルコールの中でも2,2,2-トリフルオロエタノール(TFE)は顕著なHelix誘導能を示すことが知られており,TFE水溶液の大きな濃度揺らぎがその主要な物理化学的要因であると考えられてきた.前年度は,小角X線散乱測定によって決定されたTFE水溶液のKirkwood-Buff(KB)積分に基づく解析から,TFE分子の凝集はヘリックス誘導に必ずしも必要ではなく,HelixとTFEとの直接分子間相互作用に起因する選択的溶媒和が,Helix誘導能に関与している事を示した.今年度は,TFEの選択的溶媒和の微視的メカニズムを明らかにすべく,GCN4-p1をモデルタンパク質として採用し,TFE水溶液中でのMDから,Helix二量体並びにランダムコイルとTFE分子との間のKB積分および直接分子間相互作用を解析した.その結果,Helix側鎖とTFE分子のCF3基との間の静電相互作用により,Helixへの過剰選択的溶媒和が誘起され,顕著なHelix誘導能を実現することを示した.

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  • 多彩な環境応答を示す溶媒誘起力の解明:理論・実験融合研究

    研究課題/領域番号:18KK0151  2018年10月 - 2023年03月

    日本学術振興会  科学研究費助成事業 国際共同研究加速基金(国際共同研究強化(B))  国際共同研究加速基金(国際共同研究強化(B))

    甲賀 研一郎, 岡本 隆一, 墨 智成, 望月 建爾, 植松 祐輝

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    担当区分:研究分担者 

    配分額:17940000円 ( 直接経費:13800000円 、 間接経費:4140000円 )

    引き続き,水溶液中における疎水性溶質の溶媒和自由エネルギーに対するイオン添加効果の尺度(セチェノフ係数)についての理論的研究を行った.セチェノフ係数の陽イオン・陰イオンサイズ依存性の違いの起源をより明確に理解することを目指した計算を行った.第一に,分子動力学シミュレーションおよび自由エネルギー計算を実行し,セチェノフ係数を二通りの方法で計算し,両者が良く一致することを示した.一つの方法は,溶液構造を反映する相関関数の体積積分(いわゆるKirkwood-Buff積分)から得るものである.いくつかの理論的問題を解決し,最終的に導出した式を用いた.もう一方の方法は疎水性溶質の溶媒和自由エネルギーをイオン添加水溶液と純水において計算し,セチェノフ係数を得るものである.これまで両者の一致がそれほど良くなかったが,その原因を解明することができた.これにより,信頼度の高いセチェノフ係数の計算方法の確立に寄与した.次に,セチェノフ係数の陽イオン・陰イオンサイズ依存性の微視的起源を探った.まず,広いイオンサイズ範囲において,セチェノフ係数の変化は水溶液の充填率あるいはイオンの部分モル体積の変化と相関することを示した.また,単純な疎水性溶質の溶解度は水溶液の充填率と相関することは平均場近似が示唆する.そこで,水溶液の充填率のイオンサイズ依存性について詳細な解析を行った.その結果,陽イオンの場合にはある一定サイズよりもイオンサイズが小さくなると,イオン周囲の水和水の充填率が下がること,またそれは第一水和圏の水分子の配向に依存することを明らかにした.陰イオンサイズ依存性が単調であるのは,充填率がイオン周囲の水の配向に大きく依存しないためであることがわかった.このように,セチェノフ係数のイオンサイズ依存性の微視的起源をモデル水溶液について解明することに成功した.

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  • タンパク質の構造安定性と分子間相互作用に関する実験と理論による研究

    研究課題/領域番号:16K05657  2016年04月 - 2020年03月

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    墨 智成

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    配分額:4940000円 ( 直接経費:3800000円 、 間接経費:1140000円 )

    タンパク質構造安定性は,バイオ医薬品の設計にも関係する,社会的に重要な研究課題である.これらの現象論的説明では,約60年もの間,Kauzmannによる「疎水性相互作用仮説」が,中心的役割を果たしてきた.しかしその一方で,観測事実との矛盾が数多く囁かれてきた.本研究では,本仮説の理論的検証を行うために,unfoldingに伴う自由エネルギー変化を溶媒和および分子内相互作用による寄与に分割する計算手法を開発し,モデルタンパク質シニョリンに適用した.それにより,シニョリンは分子内相互作用により安定化しており,溶媒効果はむしろunfold構造を安定化するという,本仮説とは相反する結果を得た.

