Updated on 2021/12/17

写真a

 
SUMI Tomonari
 
Organization
Research Institute for Interdisciplinary Science Associate Professor
Position
Associate Professor
External link

Degree

  • Ph. D ( 1999.3   Kyushu University )

Research Interests

  • Hippocampus

  • Statistical mechanics

  • Liquid State Theory

  • Chemical Physics

  • Biophysics

  • Soft Matter Physics

  • Density-functional Theory

  • Stochastic Modeling

  • Molecular Motor

  • Solvent effect

  • Protein

  • Protein folding

  • Synapse plasticity

  • Metabolic evolution

  • Last Universal Common Ancestor (LUCA)

  • Autotroph

  • Carbon metabolism

Research Areas

  • Life Science / Biophysics

  • Nanotechnology/Materials / Fundamental physical chemistry

  • Natural Science / Biophysics, chemical physics and soft matter physics

Education

  • Kyushu University   工学研究科   応用物理学専攻

    1994.4 - 1999.3

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    Country: Japan

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  • Yamaguchi University   理学部   物理学科

    1990.4 - 1994.3

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    Country: Japan

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Research History

  • Okayama University   Research Institute for Interdisciplinary Science   Associate Professor

    2016.4

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  • Okayama University   Graduate School of Natural Science and Technology   Associate Professor

    2013.4 - 2016.3

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  • Toyohashi University of Technology   Assistant Professor

    2007.4 - 2013.3

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  • Toyohashi University of Technology   Research Assistant

    2002.4 - 2007.3

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  • 日本学術振興会特別研究員(PD)

    1999 - 2002

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Professional Memberships

Committee Memberships

  • 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  

    2021.11 - 2021.12   

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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  

    2018.9   

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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  

    2012.2   

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    Committee type:Academic society

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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  

    2011.2   

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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  

    2010.2   

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  • 日本物理学会   領域12化学物理分野運営委員  

    2008.5 - 2009.4   

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    Committee type:Academic society

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  •   量子化学データーベースQCLDB収集  

    2006.10 - 2011.3   

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Papers

  • Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea Reviewed International journal

    Tomonari Sumi, Kouji Harada

    Communications Chemistry   4 ( 1 )   149-1 - 149-9   2021.12

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher: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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    Other Link: https://www.nature.com/articles/s42004-021-00585-0

  • Water‐mediated interactions destabilize proteins Reviewed International journal

    Tomonari Sumi, Hiroshi Imamura

    Protein Science   30 ( 10 )   2132 - 2143   2021.8

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

    DOI: 10.1002/pro.4168

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    Other Link: 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 Reviewed International journal

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

    iScience   24 ( 8 )   102920 - 102920   2021.8

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    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 Reviewed International journal

    Hiroyuki Katsuto, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga

    The Journal of Physical Chemistry B   125 ( 23 )   6296 - 6305   2021.6

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher: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 Invited Reviewed International journal

    Kouji Harada, Tomonari Sumi

    Artificial Life and Robotics   26 ( 2 )   210 - 215   2021.5

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    Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1007/s10015-020-00664-w

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    Other Link: 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 Reviewed International journal

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

    Nano Letters   21 ( 3 )   1303 - 1310   2021.2

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    Authorship:Last author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher: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 Reviewed International coauthorship International journal

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

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

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    Authorship:Corresponding author   Publishing type:Research paper (scientific journal)   Publisher: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 Reviewed International journal

    Tomonari Sumi, Kouji Harada

    Scientific Reports   10 ( 14711 )   14711-1 - 14711-14   2020.12

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    Authorship:Lead author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher: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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    Other Link: 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 Reviewed International journal

    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   2020.9

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    Publishing type:Research paper (scientific journal)   Publisher:The Chemical Society of Japan  

    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 International coauthorship

    Tomonari Sumi, Stefan Klumpp

    Nano Letters   19 ( 5 )   3370 - 3378   2019.5

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    Authorship:Lead author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher: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 Reviewed International journal

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

    Phys. Chem. Chem. Phys.   21 ( 31 )   16889 - 16894   2019.5

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

    © 2019 the Owner Societies. A novel Raman scattering enhancement was discovered using colloid nanoparticles conjugated with an amine-based copolymer. The interaction potential surface between Raman scattering enhancing nanoparticles was clarified by combining a small-angle scattering method and a model-potential-free liquid-state theory as an in situ observation in the solution state. The potential surface indicates that the most stable position is located around 0.9 nm from the particle surface, suggesting the existence of a nanogap structure between the nanocomposites. The change in Raman scattering enhancement was also acquired during the dispersion process of the aggregated nanocomposites through a glutathione-triggered nanosensing reaction.

