N. Matubayasi

发表

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

Nobuyuki Matubayasi, Akio Kitao, Kazuhiro Takemura, 2018, The Journal of chemical physics.

Hydration structure of CO2-absorbed 2-aminoethanol studied by neutron diffraction with the 14N/15N isotopic substitution method.

H. Deguchi, N. Watari, N. Matubayasi, 2014, The journal of physical chemistry. B.

The Hofmeister series and protein-salt interactions.

W. McLaren, N. Matubayasi, S. Shimizu, 2006, The Journal of chemical physics.

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

N. Matubayasi, M. Nakahara, Y. Yasaka, 2007, The Journal of chemical physics.

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

N. Matubayasi, 2017, Current opinion in structural biology.

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

Bin W. Zhang, R. Levy, N. Matubayasi, 2017, The journal of physical chemistry. B.

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

N. Matubayasi, M. Nakahara, Y. Yasaka, 2006, The journal of physical chemistry. A.

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

R. Levy, L. Murphy, N. Matubayasi, 1998, Folding & design.

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

N. Matubayasi, R. Ishizuka, Minoru Sayou, 2017, The journal of physical chemistry. B.

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

N. Matubayasi, T. Kawakami, Isamu Shigemoto, 2012, The Journal of chemical physics.

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

N. Matubayasi, Tatsuya Mori, Naoya Tomoshige, 2020, Journal of physics. Condensed matter : an Institute of Physics journal.

Probabilistic analysis for identifying the driving force of protein folding.

N. Matubayasi, Y. Yamamori, Yoshihiko Tokunaga, 2018, The Journal of chemical physics.

Solvation Thermodynamics from the Perspective of Endpoints DFT.

Bin W. Zhang, R. Levy, N. Matubayasi, 2020, The journal of physical chemistry. B.

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

Bin W. Zhang, R. Levy, N. Matubayasi, 2019, Journal of chemical theory and computation.

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

N. Matubayasi, Y. Ishii, Keisuke Mizuta, 2019, Soft matter.

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

Bin W. Zhang, R. Levy, N. Matubayasi, 2018, Journal of chemical theory and computation.

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.

N. Matubayasi, A. Morita, Hideaki Takahashi, 2012, The Journal of chemical physics.

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.

A. Kitao, N. Matubayasi, S. Sakuraba, 2013, Physical chemistry chemical physics : PCCP.

Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T1 measurements.

M. Klein, N. Matubayasi, M. Nakahara, 2012, The Journal of chemical physics.

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

N. Matubayasi, E. Okamura, M. Nakahara, 2004, Biophysical journal.

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

N. Matubayasi, M. Nakahara, 2005, The Journal of chemical physics.

In situ kinetic study on hydrothermal transformation of D-glucose into 5-hydroxymethylfurfural through D-fructose with 13C NMR.

N. Matubayasi, M. Nakahara, H. Kimura, 2011, The journal of physical chemistry. A.

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

M. Klein, N. Matubayasi, M. Nakahara, 2011, The Journal of chemical physics.

Structural study of supercritical water. II. Computer simulations

N. Matubayasi, M. Nakahara, C. Wakai, 1999 .

Finite-size effect on the charging free energy of protein in explicit solvent.

M. Ikeguchi, N. Matubayasi, Toru Ekimoto, 2015, Journal of chemical theory and computation.

Gelation: the role of sugars and polyols on gelatin and agarose.

N. Matubayasi, S. Shimizu, 2014, The journal of physical chemistry. B.

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

Nobuyuki Matubayasi, Ken Yoshida, N. Matubayasi, 2007, The Journal of chemical physics.

Effect of Rotation on Vibrational Spectrum of Supercritical Water: Analysis of Dependencies on Density and Hydrogen Isotopes

N. Matubayasi, M. Nakahara, Ken Yoshida, 2016 .

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

N. Matubayasi, M. Nakahara, Y. Yasaka, 2012 .

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

N. Matubayasi, M. Nakahara, Ken Yoshida, 2012, The Journal of chemical physics.

Self-diffusion in supercritical water and benzene in high-temperature high-pressure conditions studied by NMR and dynamic solvation-shell model

N. Matubayasi, M. Nakahara, Ken Yoshida, 2010 .

Dynamics of Hydrophobic Hydration of Benzene

N. Matubayasi, M. Nakahara, C. Wakai, 1996 .

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

R. Levy, E. Gallicchio, N. Matubayasi, 1998 .

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

N. Matubayasi, M. Nakahara, 2003 .

Erratum: “Self-diffusion of supercritical water in extremely low-density region” [J. Chem. Phys.125, 074307 (2006)]

N. Matubayasi, M. Nakahara, Ken Yoshida, 2007 .

Molecular dynamics simulations of yeast F1-ATPase before and after 16° rotation of the γ subunit.