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  • 粒子間相互作用のモデルポテンシャルフリー解析

    2015年06月 - 2017年03月

    墨智成

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    担当区分:研究代表者 

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  • 微小管系分子モーターの化学-力学共役機構と力学的破断特性の統一的解明

    研究課題/領域番号:25610121  2013年04月 - 2016年03月

    日本学術振興会  科学研究費助成事業 挑戦的萌芽研究  挑戦的萌芽研究

    墨 智成

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    配分額:3900000円 ( 直接経費:3000000円 、 間接経費:900000円 )

    本研究では,観測結果に基づいて,キネシンの化学-力学状態遷移ネットワークモデルを論理的に構築し,動力学的特性の統一的再現を実現した.主要サイクルの解析により,一般に信じられている標準的モデルとは本質的に異なる次の結果を得た.
    (1)特定のサイクルのみに依存せず,ATP濃度および外部負荷に応じてサイクルの反応経路を変化させながらdead endを回避して,安定した前進ステップ運動を実現する.(2)後方への外部負荷に対するロバスト性を維持するために,ATP濃度にかかわらず,主要サイクルに対するネットワーク上での適切な反応経路を選択している.

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  • ソフトマターを対象とした液体論的マルチスケール解析手法の開発とその応用

    研究課題/領域番号:21015012  2009年 - 2010年

    日本学術振興会  科学研究費助成事業 特定領域研究  特定領域研究

    墨 智成

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    配分額:3300000円 ( 直接経費:3300000円 )

    本研究では,液体の密度汎関数理論(DFT)に基づくマルチスケールシミュレーション法の,高分子-水溶液系への適用において必要な自由エネルギー汎関数を開発と,1.蛋白質の高圧変性機構の解析,2.過冷却水中での液-液相転移近傍での疎水性高分子挙動の解析への応用を行った.
    1.蛋白質の高圧変性機構
    蛋白質の高圧変性は古くから知られているにも関わらず,その分子機構は現在も論争中の問題である.本研究では,水の水素結合ネットワークによる寄与を考慮した自由エネルギー汎関数に基づくマルチスケールシミュレーション法を水中での疎水性高分子鎖に適用し,圧力上昇に伴うunfolding転移および負の体積変化ΔVの再現に成功した.Unfoldingに伴うギブスの自由エネルギー変化ΔGの圧力依存性が非線形である事から,水和水の圧縮率変化が重要な役割を果たしている事を示した.さらに,ΔVの圧力依存性(ΔGの非線形性)は,unfoldingにおける露出用面積の増大に伴う周期が短く隙間の少ない高密度水和層の形成に帰着し,表面誘起の水素結合ネットワークの破壊に起因した水和特性である事を示した.
    2.過冷却水中での液-液相転移近傍での疎水性水和物性
    水の4℃での密度極大や温度低下に伴う疎水性物質の溶解度の増加等は,過冷却領域において存在する可能性が示唆されている水の液-液相転移による影響ではないかと指摘されている.そこで本研究では,水4000分子によるバルク水の分子動力学シミュレーションを実行し,過冷却水の液-液相転移の相図を完成させると共に,過冷却水中での疎水性高分子鎖のマルチスケールシミュレーションを実行し,その水和物性の解析を行った.高圧下での高密度液体(HDL)側への冷却では,顕著な変化は見られなかったが,低密度液体(LDL)側への冷却では,高分子鎖のunfolding転移が観測された.このLDL側でのunfolding転移は,高分子表面によって誘起される周期が長くて密度の高い安定なネットワークを有する低エントロピー水和殻の形成に起因する事が明らかと成った.

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  • 大きな揺らぎの存在する媒体中での高分子挙動に関する理論的解析手法の開発とその応用

    研究課題/領域番号:19031013  2007年 - 2008年

    日本学術振興会  科学研究費助成事業 特定領域研究  特定領域研究

    墨 智成

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    配分額:4700000円 ( 直接経費:4700000円 )