    DOI: 10.1039/C9CP01946D

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  • Theoretical analysis on thermodynamic stability of chignolin Reviewed International journal

    Tomonari Sumi, Kenichiro Koga

    Sci. Rept.   8   5186-1 - 5186-9   2019.3

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

    Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann's hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small, designed protein, chignolin. The resulting free energy profile quantitatively agreed with the molecular dynamics simulations. Decomposition of the free energy profile indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with the site-directed mutagenesis and calorimetry experiments for globular proteins with hydrophobic interior cores.

    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 Reviewed International journal

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

    JOURNAL OF COMPUTATIONAL CHEMISTRY   39 ( 4 )   202 - 216   2018.2

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

    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

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    Language:English   Publishing type:Research paper (scientific journal)  

    Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.

    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 Reviewed International journal

    Tomonari Sumi, Atsushi Okumoto, Hitoshi Goto, Hideo Sekino

    PHYSICAL REVIEW E   96 ( 4 )   042410-1 - 042410-10   2017.10

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

    Tomonari Sumi

    SCIENTIFIC REPORTS   7   13489-1 - 13489-12   2017.10

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

    Kenji Mochizuki, Tomonari Sumi, Kenichiro Koga

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   19 ( 35 )   23915 - 23918   2017.9

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher: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 Reviewed International journal

    Tomonari Sumi

    SCIENTIFIC REPORTS   7   1163-1 - 1163-13   2017.4

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

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

    JOURNAL OF PHYSICAL CHEMISTRY B   120 ( 47 )   12127 - 12134   2016.12

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher: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 Reviewed International journal

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

    JOURNAL OF PHYSICAL CHEMISTRY C   120 ( 44 )   25564 - 25571   2016.11

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    Authorship:Last author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER CHEMICAL SOC  

    Biological sensing technology utilizing nanoparticles extends through a diverse range of fields. The nanosensing is controlled using the assembly/disassembly of nanoparticles dominated by interaction forces between them. Although the interaction potential surface gives decisive information on the sensing mechanism, evaluating the quantitative profile has been impossible due to extremely complicated interactions of conjugated soft matter. In this study, a model-potential-free determination of the interaction potential surfaces was devised by combining small-angle scattering and liquid-state theory. The model-potential-free liquid theory was developed for colloidal nanoparticles inherently with strong van der Waals attraction forces by their nanoscopic size. The present method extracts interaction potential between nanoparticles even in systems with complicated interactions due to conjugated soft matter. By applying this determination method to a glutathione-triggered biosensing reaction, interaction potential curves between biosensing nanoparticles were realized for the first time. The analysis revealed peculiar potential surfaces of the sensing nanoparticles. The mechanism of colorimetric nanosensing function based on surface plasmon resonance is discussed from the viewpoint of the assembly/disassembly of nanoparticles in nanocomposites dominated by the interaction potential surfaces.

    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 Reviewed International journal

    Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenichiro Koga

    JOURNAL OF CHEMICAL PHYSICS   144 ( 22 )   224104-1 - 224104-15   2016.6

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

    Kenji Mochizuki, Tomonari Sumi, Kenichiro Koga

    SCIENTIFIC REPORTS   6   24657-1 - 24657-10   2016.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

    We investigate driving forces of the liquid-liquid phase separation of N-isopropylpropionamide (NiPPA) aqueous solutions above the lower critical solution temperature using molecular dynamics simulations. Spontaneous phase separations of the model aqueous solution with a modified OPLS-AA force field are observed above the experimentally determined cloud point. The destabilization toward the phase separation is confirmed by temperature dependence of the long-wavelength limit of the concentration-concentration structure factor, the dominant component of which is found to be an increasing effective attraction between NiPPA molecules. At varying temperatures, the potentials of mean force (PMFs) between a pair of NiPPA molecules at infinite dilution are obtained and decomposed into the nonpolar and Coulombic contributions. The nonpolar contribution, arising essentially from molecular volume, promotes association of NiPPA molecules with increasing temperature while the Coulombic one antagonizes the association. Thus, our analysis leads to a conclusion that the driving force of thermally induced aggregation of NiPPA molecules is the temperature dependence of the nonpolar contribution in PMF between NiPPA molecules, not the temperature dependence of the number or strength of hydrogen bonds between NiPPA and water molecules.

