Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures

Kokoro Shikata, Kento Kasahara, Nozomi Morishita Watanabe, Hiroshi Umakoshi, Kang Kim, Nobuyuki Matubayasi

The Journal of Chemical Physics　Vol. 161　No. 1　2024/07/03　Research paper (scientific journal)

Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach

Kazushi Okada, Takuma Kikutsuji, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi

The Journal of Chemical Physics　Vol. 160　No. 17　2024/05/07　Research paper (scientific journal)

Solvation dynamics on the diffusion timescale elucidated using energy-represented dynamics theory

Kazuya Okita, Natsuumi Ito, Nozomi Morishita-Watanabe, Hiroshi Umakoshi, Kento Kasahara, Nobuyuki Matubayasi

Physical Chemistry Chemical Physics　2024　Research paper (scientific journal)

Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects

Stefan Hervø-Hansen, Daoyang Lin, Kento Kasahara, Nobuyuki Matubayasi

Chemical Science　Vol. 15　No. 2　p. 477-489　2024　Research paper (scientific journal)

Elucidating protein–ligand binding kinetics based on returning probability theory

Kento Kasahara, Ren Masayama, Kazuya Okita, Nobuyuki Matubayasi

The Journal of Chemical Physics　Vol. 159　No. 13　2023/10/03　Research paper (scientific journal)

Unraveling the Glass-like Dynamic Heterogeneity in Ring Polymer Melts: From Semiflexible to Stiff Chain

Shota Goto, Kang Kim, Nobuyuki Matubayasi

ACS Polymers Au　2023/08/22　Research paper (scientific journal)

Revealing the hidden dynamics of confined water in acrylate polymers: Insights from hydrogen-bond lifetime analysis

Kokoro Shikata, Takuma Kikutsuji, Nobuhiro Yasoshima, Kang Kim, Nobuyuki Matubayasi

The Journal of Chemical Physics　Vol. 158　No. 17　2023/05/01　Research paper (scientific journal)

Arylazopyrazole-Based Photoswitchable Inhibitors Selective for Escherichia coli Dihydrofolate Reductase

Himadri S. Sarkar, Takato Mashita, Toshiyuki Kowada, Satoshi Hamaguchi, Toshizo Sato, Kento Kasahara, Nobuyuki Matubayasi, Toshitaka Matsui, Shin Mizukami

ACS Chemical Biology　Vol. 18　No. 2　p. 340-346　2023/01/20　Research paper (scientific journal)

Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models

Ryo Kawada, Katsuhiro Endo, Kenji Yasuoka, Hidekazu Kojima, Nobuyuki Matubayasi

Journal of Chemical Information and Modeling　Vol. 63　No. 1　p. 76-86　2023/01/09　Research paper (scientific journal)

Diffusion theory of molecular liquids in the energy representation and application to solvation dynamics

Kazuya Okita, Kento Kasahara, Nobuyuki Matubayasi

The Journal of Chemical Physics　Vol. 157　No. 24　p. 244505-244505　2022/12/28　Research paper (scientific journal)

Hyper-mobile Water and Raman 2900 cm-1 Peak Band of Water Observed around Backbone Phosphates of Double Stranded DNA by High-Resolution Spectroscopies and MD Structural Feature Analysis of Water.

Makoto Suzuki, Akira Tsuchiko, Yoshiyuki Tanaka, Nobuyuki Matubayasi, George Mogami, Nobuyuki Uozumi, Satoshi Takahashi

The journal of physical chemistry. B　2022/12/27　Research paper (scientific journal)

Erratum: Construction of isostructural hydrogen-bonded organic frameworks: limitations and possibilities of pore expansion (Chem. Sci. (2021) 12 (9607–9618) DOI: 10.1039/D1SC02690A)

Yuto Suzuki, Mario Gutiérrez, Senri Tanaka, Eduardo Gomez, Norimitsu Tohnai, Nobuhiro Yasuda, Nobuyuki Matubayasi, Abderrazzak Douhal, Ichiro Hisaki

Chemical Science　Vol. 13　No. 48　2022/11/29　Research paper (scientific journal)

Corrigendum to “Ensemble transformations in the fluctuation theory” [Physica A 585 (2022) 126430] (Physica A: Statistical Mechanics and its Applications (2022) 585, (S0378437121007032), (10.1016/j.physa.2021.126430))

Seishi Shimizu, Nobuyuki Matubayasi

Physica A: Statistical Mechanics and its Applications　Vol. 605　2022/11/01　Research paper (scientific journal)

Cooperative Sorption on Heterogeneous Surfaces

Olivia P.L. Dalby, Steven Abbott, Nobuyuki Matubayasi, Seishi Shimizu

Langmuir　Vol. 38　No. 43　p. 13084-13092　2022/11/01　Research paper (scientific journal)

Constructing a Memory Kernel of the Returning Probability to Efficiently Describe Molecular Binding Processes

Kento Kasahara, Ren Masayama, Yuya Matsubara, Nobuyuki Matubayasi

Chemistry Letters　Vol. 51　No. 8　p. 823-827　2022/08　Research paper (scientific journal)

Crystal Growth of Urea and Its Modulation by Additives as Analyzed by All-Atom MD Simulation and Solution Theory

Senri Tanaka, Naoki Yamamoto, Kento Kasahara, Yoshiki Ishii, Nobuyuki Matubayasi

The Journal of Physical Chemistry B　Vol. 126　No. 28　p. 5274-5290　2022/07/06　Research paper (scientific journal)

Surface Area Estimation: Replacing the Brunauer-Emmett-Teller Model with the Statistical Thermodynamic Fluctuation Theory

Seishi Shimizu, Nobuyuki Matubayasi

Langmuir　Vol. 38　No. 26　p. 7989-8002　2022/07/05　Research paper (scientific journal)

All-atom molecular simulation study of cellulose acetate: amorphous structure and the dissolution of small molecule

Ryota Matsuba, Hiroyuki Kubota, Nobuyuki Matubayasi

Cellulose　Vol. 29　No. 10　p. 5463-5478　2022/07　Research paper (scientific journal)

Nonpolarizable Force Fields through the Self-Consistent Modeling Scheme with MD and DFT Methods: From Ionic Liquids to Self-Assembled Ionic Liquid Crystals.

Yoshiki Ishii, Nobuyuki Matubayasi, Hitoshi Washizu

The journal of physical chemistry. B　2022/06/13　Research paper (scientific journal)

Adsorption Energetics of Amino Acid Analogs on Polymer/Water Interfaces Studied by All-Atom Molecular Dynamics Simulation and a Theory of Solutions

Nobuhiro Yasoshima, Tatsuya Ishiyama, Nobuyuki Matubayasi

The Journal of Physical Chemistry B　2022/06/02　Research paper (scientific journal)

Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)

Takuma Kikutsuji, Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi

The Journal of Chemical Physics　2022/03/31　Research paper (scientific journal)

Anion-cation contrast of small molecule solvation in salt solutions

Stefan Hervø-Hansen, Jan Heyda, Mikael Lund, Nobuyuki Matubayasi

Physical Chemistry Chemical Physics　Vol. 24　No. 5　p. 3238-3249　2022/02/07　Research paper (scientific journal)

Simulating the nematic-isotropic phase transition of liquid crystal model via generalized replica-exchange method.

Kengo Takemoto, Yoshiki Ishii, Hitoshi Washizu, Kang Kim, Nobuyuki Matubayasi

The Journal of chemical physics　Vol. 156　No. 1　p. 014901-014901　2022/01/07　Research paper (scientific journal)

Ensemble transformation in the fluctuation theory

Seishi Shimizu, Nobuyuki Matubayasi

Physica A: Statistical Mechanics and its Applications　Vol. 585　2022/01/01　Research paper (scientific journal)

Molecular dynamics study of the interactions between a hydrophilic polymer brush on graphene and amino acid side chain analogues in water

Takuma Yagasaki, Nobuyuki Matubayasi

Physical Chemistry Chemical Physics　Vol. 24　No. 37　p. 22877-22888　2022　Research paper (scientific journal)

Atomistic description of molecular binding processes based on returning probability theory

Kento Kasahara, Ren Masayama, Kazuya Okita, Nobuyuki Matubayasi

Journal of Chemical Physics　Vol. 155　No. 20　2021/11/28　Research paper (scientific journal)

Molecular Structure and Vibrational Spectra of Water Molecules Sorbed in Poly(2-methoxyethylacrylate) Revealed by Molecular Dynamics Simulation

Nobuhiro Yasoshima, Tatsuya Ishiyama, Makoto Gemmei-Ide, Nobuyuki Matubayasi

The Journal of Physical Chemistry B　Vol. 125　No. 43　p. 12095-12103　2021/11/04　Research paper (scientific journal)

Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation.