    本研究の目的は大きな揺らぎが存在する媒体中での高分子挙動を理論的に調べる事であるが, 昨年度に行った, 一成分溶媒の気-液臨界点近傍および二成分混合溶媒の液-液相分離臨界点近傍での高分子鎖の解析に引き続き, 今年度は, 電解質水溶液中でのDNA鎖の自己凝縮転移に関する研究を行った.
    DNA鎖は電解質水溶液中において, 負に帯電した荷電高分子鎖となり, 鎖内のクーロン反発によって, ランダムコイルを形状する. この状態に, 三価ポリアミンであるスペルミジン(SPD^<3+>)を数から数十mM程度添加すると, 環状コイル形状へ自己凝縮転移する現象が観測されている.また, 温度変化に関しては, 低温でランダムコイル形成をとるDNA鎖は, 温度上昇に伴い環状コイルへ自己凝縮転移する観測結果が報告されている.
    一般に電解質水溶液中での荷電高分子鎖(DNAの粗視化モデル)のブラウニアン動力学法では, 水は連続誘電体とし, イオンは荷電粒子としてモデル化する.このモデルにおける自己凝縮転移のメカニズムとしては, 多価イオンのイオン強結合による電荷秩序状態の形成が考えられるが, 水を露に考慮しないこのモデル化では, 自己凝縮転移を再現する事は出来なかった. また, 温度変化に関しては, 温度の上昇により慣性半径が増加する(実験とは逆の)結果が得られた. そこで我々は, タンパク質の天然構造の安定性において重要となる疎水性相互作用に着目し, 水の凝集性液体としての性質(強い界面張力)を考慮した電解質水溶液モデルを構築した. この粗視化モデルに対して, 密度汎関数理論(DFT)に基づく液体論的手法を用いたマルチスケールシミュレーション法を適用し, 荷電高分子鎖(DNA鎖)の自己凝縮現象について解析を行った.その結果, SPD^<3+>の添加および温度上昇に伴う自己凝縮転移を定性的に再現出来る事が示された.また, 溶媒和自由エネルギーの解析から, SPD^<3+>の添加および温度上昇により, 溶媒和自由エネルギーが大きく上昇する事が分かった.これらの結果から, (a)SPD^<3+>の添加に伴う疎水性相互作用の強化, (b)温度上昇に伴う水和エントロピーの増加に起因した疎水性相互作用の強化, が電解質水溶液の貧溶媒化を導き, これが自己凝縮転移の駆動力となる事が示された.本研究で考慮した電解質水溶液における水の寄与は, タンパク質やコロイドの塩析に関する現象を記述するのに必要不可欠であり, ソフトマター物理においても重要な要素の一つであると考えられる.

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  • イオン液体の統計力学

    研究課題/領域番号:18540407  2006年 - 2008年

    日本学術振興会  科学研究費助成事業  基盤研究(C)

    吉森 明, 小田 垣孝, 墨 智成, 吉留 崇

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    配分額:3700000円 ( 直接経費:3100000円 、 間接経費:600000円 )

    イオン液体における融点の問題を密度汎関数法を使って研究した。ただし、ここでいう密度汎関数理論は古典液体の理論で、電子状態理論とは違う。まず、点電荷を持った剛体球系の融点を計算し、現実のイオン液体の低融点を説明した。次に、より複雑な系の融点を計算する理論を開発し、極小が2つあるポテンシャルの系で、広い範囲の相図を計算した。また、ガラス転移における配置エントロピーと比熱の関係を明らかにした。

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  • 大規模分散処理に適したマルチ分子オブジェクト法による分子計算技術の研究

    研究課題/領域番号:17300094  2005年 - 2007年

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    後藤 仁志, 関野 秀男, 墨 智成, 市川 周一

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    配分額:16390000円 ( 直接経費:15400000円 、 間接経費:990000円 )

    本研究は大きく分けて(1)マルチ分子オブジェクト法のための分子計算プラットフォームの構築、(2)階層化分子シミュレーションのための分子計算技術の開発、(3)不均一計算タスクの負荷分散アルゴリズムの開発、の3つの部分からなる。それぞれに関する研究実績の概要を以下に示す。
    (1)マルチ分子オブジェクト法による並列化効率と計算精度の向上を目指し,大規模系の結晶シミュレーション技術の開発を行った。その結果,分子間相互作用エネルギー和で14桁までの精度保障を実現すると伴に,およそ4億原子で構成された直径0.1μmもの分子性結晶計算に成功した.また、実用化レベルで結晶多形間の相転移シミュレーションによる熱力学解析法の開発に成功した.
    (2)マルチウェーブレット基底を用いたTDHF/TDDFT時間依存シュレディンガー方程式の解法や超分極率の算定法などの開発を行なった.これらは,現時点では大規模系への適用は容易ではないが,今後,不均一系に対する密度汎関数理論の開発へ展開することが大いに期待できる結果となった.
    (3)分子シミュレーションの計算タスクに対して演算性能が不十分なヘテロ分散計算環境では,実践的な負荷分散アルゴリズムは困難であることが分かった.そこで,分子シミュレーションに利用されることが多いマルチコアCPUをクラスター化したヘテロ分散環境を想定し,マルチコア/マルチスレッドシステムの負荷分散アルゴリズムめ開発に着手した.