    DOI: 10.1038/srep24657

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  • Mean-Field Approximation to the Hydrophobic Hydration in the Liquid-Vapor Interface of Water Reviewed International journal

    Kiharu Abe, Tomonari Sumi, Kenichiro Koga

    JOURNAL OF PHYSICAL CHEMISTRY B   120 ( 8 )   2012 - 2019   2016.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER CHEMICAL SOC  

    A mean-field approximation to the solvation of nonpolar solutes in the liquid vapor interface of aqueous solutions is proposed. It is first remarked with a numerical illustration that the solvation of a methane like solute in bulk liquid water is accurately described by the mean-field theory of liquids, the main idea of which is that the probability (P-cav) of finding a cavity in the solvent that can accommodate the solute molecule and the attractive interaction energy (watt) that the solute would feel if it is inserted in such a cavity are both functions of the solvent density alone. It is then assumed that the basic idea is still valid in the liquid vapor interface, but Pcav and watt are separately functions of different coarse-grained local densities, not functions of a common local density. Validity of the assumptions is confirmed for the solvation of the methane-like particle in the interface of model water at temperatures between 253 and 613 K. With the mean-field approximation extended to the inhomogeneous system the local solubility profiles across the interface at various temperatures are calculated from P-cav and u(att) obtained at a single temperature. The predicted profiles are in excellent agreement with those obtained by the direct calculation of the excess chemical potential over an interfacial region where the solvent local density varies most rapidly.

    DOI: 10.1021/acs.jpcb.5b10169

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  • Driving forces for the pressure-induced aggregation of poly(N-isopropylacrylamide) in water Reviewed International journal

    Kenji Mochizuki, Tomonari Sumi, Kenichiro Koga

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   18 ( 6 )   4697 - 4703   2016.2

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher: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.

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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 Reviewed

    Atsushi OKUMOTO, Tomonari SUMI, Hideo SEKINO, Hitoshi GOTO

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

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  • A solvation-Free-Energy Functional: A Reference-Modified Density Functional Formulation (vol 36, pg 1359, 2015) Reviewed International journal

    Tomonari Sumi, Ayori Mitsutake, Yutaka Maruyama

    JOURNAL OF COMPUTATIONAL CHEMISTRY   36 ( 26 )   2009 - 2011   2015.10

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  • A solvation-free-energy functional: A reference-modified density functional formulation Reviewed International journal

    Tomonari Sumi, Ayori Mitsutake, Yutaka Maruyama

    JOURNAL OF COMPUTATIONAL CHEMISTRY   36 ( 18 )   1359 - 1369   2015.7

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    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.

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  • A model-free method for extracting interaction potential between protein molecules using small-angle X-ray scattering Reviewed International journal

    Tomonari Sumi, Hiroshi Imamura, Takeshi Morita, Keiko Nishikawa

    JOURNAL OF MOLECULAR LIQUIDS   200   42 - 46   2014.12

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    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.

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  • Temperature dependence of local solubility of hydrophobic molecules in the liquid-vapor interface of water Invited Reviewed International journal

    Kiharu Abe, Tomonari Sumi, Kenichiro Koga

    JOURNAL OF CHEMICAL PHYSICS   141 ( 18 )   18C516-1 - 18C516-8   2014.11

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    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 Reviewed International journal

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

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   16 ( 46 )   25492 - 25497   2014

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    To extract protein-protein interaction from experimental small-angle scattering of proteins in solutions using liquid state theory, a model potential consisting of a hard-sphere repulsive potential and the excess interaction potential has been introduced. In the present study, we propose a model-potential-free integral equation method that extracts the excess interaction potential by using the experimental small-angle scattering data without specific model potential such as the Derjaguin-Landau-Verwey-Overbeek (DLVO)-type model. Our analysis of experimental small-angle X-ray scattering data for lysozyme solution shows both the stabilization of contact configurations of protein molecules and a large activation barrier against the formation of the contact configurations in addition to the screened Coulomb repulsion. These characteristic features, which are not well-described by the DLVO-type model, are interpreted as solvent effects.

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  • Time series data analysis using DFA Reviewed International journal

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

    IRAGO CONFERENCE 2013   1585   175 - 180   2014

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    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.

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  • Modulation of the intermolecular interaction of myoglobin by removal of the heme Reviewed International journal

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

    JOURNAL OF SYNCHROTRON RADIATION   20   919 - 922   2013.11

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    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.

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  • Effects of hydrophobic hydration on polymer chains immersed in supercooled water Reviewed International journal

    Tomonari Sumi, Hideo Sekino

    RSC Advances   3 ( 31 )   12743 - 12750   2013.8

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    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.

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  • Generality of anomalous expansion of polymer chains in supercritical fluids Reviewed International coauthorship International journal

    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   2011.9

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    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.