Nobuyuki Matubayasi

Chemical communications (Cambridge, England)　Vol. 57　No. 78　p. 9968-9978　2021/09/30　Research paper (scientific journal)

Crystallization of Polyethylene Brushes and Its Effect on Interactions with Water

Takuma Yagasaki, Nobuyuki Matubayasi

Macromolecules　Vol. 54　No. 18　p. 8303-8313　2021/09/28　Research paper (scientific journal)

Effects of chain length on Rouse modes and non-Gaussianity in linear and ring polymer melts

Shota Goto, Kang Kim, Nobuyuki Matubayasi

The Journal of Chemical Physics　Vol. 155　No. 12　p. 124901-124901　2021/09/28　Research paper (scientific journal)

Temperature Dependence of Sorption

Seishi Shimizu, Nobuyuki Matubayasi

Langmuir　Vol. 37　No. 37　p. 11008-11017　2021/09/21　Research paper (scientific journal)

Breakdown of the Stokes–Einstein relation in supercooled liquids: A cage-jump perspective

Raffaele Pastore, Takuma Kikutsuji, Francesco Rusciano, Nobuyuki Matubayasi, Kang Kim, Francesco Greco

The Journal of Chemical Physics　Vol. 155　No. 11　p. 114503-114503　2021/09/21　Research paper (scientific journal)

Cooperative Sorption on Porous Materials

Seishi Shimizu, Nobuyuki Matubayasi

Langmuir　Vol. 37　No. 34　p. 10279-10290　2021/08/31　Research paper (scientific journal)

Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions

Hidekazu Kojima, Kazuya Handa, Kazuo Yamada, Nobuyuki Matubayasi

Journal of Physical Chemistry B　Vol. 125　No. 32　p. 9357-9371　2021/08/19　Research paper (scientific journal)

Adsorbate-adsorbate interactions on microporous materials

Seishi Shimizu, Nobuyuki Matubayasi

Microporous and Mesoporous Materials　Vol. 323　2021/08　Research paper (scientific journal)

Construction of isostructural hydrogen-bonded organic frameworks: limitations and possibilities of pore expansion.

Yuto Suzuki, Mario Gutiérrez, Senri Tanaka, Eduardo Gomez, Norimitsu Tohnai, Nobuhiro Yasuda, Nobuyuki Matubayasi, Abderrazzak Douhal, Ichiro Hisaki

Chemical science　Vol. 12　No. 28　p. 9607-9618　2021/07/21　Research paper (scientific journal)

Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal

Yoshiki Ishii, Nobuyuki Matubayasi, Go Watanabe, Takashi Kato, Hitoshi Washizu

Science Advances　Vol. 7　No. 31　p. eabf0669-eabf0669　2021/07　Research paper (scientific journal)

Sorption: A Statistical Thermodynamic Fluctuation Theory

Seishi Shimizu, Nobuyuki Matubayasi

Langmuir　Vol. 37　No. 24　p. 7380-7391　2021/06/22　Research paper (scientific journal)

Transition pathway of hydrogen bond switching in supercooled water analyzed by the Markov state model

Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi

The Journal of Chemical Physics　Vol. 154　No. 23　p. 234501-234501　2021/06/21　Research paper (scientific journal)

Implicit function theorem and Jacobians in solvation and adsorption

Seishi Shimizu, Nobuyuki Matubayasi

Physica A: Statistical Mechanics and its Applications　Vol. 570　2021/05/15　Research paper (scientific journal)

Understanding the scaling of boson peak through elastic heterogeneity insensitive to bending rigidity in polymer glasses

Naoya Tomoshige, Shota Goto, Hideyuki Mizuno, Tatsuya Mori, Kang Kim, Nobuyuki Matubayasi

Journal of Physics: Condensed Matter　2021/04/30　Research paper (scientific journal)

Cooperativity in micellar solubilization

Seishi Shimizu, Nobuyuki Matubayasi

Physical Chemistry Chemical Physics　Vol. 23　No. 14　p. 8705-8716　2021/04　Research paper (scientific journal)

Spatial-Decomposition Analysis of Electrical Conductivity in Mixtures of Ionic Liquid and Sodium Salt for Sodium-Ion Battery Electrolytes

Lukman Hakim, Yoshiki Ishii, Nobuyuki Matubayasi

The Journal of Physical Chemistry B　2021/03/24　Research paper (scientific journal)

Phase stability condition and liquid–liquid phase separation under mesoscale confinement

Seishi Shimizu, Nobuyuki Matubayasi

Physica A: Statistical Mechanics and its Applications　Vol. 563　2021/02/01　Research paper (scientific journal)

Application of replica-exchange method in molecular dynamics analysis of nematic phase transition of 5CB liquid crystal

Kengo Takemoto, Yoshiki Ishii, Kang Kim, Nobuyuki Matubayasi

Proceedings of Japanese Liquid Crystal Society Annual meeting　Vol. 2021　2021

Solvation Thermodynamics from the Perspective of Endpoints DFT

Ronald M. Levy, Nobuyuki Matubayasi, Bin W. Zhang

Journal of Physical Chemistry B　Vol. 124　No. 52　p. 11771-11782　2020/12/31　Research paper (scientific journal)

Fluctuation adsorption theory: Quantifying adsorbate-adsorbate interaction and interfacial phase transition from an isotherm

Seishi Shimizu, Nobuyuki Matubayasi

Physical Chemistry Chemical Physics　Vol. 22　No. 48　p. 28304-28316　2020/12/28　Research paper (scientific journal)

Intensive nature of fluctuations: Reconceptualizing Kirkwood-Buff theory via elementary algebra

Seishi Shimizu, Nobuyuki Matubayasi

Journal of Molecular Liquids　Vol. 318　2020/11/15　Research paper (scientific journal)

Solubilization power of surfactant-free microemulsions

Sebastian Schöttl, Nobuyuki Matubayasi, Dominik Horinek

Physical Chemistry Chemical Physics　Vol. 22　No. 39　p. 22185-22189　2020/10/21　Research paper (scientific journal)

Thermodynamic stability condition can judge whether a nanoparticle dispersion can be considered a solution in a single phase

Seishi Shimizu, Nobuyuki Matubayasi

Journal of Colloid and Interface Science　Vol. 575　p. 472-479　2020/09/01　Research paper (scientific journal)

Transport Properties of Ionic Liquid and Sodium Salt Mixtures for Sodium-Ion Battery Electrolytes from Molecular Dynamics Simulation with a Self-Consistent Atomic Charge Determination

Lukman Hakim, Yoshiki Ishii, Kazuhiko Matsumoto, Rika Hagiwara, Koji Ohara, Yasuhiro Umebayashi, Nobuyuki Matubayasi

The Journal of Physical Chemistry B　Vol. 124　No. 33　p. 7291-7305　2020/08/06　Research paper (scientific journal)

Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals

Bin W. Zhang, Nobuyuki Matubayasi, Ronald M. Levy

Journal of Physical Chemistry B　Vol. 124　No. 25　p. 5220-5237　2020/06/25　Research paper (scientific journal)

周期境界DFT計算とBlöchl電荷解析を基にした非分極力場の開発：イオン液体の輸送物性予測への応用

石井良樹, 松林伸幸

アンサンブル　Vol. 22　p. 142-150　2020/04　Research paper (scientific journal)

Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide

Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi

2020/03/30

Vibrational state of glass-forming liquid and its dependence on fragility

Daimon Shota, Mizuno Hideyuki, Kim Kang, Matubayasi Nobuyuki

Meeting Abstracts of the Physical Society of Japan　Vol. 75.1　p. 2508-2508　2020

Chain-Increment Method for Free-Energy Computation of a Polymer with All-Atom Molecular Simulations

Yamada, K., Matubayasi, N.

Macromolecules　Vol. 53　No. 3　p. 775-788　2020　Research paper (scientific journal)

Self-Consistent Scheme Combining MD and Order-N DFT Methods: An Improved Set of Nonpolarizable Force Fields for Ionic Liquids

Ishii, Y., Matubayasi, N.

Journal of Chemical Theory and Computation　Vol. 16　No. 1　p. 651-665　2020　Research paper (scientific journal)

Boson peak, elasticity, and glass transition temperature in polymer glasses: Effects of the rigidity of chain bending

Naoya Tomoshige, Hideyuki Mizuno, Tatsuya Mori, Kang Kim, Nobuyuki Matubayasi

Scientific Reports　Vol. 9　No. 1　2019/12　Research paper (scientific journal)

Consistency of geometrical definitions of hydrogen bonds based on the two-dimensional potential of mean force with respect to the time correlation in liquid water over a wide range of temperatures

Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi

Journal of Molecular Liquids　Vol. 294　No. 15　p. 111603-111603　2019/11　Research paper (scientific journal)

Local viscoelasticity at resin-metal interface analyzed with spatial-decomposition formula for relaxation modulus.

Mori H, Matubayasi N

The Journal of chemical physics　Vol. 151　No. 11　2019/09　Research paper (scientific journal)

Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method.

Ishii Y, Yamamoto N, Matubayasi N, Zhang BW, Cui D, Levy RM

Journal of chemical theory and computation　Vol. 15　No. 5　p. 2896-2912　2019/05　Research paper (scientific journal)

Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation.

Masutani K, Yamamori Y, Kim K, Matubayasi N

The Journal of chemical physics　Vol. 150　No. 14　2019/04　Research paper (scientific journal)

Structure and Dynamics of the Hydration Shell: Spatially Decomposed Time Correlation Approach.