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  • 統合的分子シミュレーションによる新規ナノ光機能材料の提案

    研究課題/領域番号:15310105  2003年 - 2004年

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    関野 秀男, 栗田 典之, 墨 智成

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    配分額:13300000円 ( 直接経費:13300000円 )

    デンドリマー分子の構造は柔軟性に富むが、ポリマーと異なり各ユニット分子の物理化学的性質がたもたれていることから、並列処理巨大量子化学計算アルゴリズムによる理論解明に期待がもたれる。光機能物質として興味ある高世代のデンドリマーは巨大分子であるがその分極率および超分極率の算定を第一原理法によって行った。ペア相互作近似(FMO)は数千から万原子分子の分子の電子状態を量子論的に扱うことができるが、我々は同様の近似をCoupled Perturbed Hartree Fock (CPHF)に応用実装を行った。デンドリマー分子に適用することにより分極率、超分極率を算定、ペア相互作用近似(FMO)が全エネルギーのみならず、こうした光物性算定にも有効であることを示した。また世代依存性を調べたが、他のユニットとの部分的電荷移動に対応する量子論的補正を伴ったシンプルな加算性がみいだされた。さらに精度の高い計算Coupled Perturbed Density Functional Theory (CPDFT)によるcorrelationの考慮が必要であるが、巨大系では中距離以上の相互作用が重要で従来のDFTでは十分でない。PW型のファンクショナルを改良することによってDNA-stackingをうまく表現できる方法を開発した。更に現行のDFT汎関数による分極率算定が巨大分子系で破綻することが知られているが、われわれはクーロン力を分割することによりDFT長距離交換相互作用を補正する方法を開発巨大系での分極率、超分極率算定に成功した。またエネルギーの溶媒への散逸の見積もりとして単純な高分子ビーズモデルとDFT法を組み合わせ、量子、古典溶質の溶媒へのエネルギー散逸を統一的且つ第一原理的にあつかえる理論を構築、過剰電子の非局在化や高分子の異常膨張のメカニズム、ポジトロン消滅の異常増大メカニズム解析へ応用し大きな成功を収めた。

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担当授業科目

  • 分子科学演習(理論物理化学) (2023年度) 通年  - その他

  • 化学数学1 (2023年度) 第1学期  - 水1~2

  • 化学数学1 (2023年度) 第1学期  - 水1~2

  • 化学数学2 (2023年度) 第2学期  - 水1~2

  • 化学数学I (2023年度) 1・2学期  - 水1~2

  • 基礎化学実験 (2023年度) 第4学期  - 木5~8

  • 教養化学実験 (2023年度) 第2学期  - 金5~8

  • 液体論特論 (2023年度) 前期  - 火3~4

  • 液体論特論 (2023年度) 前期  - 火3~4

  • 物理化学7 (2023年度) 第3学期  - 金1~2

  • 物理化学IV (2023年度) 3・4学期  - 金1~2

  • 理論物理化学演習 (2023年度) 通年  - その他

  • 理論物理化学特別演習 (2023年度) 通年  - その他

  • 統計力学 (2023年度) 後期  - その他

  • 統計力学 (2023年度) 後期  - その他

  • 化学数学1 (2022年度) 第1学期  - 水1~2

  • 化学数学2 (2022年度) 第2学期  - 水1~2

  • 化学数学I (2022年度) 1・2学期  - 水1~2

  • 基礎化学実験 (2022年度) 第4学期  - 木5~8

  • 教養化学実験 (2022年度) 第2学期  - 金5~8

  • 液体論特論 (2022年度) 前期  - 火3~4

  • 物理化学7 (2022年度) 第3学期  - 金1~2

  • 理論物理化学演習 (2022年度) 通年  - その他

  • 統計力学 (2022年度) 後期  - その他

  • 化学数学1 (2021年度) 第1学期  - 水1,水2

  • 化学数学2 (2021年度) 第2学期  - 水1,水2

  • 化学数学I (2021年度) 1・2学期  - 水1,水2

  • 物理化学7 (2021年度) 第3学期  - 金1,金2

  • 理論物理化学演習 (2021年度) 通年  - その他

  • 統計力学 (2021年度) 後期  - その他

  • 統計熱力学 (2021年度) 前期  - 月5,月6

  • 量子化学7 (2021年度) 第4学期  - 金1,金2

  • 量子化学IV (2021年度) 3・4学期  - 金1,金2

  • 一般化学 (2020年度) 3・4学期  - 金1,金2

  • 一般化学2 (2020年度) 第4学期  - 金1,金2

  • 一般化学2 (2020年度) 第4学期  - 金1,金2

  • 化学数学1 (2020年度) 第1学期  - 水1,水2

  • 化学数学2 (2020年度) 第2学期  - 水1,水2

  • 化学数学I (2020年度) 1・2学期  - 水1,水2

  • 液体論特論 (2020年度) 前期  - 金3,金4

  • 理論物理化学演習 (2020年度) 前期

  • 理論物理化学演習 (2020年度) 通年  - その他

  • 統計力学 (2020年度) 後期  - その他

  • 量子化学7 (2020年度) 第3学期  - 水1,水2

  • 量子化学IV (2020年度) 第3学期  - 水1,水2,金1,金2

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社会貢献活動

  • 理論化学からみた身近な現象

    役割:講師

    岡山大学異分野基礎科学研究所  岡山大学異分野基礎科学研究所公開講座  2022年11月12日

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    種別:講演会

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