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  • Possible mechanism underlying high-pressure unfolding of proteins: formation of a short-period high-density hydration shell Reviewed International journal

    Tomonari Sumi, Hideo Sekino

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

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    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 Reviewed International journal

    Tomonari Sumi, Nobuyuki Imazaki, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   132 ( 16 )   165101   2010.4

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    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)]” Reviewed International journal

    Tomonari Sumi, Nobuyuki Imazaki, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   132 ( 16 )   229901-1 - 229901-1   2010.4

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    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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  • Hydrophobic effects on multivalent-salt-induced self-condensation of DNA Reviewed International journal

    Tomonari Sumi, Chiaki Suzuki, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   131 ( 16 )   161103   2009.10

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    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 Reviewed International journal

    Tomonari Sumi, Nobuyuki Imazaki, Hideo Sekino

    PHYSICAL REVIEW E   79 ( 3 )   030801   2009.3

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    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.

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  • A self-consistent density-functional approach for homogeneous and inhomogeneous classical fluids Reviewed International journal

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   77 ( 3 )   034605-1 - 034605-8   2008.3

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    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.

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  • Metal-nonmetal transition in dense fluid hydrogen Reviewed International journal

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   128 ( 4 )   044712   2008.1

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    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.

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

    Tomonari Sumi, Kazuhiko Kobayashi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   127 ( 16 )   164904   2007.10

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    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 Reviewed International journal

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   126 ( 14 )   144508-1 - 144508-7   2007.4

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    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 Reviewed International journal

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   125 ( 19 )   194526-1 - 194526-10   2006.11

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    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.

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  • An interaction site model integral equation study of molecular fluids explicitly considering the molecular orientation Reviewed International journal

    Tomonari Sumi, Hideo Sekino

    JOURNAL OF CHEMICAL PHYSICS   125 ( 3 )   034509-1 - 034509-9   2006.7

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    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.

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  • Entropy- or enthalpy-driven collapse of strongly charged polymer chains in a one-component charged fluid of counterions or coions Reviewed International journal

    T Sumi, C Suzuki, H Sekino

    JOURNAL OF CHEMICAL PHYSICS   123 ( 20 )   204907-1 - 204907-6   2005.11

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    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.

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  • A cooperative phenomenon between polymer chain and supercritical solvent: Remarkable expansions of solvophobic and solvophilic polymers Reviewed International journal

    T Sumi, H Sekino

    JOURNAL OF CHEMICAL PHYSICS   122 ( 19 )   194910-1 - 194910-11   2005.5

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    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 Reviewed International journal

    T Sumi, H Sekino

    CHEMICAL PHYSICS LETTERS   407 ( 4-6 )   294 - 297   2005.5

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

    T Sumi, H Sekino

    CHEMICAL PHYSICS LETTERS   407 ( 4-6 )   322 - 326   2005.5

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

    T Sumi, H Shirahama, H Sekino

    JOURNAL OF CHEMICAL PHYSICS   121 ( 2 )   1014 - 1019   2004.7

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    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 International journal

    T Sumi, H Sekino

    JOURNAL OF CHEMICAL PHYSICS   120 ( 17 )   8157 - 8165   2004.5

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

    T Sumi, F Hirata

    JOURNAL OF CHEMICAL PHYSICS   118 ( 5 )   2431 - 2442   2003.2

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

    T Sumi, T Imai, F Hirata

    JOURNAL OF CHEMICAL PHYSICS   115 ( 14 )   6653 - 6662   2001.10

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

    DOI: 10.1063/1.1401824

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  • Molecular-dynamics study of liquid mercury in the density region between metal and nonmetal Reviewed International journal

    Tomonari Sumi, Eisaku Miyoshi, Kiyoshi Tanaka

    Physical Review B - Condensed Matter and Materials Physics   59 ( 9 )   6153 - 6158   1999

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

    Molecular dynamics (MD) calculations of expanded liquid mercury in the density region between metal and nonmetal were made using the potential energy curve of dimeric mercury (Formula presented) determined from molecular orbital calculations. The density dependence of the thermal pressure coefficient and the internal pressure, which were observed experimentally in the density region that included the metal-nonmetal transition range, were qualitatively demonstrated with our MD calculations. The change of calculated pair distribution function and structure factor from a metallic to a nonmetallic state also explained qualitatively the change of experimental ones. The temperature dependence of the isochoric electrical conductivity was discussed using quantities obtained from the calculated pair distribution functions. It was shown that the increase of the isochoric electrical conductivity accompanying an increase in temperature, which was experimentally observed in the strong-scattering metallic region, can be realized through the increase of the density of states at the Fermi energy arising from the decrease of interatomic distance. © 1999 The American Physical Society.