Pluhařová E, Jungwirth P, Matubayasi N, Marsalek O

Journal of chemical theory and computation　Vol. 15　No. 2　p. 803-812　2019/02　Research paper (scientific journal)

The mechanism of salt effects on starch gelatinization from a statistical thermodynamic perspective

Nicol Thomas W. J, Isobe Noriyuki, Clark James H, Matubayasi Nobuyuki, Shimizu Seishi

FOOD HYDROCOLLOIDS　Vol. 87　p. 593-601　2019/02　Research paper (scientific journal)

Density of State Analysis Studied by Coarse-Grained MD Simulation

Tomoshige Naoya, Mizuno Hideyuki, Kim Kang, Matubayasi Nobuyuki

Meeting Abstracts of the Physical Society of Japan　Vol. 74.1　p. 2881-2881　2019

Molecular dynamics analysis of model dependence of silica glass

Daimon Shota, Mizuno Hideyuki, Kim Kang, Matubayasi Nobuyuki

Meeting Abstracts of the Physical Society of Japan　Vol. 74.2　p. 2619-2619　2019

Energy-representation theory of solutions: Its formulation and application to soft, molecular aggregates

Matubayasi, N.

Bulletin of the Chemical Society of Japan　Vol. 92　No. 11　p. 1910-1927　2019　Research paper (scientific journal)

Bridging the gap between molecular dynamics and hydrodynamics in nanoscale Brownian motions

Mizuta, K., Ishii, Y., Kim, K., Matubayasi, N.

Soft Matter　Vol. 15　No. 21　p. 4380-4390　2019　Research paper (scientific journal)

Diffusion dynamics of supercooled water modeled with the cage-jump motion and hydrogen-bond rearrangement

Kikutsuji, T., Kim, K., Matubayasi, N.

Journal of Chemical Physics　Vol. 150　No. 20　2019　Research paper (scientific journal)

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations

Shinobu Ai, Takemura Kazuhiro, Matubayasi Nobuyuki, Kitao Akio

JOURNAL OF CHEMICAL PHYSICS　Vol. 149　No. 19　p. 195101-195101　2018/11/21　Research paper (scientific journal)

Statistical thermodynamics of regular solutions and solubility parameters

Matubayasi Nobuyuki, Shimizu Seishi

J. Mol. Liq.　Vol. 273　p. 626-633　2018/10　Research paper (scientific journal)

Spatial-Decomposition Analysis of Electrical Conductivity.

Matubayasi N

Chemical record (New York, N.Y.)　Vol. 19　No. 4　p. 723-734　2018/10　Research paper (scientific journal)

Resin filling into nano-sized pore on metal surface analyzed by all-atom molecular dynamics simulation over a variety of resin and pore sizes

Mori Hodaka, Matubayasi Nobuyuki

POLYMER　Vol. 150　p. 360-370　2018/08/15　Research paper (scientific journal)

Free-energy analysis of physisorption on solid-liquid interface with the solution theory in the energy representation

Yamamoto Naoki, Nakakuki Ippei, Matubayasi Nobuyuki

JOURNAL OF CHEMICAL PHYSICS　Vol. 149　No. 1　2018/07/07　Research paper (scientific journal)

How do hydrogen bonds break in supercooled water?: Detecting pathways not going through saddle point of two-dimensional potential of mean force

Kikutsuji Takuma, Kim Kang, Matubayasi Nobuyuki

JOURNAL OF CHEMICAL PHYSICS　Vol. 148　No. 24　2018/06/28　Research paper (scientific journal)

Structure and permeability of ionomers studied by atomistic molecular simulation combined with the theory of solutions in the energy representation

Tomonori Kawakami, Isamu Shigemoto, Nobuyuki Matubayasi

Journal of Chemical Physics　Vol. 148　No. 21　2018/06/07　Research paper (scientific journal)

Novel intermolecular surface force unveils the driving force of the actomyosin system

Makoto Suzuki, George Mogami, Takahiro Watanabe, Nobuyuki Matubayasi

The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery　p. 257-274　2018/05/07　Part of collection (book)

All-atom analysis of free energy of protein solvation through molecular simulation and solution theory

Nobuyuki Matubayasi

The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery　p. 141-155　2018/05/07　Part of collection (book)

Spatial distribution of ionic hydration energy and hyper-mobile water

George Mogami, Makoto Suzuki, Nobuyuki Matubayasi

The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery　p. 33-52　2018/05/07　Part of collection (book)

The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations

Bin W. Zhang, Di Cui, Nobuyuki Matubayasi, Ronald M. Levy

Journal of Physical Chemistry B　Vol. 122　No. 17　p. 4700-4707　2018/05/03　Research paper (scientific journal)

Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions

Tomoko Mizuguchi, Nobuyuki Matubayasi

Journal of Physical Chemistry B　Vol. 122　No. 13　p. 3219-3229　2018/04/05　Research paper (scientific journal)

Probabilistic analysis for identifying the driving force of protein folding

Yoshihiko Tokunaga, Yu Yamamori, Nobuyuki Matubayasi

Journal of Chemical Physics　Vol. 148　No. 12　2018/03/28　Research paper (scientific journal)

Binding free energy analysis of protein-protein docking model structures by evERdock

Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao

Journal of Chemical Physics　Vol. 148　No. 10　2018/03/14　Research paper (scientific journal)

Spatial-decomposition analysis of viscosity with application to Lennard-Jones fluid

Kai-Min Tu, Kang Kim, Nobuyuki Matubayasi

Journal of Chemical Physics　Vol. 148　No. 9　2018/03/07　Research paper (scientific journal)

A unified perspective on preferential solvation and adsorption based on inhomogeneous solvation theory

Seishi Shimizu, Nobuyuki Matubayasi

Physica A: Statistical Mechanics and its Applications　Vol. 492　p. 1988-1996　2018/02/15　Research paper (scientific journal)

The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force

Di Cui, Bin W. Zhang, Nobuyuki Matubayasi, Ronald M. Levy

Journal of Chemical Theory and Computation　Vol. 14　No. 2　p. 512-526　2018/02/13　Research paper (scientific journal)

A molecular thermodynamics approach to capture non-specific flavour-macromolecule interactions

Seishi Shimizu, Steven Abbott, Nobuyuki Matubayasi

Encyclopedia of Food Chemistry　p. 522-527　2018/01/01　Part of collection (book)

MD simulation analysis of resin filling into nano-sized pore formed on metal surface

Hodaka Mori, Nobuyuki Matubayasi

APPLIED SURFACE SCIENCE　Vol. 427　p. 1084-1091　2018/01　Research paper (scientific journal)

Ion hydration: Linking self-diffusion and reorientational motion to water structure

Seishi Shimizu, Nobuyuki Matubayasi

Physical Chemistry Chemical Physics　Vol. 20　No. 8　p. 5909-5917　2018　Research paper (scientific journal)

Statistical thermodynamic foundation for mesoscale aggregation in ternary mixtures

Seishi Shimizu, Nobuyuki Matubayasi

Physical Chemistry Chemical Physics　Vol. 20　No. 20　p. 13777-13784　2018　Research paper (scientific journal)

Water activity in liquid food systems: A molecular scale interpretation

Andrew J. Maneffa, Richard Stenner, Avtar S. Matharu, James H. Clark, Nobuyuki Matubayasi, Seishi Shimizu

FOOD CHEMISTRY　Vol. 237　p. 1133-1138　2017/12　Research paper (scientific journal)

Osmolyte depletion viewed in terms of the dividing membrane and its work of expansion against osmotic pressure

Seishi Shimizu, Nobuyuki Matubayasi

BIOPHYSICAL CHEMISTRY　Vol. 231　p. 111-115　2017/12　Research paper (scientific journal)

Physical driving force of actomyosin motility based on the hydration effect

Makoto Suzuki, George Mogami, Hideyuki Ohsugi, Takahiro Watanabe, Nobuyuki Matubayasi

CYTOSKELETON　Vol. 74　No. 12　p. 512-527　2017/12　Research paper (scientific journal)

Effective Charges of Ionic Liquid Determined Self-Consistently through Combination of Molecular Dynamics Simulation and Density-Functional Theory

Ryosuke Ishizuka, Nobuyuki Matubayasi

JOURNAL OF COMPUTATIONAL CHEMISTRY　Vol. 38　No. 30　p. 2559-2569　2017/11　Research paper (scientific journal)

Hydrotropy and scattering: pre-ouzo as an extended near-spinodal region

Seishi Shimizu, Nobuyuki Matubayasi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 19　No. 39　p. 26734-26742　2017/10　Research paper (scientific journal)

Unifying hydrotropy under Gibbs phase rule

Seishi Shimizu, Nobuyuki Matubayasi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 19　No. 35　p. 23597-23605　2017/09　Research paper (scientific journal)

Quantifying non-specific interactions between flavour and food biomolecules

Seishi Shimizu, Steven Abbott, Nobuyuki Matubayasi

FOOD & FUNCTION　Vol. 8　No. 9　p. 2999-3009　2017/09

Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points

Robert C. Harris, Nanjie Deng, Ronald M. Levy, Ryosuke Ishizuka, Nobuyuki Matubayasi

JOURNAL OF COMPUTATIONAL CHEMISTRY　Vol. 38　No. 15　p. 1198-1208　2017/06　Research paper (scientific journal)

Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme

Yu Yamamori, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 146　No. 22　2017/06　Research paper (scientific journal)

Energetic Analysis of Adsorption and Absorption of Small Molecule to Nanodroplet of Water

Minoru Sayou, Ryosuke Ishizuka, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 121　No. 24　p. 5995-6001　2017/06　Research paper (scientific journal)

Fragment ER: Efficient and accurate binding free energy calculation method for protein-ligand complex

Masuda Tomohide, Tanimura Ryuji, Matubayasi Nobuyuki

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY　Vol. 253　2017/04/02

Relationship between Solvation Thermodynamics from IST and DFT Perspectives

Ronald M. Levy, Di Cui, Bin W. Zhang, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 121　No. 15　p. 3825-3841　2017/04　Research paper (scientific journal)

Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions

Nobuyuki Matubayasi

CURRENT OPINION IN STRUCTURAL BIOLOGY　Vol. 43　p. 45-54　2017/04　Research paper (scientific journal)

Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions

Hideaki Takahashi, Satoru Umino, Yuji Miki, Ryosuke Ishizuka, Shu Maeda, Akihiro Morita, Makoto Suzuki, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 121　No. 10　p. 2279-2287　2017/03　Research paper (scientific journal)

Protein-Protein Complex Structure Prediction using the Solution Theory in the Energy Representation

Kazuhiro Takemura, Akio Kitao, Nobuyuki Matubayasi

BIOPHYSICAL JOURNAL　Vol. 112　No. 3　p. 53A-54A　2017/02

Gastrophysics: Statistical thermodynamics of biomolecular denaturation and gelation from the Kirkwood-Buff theory towards the understanding of tofu

Seishi Shimizu, Richard Stenner, Nobuyuki Matubayasi

FOOD HYDROCOLLOIDS　Vol. 62　p. 128-139　2017/01

Pseudomonas aeruginosa cytochrome c(551) denaturation by five systematic urea derivatives that differ in the alkyl chain length

Shinya Kobayashi, Sotaro Fujii, Aya Koga, Satoshi Wakai, Nobuyuki Matubayasi, Yoshihiro Sambongi

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　Vol. 81　No. 7　p. 1274-1278　2017　Research paper (scientific journal)

The origin of cooperative solubilisation by hydrotropes

Seishi Shimizu, Nobuyuki Matubayasi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 18　No. 36　p. 25621-25628　2016/09　Research paper (scientific journal)

Origin of non-linearity in phase solubility: solubilisation by cyclodextrin beyond stoichiometric complexation

Thomas W. J. Nicol, Nobuyuki Matubayasi, Seishi Shimizu

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 18　No. 22　p. 15205-15217　2016/06　Research paper (scientific journal)

Morphology study of DMPC/DHPC mixtures by solution-state H-1, P-31 NMR, and NOE measurements

Megumi Shintani, Nobuyuki Matubayasi

JOURNAL OF MOLECULAR LIQUIDS　Vol. 217　p. 62-69　2016/05　Research paper (scientific journal)

Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions

Atsushi Date, Ryosuke Ishizuka, Nobuyuki Matubayasi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 18　No. 19　p. 13223-13231　2016/05　Research paper (scientific journal)

Effect of Diffuseness of Micelle Boundary on the Solute Bound to Micelle

Tomoko Mizuguchi, Nobuyuki Matubayasi

SEN-I GAKKAISHI　Vol. 72　No. 5　p. 266-269　2016/05　Research paper (scientific journal)

Gelation of carrageenan: Effects of sugars and polyols

Richard Stenner, Nobuyuki Matubayasi, Seishi Shimizu

FOOD HYDROCOLLOIDS　Vol. 54　p. 284-292　2016/03　Research paper (scientific journal)

Spatial-Decomposition Analysis of Energetics of Ionic Hydration

George Mogami, Makoto Suzuki, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 120　No. 8　p. 1813-1821　2016/03　Research paper (scientific journal)

Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory

Ryosuke Ishizuka, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL THEORY AND COMPUTATION　Vol. 12　No. 2　p. 804-811　2016/02　Research paper (scientific journal)

Interaction-component analysis of the hydration and urea effects on cytochrome c

Yu Yamamori, Ryosuke Ishizuka, Yasuhito Karino, Shun Sakuraba, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 144　No. 8　2016/02　Research paper (scientific journal)

An Accurate and Efficient, Computational Method for the Hydration Free Energy of Large and Complex Molecules

Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi

BIOPHYSICAL JOURNAL　Vol. 110　No. 3　p. 328A-329A　2016/02

Effect of rotation on vibrational spectrum of supercritical water: Analysis of dependencies on density and hydrogen isotopes

Ken Yoshida, Nobuyuki Matubayasi, Masaru Nakahara, Yasuhiro Uosaki

Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu　Vol. 26　No. 4　p. 323-332　2016　Research paper (scientific journal)

Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent

Fumitaka Kamo, Ryosuke Ishizuka, Nobuyuki Matubayasi

PROTEIN SCIENCE　Vol. 25　No. 1　p. 56-66　2016/01　Research paper (scientific journal)

Free-Energy Analysis of the Preferred Configuration of Transmembrane Protein in Model Membrane: Roles of Lipid and Water

Acep Purqon, Nobuyuki Matubayasi

2ND PADJADJARAN INTERNATIONAL PHYSICS SYMPOSIUM 2015 (PIPS-2015): MATERIALS FUNCTIONALIZATION AND ENERGY CONSERVATIONS　Vol. 1712　2016　Research paper (international conference proceedings)

An accurate and efficient computation method of the hydration free energy of a large, complex molecule

Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi

JOURNAL OF CHEMICAL PHYSICS　Vol. 142　No. 17　2015/05　Research paper (scientific journal)

Effect of diffuseness of micelle boundary on the solute distribution upon solubilization

Tomoko Mizuguchi, Ryosuke Ishizuka, Nobuyuki Matubayasi

CHEMICAL PHYSICS LETTERS　Vol. 624　p. 19-23　2015/03　Research paper (scientific journal)

Free-energy Analysis of Binding Functions of Soft Molecular Aggregates on the Basis of the Extended Concept of Solvation

Nobuyuki Matubayasi

BUNSEKI KAGAKU　Vol. 64　No. 3　p. 185-188　2015/03　Research paper (scientific journal)

Development of a massively parallel QM/MM approach combined with a theory of solutions

Hideaki Takahashi, Nobuyuki Matubayasi

Challenges and Advances in Computational Chemistry and Physics　Vol. 21　p. 153-196　2015　Part of collection (book)

Energetic Contributions from the Cation and Anion to the Stability of Carbon Dioxide Dissolved in Imidazolium-Based Ionic Liquids

Ryosuke Ishizuka, Nobuyuki Matubayasi, Kai-Min Tu, Yasuhiro Umebayashi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 119　No. 4　p. 1579-1587　2015/01　Research paper (scientific journal)

Finite-Size Effect on the Charging Free Energy of Protein in Explicit Solvent

Toru Ekimoto, Nobuyuki Matubayasi, Mitsunori Ikeguchi

JOURNAL OF CHEMICAL THEORY AND COMPUTATION　Vol. 11　No. 1　p. 215-223　2015/01　Research paper (scientific journal)

Spatial-decomposition analysis of electrical conductivity in ionic liquid

Kai-Min Tu, Ryosuke Ishizuka, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 141　No. 24　2014/12　Research paper (scientific journal)

Gelation: The Role of Sugars and Polyols on Gelatin and Agarose

Seishi Shimizu, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 118　No. 46　p. 13210-13216　2014/11　Research paper (scientific journal)

Effect of Rotational Couplings on Vibrational Spectrum Line Shape of the Bending Mode in Low-Density Supercritical Water: Density and Hydrogen Isotopes Dependencies

Ken Yoshida, Nobuyuki Matubayasi, Yasuhiro Uosaki, Masaru Nakahara

JOURNAL OF SOLUTION CHEMISTRY　Vol. 43　No. 9-10　p. 1499-1508　2014/10　Research paper (scientific journal)

Hydrotropy: Monomer-Micelle Equilibrium and Minimum Hydrotrope Concentration

Seishi Shimizu, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 118　No. 35　p. 10515-10524　2014/09　Research paper (scientific journal)

ERmod: Fast and Versatile Computation Software for Solvation Free Energy with Approximate Theory of Solutions

Shun Sakuraba, Nobuyuki Matubayasi

JOURNAL OF COMPUTATIONAL CHEMISTRY　Vol. 35　No. 21　p. 1592-1608　2014/08　Research paper (scientific journal)

Spatial-decomposition analysis of electrical conductivity in concentrated electrolyte solution

Kai-Min Tu, Ryosuke Ishizuka, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 141　No. 4　2014/07　Research paper (scientific journal)

Preferential Solvation: Dividing Surface vs Excess Numbers

Seishi Shimizu, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 118　No. 14　p. 3922-3930　2014/04　Research paper (scientific journal)

Comparative Study on the Properties of Hydration Water of Na- and K-Halide Ions by Raman OH/OD-stretching Spectroscopy and Dielectric Relaxation Data

Yuichiro Okazaki, Tetsuo Taniuchi, George Mogami, Nobuyuki Matubayasi, Makoto Suzuki

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 118　No. 16　p. 2922-2930　2014/04　Research paper (scientific journal)

Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation (vol 137, 234903, 2012)

Tomonori Kawakami, Isamu Shigemoto, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 140　No. 16　2014/04

Hydration Structure of CO2-Absorbed 2-Aminoethanol Studied by Neutron Diffraction with the N-14/N-15 Isotopic Substitution Method

Yasuo Kameda, Hiroshi Deguchi, Hirotoshi Furukawa, Yoshiyuki Kubota, Yasuyuki Yagi, Yoshihiro Imai, Noriko Yamazaki, Noriko Watari, Takuya Hirata, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 118　No. 5　p. 1403-1410　2014/02　Research paper (scientific journal)

2SDP-06 Interaction-Component Analysis on Protein Structure in Explicit Solvent(Biomolecular machinery driven by surrounding water,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Matubayasi Nobuyuki

Seibutsu Butsuri　Vol. 54　No. 1　2014

3P132 On the Hydration Dynamics and Energetics of Alkali halide and Phosphate Ions by Dielectric Relaxation Spectroscopy and Molecular Dynamics(07. Water & Hydration & Electrolyte,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Mogami George, Ishimori Kazuki, Matubayasi Nobuyuki, Takahashi Hideaki, Suzuki Makoto

Seibutsu Butsuri　Vol. 54　No. 1　2014

1P007 Protein-protein complex structure prediction using the solution theory in the energy representation(Protein: Structure,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao

Seibutsu Butsuri　Vol. 54　No. 1　2014

Anion-Dependence of Fast Relaxation Component in Na-, K-Halide Solutions at Low Concentrations Measured by High-Resolution Microwave Dielectric Spectroscopy

George Mogami, Takashi Miyazaki, Tetsuichi Wazawa, Nobuyuki Matubayasi, Makoto Suzuki

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 117　No. 23　p. 4851-4862　2013/06　Research paper (scientific journal)

Effect of heavy hydrogen isotopes on the vibrational line shape for supercritical water through rotational couplings

Ken Yoshida, Nobuyuki Matubayasi, Yasuhiro Uosaki, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 138　No. 13　2013/04　Research paper (scientific journal)

Solvent effect on pathways and mechanisms for d-fructose conversion to 5-hydroxymethyl-2-furaldehyde: In situ 13C NMR study

Hiroshi Kimura, Masaru Nakahara, Nobuyuki Matubayasi

Journal of Physical Chemistry A　Vol. 117　No. 10　p. 2102-2113　2013/03/14　Research paper (scientific journal)

Molecular Dynamics Simulations of Yeast F-1-ATPase before and after 16 degrees Rotation of the gamma Subunit

Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori Ikeguchi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 117　No. 12　p. 3298-3307　2013/03　Research paper (scientific journal)

Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

Kazuhiro Takemura, Raghunadha Reddy Burri, Takeshi Ishikawa, Takakazu Ishikura, Shun Sakuraba, Nobuyuki Matubayasi, Kazuo Kuwata, Akio Kitao

CHEMICAL PHYSICS LETTERS　Vol. 559　p. 94-98　2013/02　Research paper (scientific journal)

3P164 All-atom hydration analysis of the β subunit in F1-ATPase(11. Molecular motor,Poster)

Ekimoto Toru, Ikeguchi Mitsunori, Matubayasi Nobuyuki

Seibutsu Butsuri　Vol. 53　No. 1　2013

A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method

Takeshi Ishikawa, Raghunadha Reddy Burri, Yuji O. Kamatari, Shun Sakuraba, Nobuyuki Matubayasi, Akio Kitao, Kazuo Kuwata

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 15　No. 10　p. 3646-3654　2013　Research paper (scientific journal)

Interaction-component analysis of the urea effect on amino acid analogs

Yasuhito Karino, Nobuyuki Matubayasi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 15　No. 12　p. 4377-4391　2013　Research paper (scientific journal)

High-Energy X-ray Diffraction Study on the Intramolecular Structure of 2-Aminoethanol in the Liquid State

Yasuo Kameda, Hiroshi Deguchi, Yoshiyuki Kubota, Hirotoshi Furukawa, Yasuyuki Yagi, Yoshihiro Imai, Masahiko Tatsumi, Noriko Yamazaki, Noriko Watari, Takuya Hirata, Nobuyuki Matubayasi

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN　Vol. 86　No. 1　p. 99-103　2013/01　Research paper (scientific journal)

Molecular Dynamics Simulations of Yeast F-1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit

Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori Ikeguchi

BIOPHYSICAL JOURNAL　Vol. 104　No. 2　p. 332A-332A　2013/01

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

Kazuhiro Takemura, Hao Guo, Shun Sakuraba, Nobuyuki Matubayasi, Akio Kitao

JOURNAL OF CHEMICAL PHYSICS　Vol. 137　No. 21　2012/12　Research paper (scientific journal)

Molecular dynamics study of fast dielectric relaxation of water around a molecular-sized ion

Yoji Kubota, Akira Yoshimori, Nobuyuki Matubayasi, Makoto Suzuki, Ryo Akiyama

JOURNAL OF CHEMICAL PHYSICS　Vol. 137　No. 22　2012/12　Research paper (scientific journal)

Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation

Tomonori Kawakami, Isamu Shigemoto, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 137　No. 23　2012/12　Research paper (scientific journal)

Nuclear magnetic resonance study on rotational dynamics of water and benzene in a series of ionic liquids: Anion and cation effects

Hiroshi Kimura, Yoshiro Yasaka, Masaru Nakahara, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 137　No. 19　2012/11　Research paper (scientific journal)

Density effect on infrared spectrum for supercritical water in the low- and medium-density region studied by molecular dynamics simulation

Ken Yoshida, Nobuyuki Matubayasi, Yasuhiro Uosaki, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 137　No. 19　2012/11　Research paper (scientific journal)

Noncatalytic Hydrothermal Elimination of the Terminal D-Glucose Unit from Malto- and Cello-Oligosaccharides through Transformation to D-Fructose

Hiroshi Kimura, Masaru Nakahara, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 116　No. 41　p. 10039-10049　2012/10　Research paper (scientific journal)

A possible molecular mechanism for the pressure reversal of general anaesthetics: Aggregation of halothane in POPC bilayers at high pressure

K. M. Tu, N. Matubayasi, K. K. Liang, I. T. Todorov, S. L. Chan, P. -L. Chau

CHEMICAL PHYSICS LETTERS　Vol. 543　p. 148-154　2012/08　Research paper (scientific journal)

Structural characteristics of yeast F-1-ATPase before and after 16-degree rotation of the gamma subunit: Theoretical analysis focused on the water-entropy effect

Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayasi, Mitunori Ikeguchi, Masahiro Kinoshita

JOURNAL OF CHEMICAL PHYSICS　Vol. 137　No. 3　2012/07　Research paper (scientific journal)

Free-Energy and Structural Analysis of Ion Solvation and Contact Ion-Pair Formation of Li+ with BF4- and PF6- in Water and Carbonate Solvents

Munetaka Takeuchi, Nobuyuki Matubayasi, Yasuo Kameda, Babak Minofar, Shin-ichi Ishiguro, Yasuhiro Umebayashi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 116　No. 22　p. 6476-6487　2012/06　Research paper (scientific journal)

Simple and exact approach to the electronic polarization effect on the solvation free energy: Formulation for quantum-mechanical/molecular-mechanical system and its applications to aqueous solutions

Hideaki Takahashi, Atsushi Omi, Akihiro Morita, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 136　No. 21　2012/06　Research paper (scientific journal)

Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T-1 measurements

Yoshiro Yasaka, Michael L. Klein, Masaru Nakahara, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 136　No. 7　2012/02　Research paper (scientific journal)

1PS034 Molecular Dynamics Simulation on Structural Characteristics of Yeast F1-ATPase before and after 16-degree Rotation of Gamma Subunit(The 50th Annual Meeting of the Biophysical Society of Japan)

Ito Yuko, Yoshidome Takashi, Matsubayashi Nobuyuki, Kinoshita Masahiro, Ikeguchi Mitsunori

Seibutsu Butsuri　Vol. 52　2012

Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation

Nobuyuki Matubayasi, Hideaki Takahashi

JOURNAL OF CHEMICAL PHYSICS　Vol. 136　No. 4　2012/01　Research paper (scientific journal)

Pathways and Kinetics of Anisole Pyrolysis Studied by NMR and Selective C-13 Labeling. Heterolytic Carbon Monoxide Generation

Yasuo Tsujino, Yoshiro Yasaka, Nobuyuki Matubayasi, Masaru Nakahara

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN　Vol. 85　No. 1　p. 124-132　2012/01　Research paper (scientific journal)

The effect of pressure on halothane binding to hydrated DMPC bilayers

P. -L. Chau, K. M. Tu, K. K. Liang, I. T. Todorov, S. J. Roser, Robert Barker, Nobuyuki Matubayasi

MOLECULAR PHYSICS　Vol. 110　No. 13　p. 1461-1467　2012　Research paper (scientific journal)

Interaction of naphthalene derivatives with lipids in membranes studied by the H-1-nuclear Overhauser effect and molecular dynamics simulation

Megumi Shintani, Yushi Matsuo, Shun Sakuraba, Nobuyuki Matubayasi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 14　No. 40　p. 14049-14060　2012　Research paper (scientific journal)

A Novel Rotation Mechanism of F1-ATPase Based on the Water-Entropy Effect

Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayasi, Mitunori Ikeguchi, Masahiro Kinoshita

BIOPHYSICAL JOURNAL　Vol. 102　No. 3　p. 246A-246A　2012/01

In Situ Kinetic Study on Hydrothermal Transformation of D-Glucose into 5-Hydroxymethylfurfural through D-Fructose with C-13 NMR

Hiroshi Kimura, Masaru Nakahara, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 115　No. 48　p. 14013-14021　2011/12　Research paper (scientific journal)

Frequency-Domain Investigation of the Ionic Mobility of Inflate Salts in Tetrahydrofuran

Tsuyoshi Yamaguchi, Yukihiro Yamada, Tatsuro Matsuoka, Shinobu Koda, Yoshiro Yasaka, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 115　No. 43　p. 12558-12565　2011/11　Research paper (scientific journal)