    DOI: 10.1103/PhysRevB.59.6153

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  • Molecular-orbital and molecular-dynamics study of mercury Reviewed International journal

    Tomonari Sumi, Eisaku Miyoshi, Yoshiko Sakai, Osamu Matsuoka

    Physical Review B - Condensed Matter and Materials Physics   57 ( 2 )   914 - 918   1998

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

    A potential curve and spectroscopic constants of (Formula presented) were calculated using multireference single- and double-excitations configuration interaction calculations, where (Formula presented) and (Formula presented) electrons were correlated. The calculated constants were consistent with experimental data. Using the potential curves of (Formula presented) we performed molecular-dynamics (MD) calculations to identify the melting point of mercury. A characteristic feature of liquid metal, cooperative motion, was observed in the MD calculations. On the other hand, MD calculations using a Lennard-Jones potential gave the cooperative motion only in very short time intervals (Formula presented). © 1998 The American Physical Society.

    DOI: 10.1103/PhysRevB.57.914

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  • Ab initio CASSCF and MRSDCI calculations of the (C6H6)(2)(+) radical Reviewed International journal

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

    CHEMICAL PHYSICS LETTERS   275 ( 3-4 )   404 - 408   1997.8

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher: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 Reviewed

    Tomonari Sumi, Yoshiko Sakai, Eisaku Miyoshi

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

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    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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MISC

  • Model-potential-free determination of the interaction potential between biological sensing nanoparticles Invited Reviewed

    Takeshi Morita, Nobuo Uehara, Hiroshi Imamura, Tomonari Sumi

    Photon Factory Highlights   38 - 39   2016.12

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    Authorship:Last author   Language:English   Publishing type:Article, review, commentary, editorial, etc. (bulletin of university, research institution)   Publisher:High Energy Accelerator Research Organization (KEK)  

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  • X 線小角散乱と液体論に基づくコロイド粒子 間相互作用のモデルポテンシャルフリー解析 Invited Reviewed

    墨智成

    Colloid and Interface Communication   41   1 - 3   2016.12

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    Authorship:Lead author, Corresponding author   Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)   Publisher: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 Invited

    墨智成

    アンサンブル   14   206 - 210   2012

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

    Tomonari Sumi

    物性研究   95   310 - 313   2010.12

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  • 塩による疎水性相互作用とDNAの自己凝縮転移 Invited

    墨智成

    アンサンブル   12   22 - 26   2010.12

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Research Projects

  • Verification of the hydrophobic interaction hypothesis in protein structural stability and theoretical/experimental study on cosolvent effects

    Grant number:20K05431  2020.04 - 2023.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    墨 智成

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    Grant amount:\4420000 ( Direct expense: \3400000 、 Indirect expense:\1020000 )

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  • Experimental/theoretical studies on the structural stability and intermolecular interactions of proteins

    Grant number:16K05657  2016.04 - 2020.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    Tomonari Sumi

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    Grant amount:\4940000 ( Direct expense: \3800000 、 Indirect expense:\1140000 )

    Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann’s hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small model chignolin. Decomposition of the free energy indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with experimental observations for globular proteins.

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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

    2015.06 - 2017.03

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  • Chemomechanical network modeling for molecular motor dynamics of kinesin

    Grant number:25610121  2013.04 - 2016.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research  Grant-in-Aid for Challenging Exploratory Research

    Sumi Tomonari, Klumpp Stefan

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    Grant amount:\3900000 ( Direct expense: \3000000 、 Indirect expense:\900000 )

    We present a chemomechanical network model of molecular motor kinesin that is systematically developed on the basis of experimental observations, and demonstrate that it can qualitatively reproduce available all the experimental results of motor dynamics. The analysis of the local excess fluxes shows that an ATP-concentration dependence of the dominant forward stepping cycle and (2) supports a gated rear head mechanism where the forward step is controlled by ATP hydrolysis and the resulting ADP-bound state of the rear head at saturating ATP levels. The network picture suggests that for saturating ATP concentration, the energy from ATP hydrolysis is used to concentrate the chemical transition flux on the network to a force-generating state that can produce the power stroke. At low ATP levels, the energy is used to avoid states that are fragile against backward load because the leading head is weakly bound to microtubule.

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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

    Grant number:21015012  2009 - 2010

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Priority Areas  Grant-in-Aid for Scientific Research on Priority Areas

    墨 智成

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    Grant amount:\3300000 ( Direct expense: \3300000 )

    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

    Grant number:19031013  2007 - 2008

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Priority Areas  Grant-in-Aid for Scientific Research on Priority Areas

    墨 智成

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    Grant amount:\4700000 ( Direct expense: \4700000 )

    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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