Hydration structure around CO2 captured in aqueous amine solutions observed by high energy X-ray scattering

Hiroshi Deguchi, Yoshiyuki Kubota, Hirotoshi Furukawa, Yasuyuki Yagi, Yoshihiro Imai, Masahiko Tatsumi, Noriko Yamazaki, Noriko Watari, Takuya Hirata, Nobuyuki Matubayasi, Yasuo Kameda

INTERNATIONAL JOURNAL OF GREENHOUSE GAS CONTROL　Vol. 5　No. 6　p. 1533-1539　2011/11　Research paper (scientific journal)

Distribution-function approach to free energy computation

Shun Sakuraba, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 135　No. 11　2011/09　Research paper (scientific journal)

NMR-NOE and MD Simulation Study on Phospholipid Membranes: Dependence on Membrane Diameter and Multiple Time Scale Dynamics

Megumi Shintani, Ken Yoshida, Shun Sakuraba, Masaru Nakahara, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 115　No. 29　p. 9106-9115　2011/07　Research paper (scientific journal)

Communication: Exploring the reorientation of benzene in an ionic liquid via molecular dynamics: Effect of temperature and solvent effective charge on the slow dynamics

Yoshiro Yasaka, Michael L. Klein, Masaru Nakahara, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 134　No. 19　2011/05　Research paper (scientific journal)

Energetic Origin of Proton Affinity to the Air/Water Interface

Hideaki Takahashi, Kunihiro Maruyama, Yasuhito Karino, Akihiro Morita, Masayoshi Nakano, Pavel Jungwirth, Nobuyuki Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 115　No. 16　p. 4745-4751　2011/04　Research paper (scientific journal)

1SG-07 Summary and Near-Future Perspective of the Symposium "Asymmetry Produced by Water and ATP"(1SG Asymmetryproduced by water and ATP,The 49th Annual Meeting of the Biophysical Society of Japan)

Matubayasi Nobuyuki

Seibutsu Butsuri　Vol. 51　2011

Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c

Yasuhito Karino, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 134　No. 4　2011/01　Research paper (scientific journal)

Hydration property of globular proteins: An analysis of solvation free energy by energy representation method

Hiroaki Saito, Nobuyuki Matubayasi, Kiyoshi Nishikawa, Hidemi Nagao

CHEMICAL PHYSICS LETTERS　Vol. 497　No. 4-6　p. 218-222　2010/09　Research paper (scientific journal)

Insights into the Origins of Configurational Stability of Axially Chiral Biaryl Amines with an Intramolecular N-H-N Hydrogen Bond

Kazuhiro Hayashi, Nobuyuki Matubayasi, Changsheng Jiang, Tomoyuki Yoshimura, Swapan Majumdar, Takahiro Sasamori, Norihiro Tokitoh, Takeo Kawabata

JOURNAL OF ORGANIC CHEMISTRY　Vol. 75　No. 15　p. 5031-5036　2010/08　Research paper (scientific journal)

Scaled Polynomial Expression for Self-Diffusion Coefficients for Water, Benzene, and Cyclohexane over a Wide Range of Temperatures and Densities

Ken Yoshida, Nobuyuki Matubayasi, Yasuhiro Uosaki, Masaru Nakahara

JOURNAL OF CHEMICAL AND ENGINEERING DATA　Vol. 55　No. 8　p. 2815-2823　2010/08　Research paper (scientific journal)

End-point calculation of solvation free energy of amino-acid analogs by molecular theories of solution

Yasuhito Karino, Maxim V. Fedorov, Nobuyuki Matubayasi

CHEMICAL PHYSICS LETTERS　Vol. 496　No. 4-6　p. 351-355　2010/08　Research paper (scientific journal)

Controlling the Equilibrium of Formic Acid with Hydrogen and Carbon Dioxide Using Ionic Liquid

Yoshiro Yasaka, Chihiro Wakai, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 114　No. 10　p. 3510-3515　2010/03　Research paper (scientific journal)

2SB1105 Structure and Energetics of Hydration for Functional Molecules in Solution(2SB Molecular Basis of ATP Energy,The 48th Annual Meeting of the Biophysical Society of Japan)

Matubayasi Nobuyuki

Seibutsu Butsuri　Vol. 50　No. 2　2010

Recent advances in studies on organic reactions in water at high temperatures and high pressures

Masaru Nakahara, Yasuo Tsujino, Yoshiro Yasaka, Ken Yoshida, Yasuhiro Uosaki, Chihiro Wakai, Nobuyuki Matubayasi

Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu　Vol. 20　No. 1　p. 40-49　2010　Research paper (scientific journal)

Newly Designed Neutron Diffraction Cell for Fluids at High Temperatures and High Pressures

Hiroki Iwase, Nobuyuki Matubayasi, Yasuo Kameda, Keiji Itoh, Toshiya Otomo, Masaru Nakahara

JAPANESE JOURNAL OF APPLIED PHYSICS　Vol. 49　No. 1　2010　Research paper (scientific journal)

Development of a Quantum Chemical Method Combined with a Theory of Solutions-Free-Energy Calculation for Chemical Reactions by Condensed Phase Simulations

Hideaki Takahashi, Nobuyuki Matubayasi, Masayoshi Nakano

ADVANCES IN QUANTUM CHEMISTRY, VOL 59　Vol. 59　p. 283-351　2010　Part of collection (book)

Self-Diffusion in Supercritical Water and Benzene in High-Temperature High-Pressure Conditions Studied by NMR and Dynamic Solvation-Shell Model

Ken Yoshida, Nobuyuki Matubayasi, Yasuhiro Uosaki, Masaru Nakahara

INTERNATIONAL CONFERENCE ON HIGH PRESSURE SCIENCE AND TECHNOLOGY, JOINT AIRAPT-22 AND HPCJ-50　Vol. 215　2010　Research paper (international conference proceedings)

Self-diffusion coefficients for water and organic solvents in extremely low-density supercritical states

Ken Yoshida, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF MOLECULAR LIQUIDS　Vol. 147　No. 1-2　p. 96-101　2009/07　Research paper (scientific journal)

Water as an in Situ NMR Indicator for Impurity Acids in Ionic Liquids

Yoshiro Yasaka, Chihiro Wakai, Nobuyuki Matubayasi, Masaru Nakahara

ANALYTICAL CHEMISTRY　Vol. 81　No. 1　p. 400-407　2009/01　Research paper (scientific journal)

Free-Energy Analysis of Solvation with the Method of Energy Representation

Nobuyuki Matubayasi

FRONTIERS IN BIOSCIENCE　Vol. 14　p. 3536-3549　2009/01　Research paper (scientific journal)

Self-diffusion coefficients for water and organic solvents at high temperatures along the coexistence curve

Ken Yoshida, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 129　No. 21　2008/12　Research paper (scientific journal)

Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: A novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation

Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Masayoshi Nakano, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 129　No. 20　2008/11　Research paper (scientific journal)

Free-energy change of inserting halothane into different depths of a hydrated DMPC bilayer

P. -L. Chau, K. -M. Tu, K. K. Liang, S. L. Chan, Nobuyuki Matubayasi

CHEMICAL PHYSICS LETTERS　Vol. 462　No. 1-3　p. 112-115　2008/09　Research paper (scientific journal)

Hydrothermal C - C bond formation and disproportionation of acetaldehyde with formic acid

Saiko Morooka, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 112　No. 30　p. 6950-6959　2008/07　Research paper (scientific journal)

Computation of the reduction free energy of coenzyme in aqueous solution by the QM/MM-ER method

Hideaki Takahashi, Hajime Ohno, Ryohei Kishi, Masayoshi Nakano, Nobuyuki Matubayasi

CHEMICAL PHYSICS LETTERS　Vol. 456　No. 4-6　p. 176-180　2008/05　Research paper (scientific journal)

Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation

Nobuyuki Matubayasi, Wataru Shinoda, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 128　No. 19　2008/05　Research paper (scientific journal)

Partial pair correlation functions of low-density Supercritical water determined by neutron diffraction with the H/D isotopic substitution method

Toshiya Otomo, Hiroki Iwase, Yasuo Kameda, Nobuyuki Matubayasi, Keiji Itoh, Susumu Ikeda, Masaru Nakahara

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 112　No. 15　p. 4687-4693　2008/04　Research paper (scientific journal)

Cholesterol location and orientation in aqueous suspension of large unilamellar vesicles of phospholipid revealed by intermolecular nuclear Overhauser effect

Cristiano Giordani, Chihiro Wakai, Ken Yoshida, Erniko Okamura, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 112　No. 9　p. 2622-2628　2008/03　Research paper (scientific journal)

Investigation of the dominant hydration structures among the ionic species in aqueous solution: Novel quantum mechanics/molecular mechanics simulations combined with the theory of energy representation

Hideaki Takahashi, Hajime Ohno, Toshihiko Yamauchi, Ryohei Kishi, Shin-ichi Furukawa, Masayoshi Nakano, Nobuyuki Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 128　No. 6　2008/02　Research paper (scientific journal)

Solvation shell dynamics studied by molecular dynamics simulation in relation to the translational and rotational dynamics of supercritical water and benzene

Ken Yoshida, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 127　No. 17　2007/11　Research paper (scientific journal)

High-sensitivity Raman Spectroscopy of Supercritical water and methanol over a wide range of density

Yoshiro Yasaka, Masahito Kubo, Nobuyuki Matubayasi, Masaru Nakahara

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN　Vol. 80　No. 9　p. 1764-1769　2007/09　Research paper (scientific journal)

Rotational dynamics of water and benzene controlled by anion field in ionic liquids: 1-butyl-3-methylimidazolium chloride and hexafluorophosphate

Yoshiro Yasaka, Chihiro Wakai, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 127　No. 10　2007/09　Research paper (scientific journal)

Chemical equilibrium of formaldehyde and methanediol in hot water: Free-energy analysis of the solvent effect

Nobuyuki Matubayasi, Saiko Morooka, Masaru Nakahara, Hideaki Takahashi

JOURNAL OF MOLECULAR LIQUIDS　Vol. 134　No. 1-3　p. 58-63　2007/05　Research paper (scientific journal)

Kinetic study on disproportionations of C1 aldehydes in supercritical water: Methanol from formaldehyde and formic acid

Saiko Morooka, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 111　No. 14　p. 2697-2705　2007/04　Research paper (scientific journal)

Self-diffusion of supercritical water in extremely low-density region (vol 125, pg 074307, 2006)

Ken Yoshida, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 126　No. 8　2007/02

Slowdown of H/D exchange reaction rate and water dynamics in ionic liquids: Deactivation of solitary water solvated by small anions in 1-butyl-3-methyl-imidazolium chloride

Yoshiro Yasaka, Chihiro Wakai, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 111　No. 4　p. 541-543　2007/02

Hydration free energy of hard-sphere solute over a wide range of size studied by various types of solution theories

N. Matubayasi, M. Kinoshita, M. Nakahara

CONDENSED MATTER PHYSICS　Vol. 10　No. 4　p. 471-480　2007　Research paper (scientific journal)

Free energy of solvation in the energetic perspective

Nobuyuki Matubayasi

COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B　Vol. 2　p. 342-345　2007　Research paper (international conference proceedings)

Intermolecular proton transfer from formaldehyde intermediate to anisole in noncatalytic pyrolysis: Phenol produced without hydrolysis

Yasuo Tsujino, Chihiro Wakai, Nobuyuki Matubayasi, Masaru Nakahara

CHEMISTRY LETTERS　Vol. 35　No. 12　p. 1334-1335　2006/12　Research paper (scientific journal)

Kinetic and equilibrium study on formic acid decomposition in relation to the water-gas-shift reaction

Yoshiro Yasaka, Ken Yoshida, Chihiro Wakai, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 110　No. 38　p. 11082-11090　2006/09　Research paper (scientific journal)

Dynamic and 2D NMR studies on hydrogen-bonding aggregates of cholesterol in low-polarity organic solvents

Cristiano Giordani, Chihiro Wakai, Emiko Okamura, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 110　No. 31　p. 15205-15211　2006/08　Research paper (scientific journal)

Self-diffusion of supercritical water in extremely low-density region

Ken Yoshida, Nobuyuki Matubayasi, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 125　No. 7　2006/08　Research paper (scientific journal)

Free-Energy Analysis of Solutions in the Method of Energy Representation

MATUBAYASI Nobuyuki

Seibutsu Butsuri　Vol. 46　No. 4　p. 228-231　2006/07/25

The Hofmeister series and protein-salt interactions

S Shimizu, WM McLaren, N Matubayasi

JOURNAL OF CHEMICAL PHYSICS　Vol. 124　No. 23　2006/06　Research paper (scientific journal)

Free-energy analysis of solubilization in micelle

N Matubayasi, KK Liang, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 124　No. 15　2006/04　Research paper (scientific journal)

Preferential hydration of proteins: A Kirkwood-Buff approach

S Shimizu, N Matubayasi

CHEMICAL PHYSICS LETTERS　Vol. 420　No. 4-6　p. 518-522　2006/03　Research paper (scientific journal)

New method for precise measurement of density of supercritical fluid over a wide range of pressure

Ken Yoshida, Nobuyuki Matubayasi, Masaru Nakahara

Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu　Vol. 16　No. 4　p. 379-380　2006　Research paper (scientific journal)

Pair-correlation entropy of hydrophobic hydration: Decomposition into translational and orientational contributions and analysis of solute-size effects

M Kinoshita, N Matubayasi, Y Harano, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 124　No. 2　2006/01　Research paper (scientific journal)

A new high-temperature multinuclear-magnetic-resonance probe and the self-diffusion of light and heavy water in sub- and supercritical conditions

K Yoshida, C Wakai, N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 123　No. 16　2005/10　Research paper (scientific journal)

Hydrothermal carbon-carbon bond formation and disproportionations of C1 aldehydes: Formaldehyde and formic acid

S Morooka, C Wakai, N Matubayasi, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 109　No. 29　p. 6610-6619　2005/07　Research paper (scientific journal)

Real-time in-cell F-19 NMR study on uptake of fluorescent and nonfluorescent F-19-octaarginines into human Jurkat cells

E Okamura, K Ninomiya, S Futaki, Y Nagai, T Kimura, C Wakai, N Matubayasi, Y Sugiura, M Nakahara

CHEMISTRY LETTERS　Vol. 34　No. 7　p. 1064-1065　2005/07　Research paper (scientific journal)

Mechanisms and kinetics of noncatalytic ether reaction in supercritical water. 2. Proton-transferred fragmentation of dimethyl ether to formaldehyde in competition with hydrolysis

Y Nagai, N Matubayasi, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 109　No. 16　p. 3558-3564　2005/04　Research paper (scientific journal)

Mechanisms and kinetics of noncatalytic ether reaction in supercritical water. 1. Proton-transferred fragmentation of diethyl ether to acetaldehyde in competition with hydrolysis

Y Nagai, N Matubayasi, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 109　No. 16　p. 3550-3557　2005/04　Research paper (scientific journal)

Hydrothermal reactions of formaldehyde and formic acid: Free-energy analysis of equilibrium

N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 122　No. 7　2005/02　Research paper (scientific journal)

46 Nuclear magnetic resonance and molecular dynamics simulation study on the reorientational relaxation of solutes in supercritical methanol T. Yamaguchi, N. Matubayasi, and M. Nakahara

J. Mol. Liq.　Vol. 119, 119-123　2005

45 An approach to the solvation free energy in terms of the distributions functions of the solute-solvent interaction energy N. Matubayasi and M. Nakahara

J. Mol. Liq.　Vol. 119, 23-29　2005

Limited slowdown of endocrine-disruptor diffusion in confined fluid lipid membranes

E Okamura, C Wakai, N Matubayasi, Y Sugiura, M Nakahara

PHYSICAL REVIEW LETTERS　Vol. 93　No. 24　2004/12　Research paper (scientific journal)

Mechanisms and kinetics of acetaldehyde reaction in supercritical water: Noncatalytic disproportionation, condensation, and decarbonylation

Y Nagai, S Morooka, N Matubayasi, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 108　No. 52　p. 11635-11643　2004/12　Research paper (scientific journal)

A quantum chemical approach to the free energy calculations in condensed systems: The QM/MM method combined with the theory of energy representation

H Takahashi, N Matubayasi, M Nakahara, T Nitta

JOURNAL OF CHEMICAL PHYSICS　Vol. 121　No. 9　p. 3989-3999　2004/09　Research paper (scientific journal)

NMR spectroscopic evidence for an intermediate of formic acid in the water-gas-shift reaction

K Yoshida, C Wakai, N Matubayasi, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 108　No. 37　p. 7479-7482　2004/09

Noncatalytic kinetic study on site-selective H/D exchange reaction of phenol in sub- and supercritical water

M Kubo, T Takizawa, C Wakai, N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 121　No. 2　p. 960-969　2004/07　Research paper (scientific journal)

Acid-catalyzed hydrothermal formation of carbon-carbon bond in glycolic acid from a series of formaldehyde producers

S Morooka, C Wakai, N Matubayasi, M Nakahara

CHEMISTRY LETTERS　Vol. 33　No. 5　p. 624-625　2004/05　Research paper (scientific journal)

Noncatalytic disproportionation and decarbonylation reactions of benzaldehyde in supercritical water

Y Nagai, N Matubayasi, M Nakahara

CHEMISTRY LETTERS　Vol. 33　No. 5　p. 622-623　2004/05　Research paper (scientific journal)

Effect of concentration, acid, temperature, and metal on competitive reaction pathways for decarbonylation and decarboxylation of formic acid in hot water

C Wakai, K Yoshida, Y Tsujino, N Matubayasi, M Nakahara

CHEMISTRY LETTERS　Vol. 33　No. 5　p. 572-573　2004/05　Research paper (scientific journal)

Hot water induces an acid-catalyzed reaction in its undissociated form

Y Nagai, N Matubayasi, M Nakahara

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN　Vol. 77　No. 4　p. 691-697　2004/04　Research paper (scientific journal)

Synthesis of dimethyl ether from supercritical methanol in the presence of aluminum

Y Usui, C Wakai, N Matubayasi, M Nakahara

CHEMISTRY LETTERS　Vol. 33　No. 4　p. 394-395　2004/04　Research paper (scientific journal)

Carbon-carbon bond formation in glycolic acid generated spontaneously from dichloromethane in hot water

C Wakai, S Morooka, N Matubayasi, M Nakahara

CHEMISTRY LETTERS　Vol. 33　No. 3　p. 302-303　2004/03　Research paper (scientific journal)

Side-chain conformational thermodynamics of aspartic acid residue in the peptides and achatin-I in aqueous solution

T Kimura, N Matubayasi, M Nakahara

BIOPHYSICAL JOURNAL　Vol. 86　No. 2　p. 1124-1137　2004/02　Research paper (scientific journal)

NMR study on the reorientational relaxation in supercritical alcohols

T Yamaguchi, N Matubayasi, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 108　No. 8　p. 1319-1324　2004/02　Research paper (scientific journal)

NMR study on the binding of neuropeptide achatin-I to phospholipid bilayer: The equilibrium, location, and peptide conformation

Kimura, T., Okamura, E., Matubayasi, N., Asami, K., Nakahara, M.

Biophysical Journal　Vol. 87　No. 1　2004　Research paper (scientific journal)

Theory of solutions in the energy representation. III. Treatment of the molecular flexibility

N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 119　No. 18　p. 9686-9702　2003/11　Research paper (scientific journal)

Noncatalytic Cannizzaro-type reaction of acetaldehyde in supercritical water

Y Nagai, C Wakai, N Matubayasi, M Nakahara

CHEMISTRY LETTERS　Vol. 32　No. 3　p. 310-311　2003/03　Research paper (scientific journal)

Erratum: Theory of solutions in the energy representation II. Functional for the chemical potential (J. Chem. Phys. (2002) 117 (3605))

Nobuyuki Matubayasi, Masaru Nakahara

Journal of Chemical Physics　Vol. 118　No. 5　2003/02/01　Research paper (scientific journal)

Enthalpy and entropy decomposition of free-energy changes for side-chain conformations of aspartic acid and asparagine in acidic, neutral, and basic aqueous solutions

T Kimura, N Matubayasi, H Sato, F Hirata, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 106　No. 47　p. 12336-12343　2002/11　Research paper (scientific journal)

Theory of solutions in the energy representation. II. Functional for the chemical potential

N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 117　No. 8　p. 3605-3616　2002/08　Research paper (scientific journal)

Structure, Dynamics, and Reaction of Supercritical Water

MATUBAYASI Nobuyuki

The Review of High Pressure Science and Technology　Vol. 12　No. 2　p. 159-166　2002/05/20

Chloride ion hydration and diffusion in supercritical water using a polarizable water model

Masahito Kubo, Ronald M. Levy, Peter J. Rossky, Nobuyuki Matubayasi, Masaru Nakahara

Journal of Physical Chemistry B　Vol. 106　No. 15　p. 3979-3986　2002/04/18　Research paper (scientific journal)

Chloride ion hydration and diffusion in supercritical water using a polarizable water model

M Kubo, RM Levy, PJ Rossky, N Matubayasi, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 106　No. 15　p. 3979-3986　2002/04　Research paper (scientific journal)

A mode-coupling approach to the attractive interaction effect on the solute diffusion in liquids

T Yamaguchi, N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 115　No. 1　p. 422-432　2001/07　Research paper (scientific journal)

Structural study of supercritical water. III. Rotational dynamics

N Matubayasi, N Nakao, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 114　No. 9　p. 4107-4115　2001/03　Research paper (scientific journal)

Structure and dynamics of water: from ambient to supercritical

M Nakahara, N Matubayasi, C Wakai, Y Tsujino

JOURNAL OF MOLECULAR LIQUIDS　Vol. 90　No. 1-3　p. 75-83　2001/02　Research paper (scientific journal)

Association and dissociation of nonpolar solutes in super- and subcritical water

N Matubayasi, N Nakahara

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 104　No. 44　p. 10352-10358　2000/11　Research paper (scientific journal)

Theory of solutions in the energetic representation. I. Formulation

N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 113　No. 15　p. 6070-6081　2000/10　Research paper (scientific journal)

Which carbon oxide is more soluble? Ab initio study on carbon monoxide and dioxide in aqueous solution

H Sato, N Matubayasi, M Nakahara, F Hirata

CHEMICAL PHYSICS LETTERS　Vol. 323　No. 3-4　p. 257-262　2000/06　Research paper (scientific journal)

Super- and subcritical hydration of nonpolar solutes. I. Thermodynamics of hydration

N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 112　No. 18　p. 8089-8109　2000/05

Dynamic structural analysis of supercritical water

N. Matubayasi, N. Nakao, M. Nakahara

Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu　Vol. 10　No. 4　p. 283-289　2000　Research paper (scientific journal)

Tumbling and spinning diffusions of acetonitrile in water and organic solvents

C Wakai, H Saito, N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 112　No. 3　p. 1462-1473　2000/01　Research paper (scientific journal)

Physical properties and structure of supercritical water

M Nakahara, N Matubayasi

ELECTROCHEMISTRY　Vol. 67　No. 10　p. 988-993　1999/10　Research paper (scientific journal)

Pressure effect on hydrophobic hydration: Rotational dynamics of benzene

C Wakai, N Matubayasi, M Nakahara

JOURNAL OF PHYSICAL CHEMISTRY A　Vol. 103　No. 34　p. 6685-6690　1999/08　Research paper (scientific journal)

Structural study of supercritical water. II. Computer simulations

N Matubayasi, C Wakai, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 110　No. 16　p. 8000-8011　1999/04　Research paper (scientific journal)

Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo

N Matubayasi, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 110　No. 7　p. 3291-3301　1999/02　Research paper (scientific journal)

Noncatalytic cannizzaro-type reaction of formaldehyde in hot water

Tsujino, Y., Wakai, C., Matubayashi, N., Nakahara, M.

Chemistry Letters　No. 4　1999　Research paper (scientific journal)

On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models

N Matubayasi, E Gallicchio, RM Levy

JOURNAL OF CHEMICAL PHYSICS　Vol. 109　No. 12　p. 4864-4872　1998/09　Research paper (scientific journal)

Protein hydration and unfolding - insights from experimental partial specific volumes and unfolded protein models

LR Murphy, N Matubayasi, VA Payne, RM Levy

FOLDING & DESIGN　Vol. 3　No. 2　p. 105-118　1998　Research paper (scientific journal)

Structural study of supercritical water .1. Nuclear magnetic resonance spectroscopy

N Matubayasi, C Wakai, M Nakahara

JOURNAL OF CHEMICAL PHYSICS　Vol. 107　No. 21　p. 9133-9140　1997/12　Research paper (scientific journal)

Monte Carlo study of the effect of pressure on hydrophobic association

VA Payne, N Matubayasi, LR Murphy, RM Levy

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 101　No. 11　p. 2054-2060　1997/03　Research paper (scientific journal)

NMR study of water structure in super- and subcritical conditions

N Matubayasi, C Wakai, M Nakahara

PHYSICAL REVIEW LETTERS　Vol. 78　No. 13　p. 2573-2576　1997/03　Research paper (scientific journal)

Structure of Water at High Temperatures and Pressures

Nobuyuki Matubayasi, Masaru Nakahara

Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu　Vol. 6　No. 1　p. 16-23　1997　Research paper (scientific journal)

N-14 NMR spectra sensitively reflect surface curvature and segmental motion of hydrophilic headgroups in lipid bilayers and micelles

E Okamura, C Wakai, N Matubayasi, M Nakahara

CHEMISTRY LETTERS　No. 10　p. 1061-1062　1997　Research paper (scientific journal)

Thermodynamics of the hydration shell .2. Excess volume and compressibility of a hydrophobic solute

N Matubayasi, RM Levy

JOURNAL OF PHYSICAL CHEMISTRY　Vol. 100　No. 7　p. 2681-2688　1996/02　Research paper (scientific journal)

Dynamics of hydrophobic hydration of benzene

M Nakahara, C Wakai, Y Yoshimoto, N Matubayasi

JOURNAL OF PHYSICAL CHEMISTRY　Vol. 100　No. 4　p. 1345-1349　1996/01　Research paper (scientific journal)

Mean-field theory of solutions: Chemical potential and solution structure in the superposition approximation

Nobuyuki Matubayasi

Journal of Chemical Physics　Vol. 104　No. 13　p. 5265-5278　1996　Research paper (scientific journal)

JUMP IN THE ROTATIONAL MOBILITY OF BENZENE INDUCED BY THE CLATHRATE HYDRATE FORMATION

M NAKAHARA, C WAKAI, N MATUBAYASI

JOURNAL OF PHYSICAL CHEMISTRY　Vol. 99　No. 5　p. 1377-1379　1995/02

THERMODYNAMICS OF THE HYDRATION SHELL .1. EXCESS ENERGY OF A HYDROPHOBIC SOLUTE

N MATUBAYASI, LH REED, RM LEVY

JOURNAL OF PHYSICAL CHEMISTRY　Vol. 98　No. 41　p. 10640-10649　1994/10　Research paper (scientific journal)

MATCHING-MISMATCHING OF WATER GEOMETRY AND HYDROPHOBIC HYDRATION

N MATUBAYASI

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY　Vol. 116　No. 4　p. 1450-1456　1994/02　Research paper (scientific journal)

DYNAMICS IN REGULAR SOLUTIONS - CONCENTRATION AND VISCOSITY DEPENDENCE OF ORIENTATIONAL CORRELATION TIME OF A BENZENE MOLECULE

N MATSUBAYASHI, M NAKAHARA

JOURNAL OF CHEMICAL PHYSICS　Vol. 94　No. 1　p. 653-661　1991/01　Research paper (scientific journal)