M. Ikeguchi, N. Matubayasi, M. Kinoshita, 2013, The journal of physical chemistry. B.

Energetics of cosolvent effect on peptide aggregation

N. Matubayasi, K. Masutani, 2019, Biophysics and physicobiology.

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

N. Matubayasi, Y. Yamamori, Kang-Sahn Kim, 2019, The Journal of chemical physics.

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

N. Matubayasi, Hiroyuki Kubota, Ryota Matsuba, 2022, Cellulose.

Structure of Water at High Temperatures and Pressures

N. Matubayasi, M. Nakahara, 1997 .

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

N. Matubayasi, Hideaki Takahashi, 2012, The Journal of chemical physics.

Matching-Mismatching of Water Geometry and Hydrophobic Hydration

N. Matubayasi, 1994 .

An approach to the solvation free energy in terms of the distribution functions of the solute–solvent interaction energy

N. Matubayasi, M. Nakahara, 2005 .

Structure and dynamics of water: from ambient to supercritical

N. Matubayasi, M. Nakahara, C. Wakai, 2001 .

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

N. Matubayasi, M. Nakahara, Y. Yasaka, 2012, The Journal of chemical physics.

Monte Carlo Study of the Effect of Pressure on Hydrophobic Association

R. Levy, N. Matubayasi, V. Payne, 1997 .

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

N. Matubayasi, T. Mizuguchi, 2018, The journal of physical chemistry. B.

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

N. Matubayasi, A. Douhal, N. Tohnai, 2021, Chemical science.

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

N. Matubayasi, H. Washizu, Yoshiki Ishii, 2022, The journal of physical chemistry. B.

Cooperative Sorption on Heterogeneous Surfaces

N. Matubayasi, S. Shimizu, Steven Abbott, 2022, Langmuir : the ACS journal of surfaces and colloids.

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

N. Matubayasi, S. Shimizu, 2020, Physical chemistry chemical physics : PCCP.

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

N. Matubayasi, S. Shimizu, 2022, Langmuir : the ACS journal of surfaces and colloids.

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

N. Matubayasi, M. Shintani, 2016 .

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

N. Matubayasi, M. Kinoshita, M. Nakahara, 2006, The Journal of chemical physics.

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

N. Matubayasi, S. Shimizu, 2018 .

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

N. Matubayasi, Hiroyuki Kubota, Ryota Matsuba, 2022, Cellulose.

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

N. Matubayasi, Kento Kasahara, Naoki Yamamoto, 2022, The journal of physical chemistry. B.

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

N. Matubayasi, T. Ishiyama, Nobuhiro Yasoshima, 2022, The journal of physical chemistry. B.

Controlling the equilibrium of formic acid with hydrogen and carbon dioxide using ionic liquid.

N. Matubayasi, M. Nakahara, Y. Yasaka, 2010, The journal of physical chemistry. A.

NMR Study of Water Structure in Super- and Subcritical Conditions [Phys. Rev. Lett. 78, 2573 (1997)]

N. Matubayasi, M. Nakahara, C. Wakai, 1997 .

NMR Study of Water Structure in Super- and Subcritical Conditions

N. Matubayasi, M. Nakahara, C. Wakai, 1997 .

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, 2007 .

The origin of cooperative solubilisation by hydrotropes.

N. Matubayasi, S. Shimizu, 2016, Physical chemistry chemical physics : PCCP.

Hydrotropy: monomer-micelle equilibrium and minimum hydrotrope concentration.

N. Matubayasi, S. Shimizu, 2014, The journal of physical chemistry. B.

Noncatalytic Cannizzaro-type Reaction of Formaldehyde in Hot Water (INTERFACE SCIENCE-Solutions and Interfaces)

N. Matubayasi, M. Nakahara, C. Wakai, 1999 .

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

N. Matubayasi, Kento Kasahara, Kazuya Okita, 2022, The Journal of chemical physics.

Pseudomonas aeruginosa cytochrome c551 denaturation by five systematic urea derivatives that differ in the alkyl chain length

N. Matubayasi, S. Wakai, Y. Sambongi, 2017, Bioscience, biotechnology, and biochemistry.

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

N. Matubayasi, S. Shimizu, 2020 .

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

N. Matubayasi, M. Nakahara, C. Wakai, 2004 .

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

N. Matubayasi, S. Sakuraba, M. Shintani, 2012, Physical chemistry chemical physics : PCCP.

Noncatalytic hydrothermal elimination of the terminal D-glucose unit from malto- and cello-oligosaccharides through transformation to D-fructose.

N. Matubayasi, M. Nakahara, H. Kimura, 2012, Journal of Physical Chemistry A.

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

N. Matubayasi, S. Shimizu, Thomas W. J. Nicol, 2016, Physical chemistry chemical physics : PCCP.

A Molecular Thermodynamics Approach to Capture Non-specific Flavour–Macromolecule Interactions

Seishi Shimizu, Steven Abbott, Nobuyuki Matubayasi, 2019, Encyclopedia of Food Chemistry.

Quantifying non-specific interactions between flavour and food biomolecules.

N. Matubayasi, S. Shimizu, Steven Abbott, 2017, Food & function.

Chloride Ion Hydration and Diffusion in Supercritical Water Using a Polarizable Water Model

P. Rossky, R. Levy, N. Matubayasi, 2002 .

Insights into the origins of configurational stability of axially chiral biaryl amines with an intramolecular N-H-N hydrogen bond.

N. Matubayasi, T. Kawabata, N. Tokitoh, 2010, The Journal of organic chemistry.

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

N. Matubayasi, E. Okamura, M. Nakahara, 2008, The journal of physical chemistry. B.

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

N. Matubayasi, M. Nakahara, Tomohiro Kimura, 2004, Biophysical journal.

Free-energy analysis of solubilization in micelle.

N. Matubayasi, M. Nakahara, K. Liang, 2006, The Journal of chemical physics.

Ensemble transformation in the fluctuation theory

Seishi Shimizu, Nobuyuki Matubayasi, N. Matubayasi, 2022, Physica A: Statistical Mechanics and its Applications.

Adsorbate-adsorbate interactions on microporous materials

N. Matubayasi, S. Shimizu, 2021, Microporous and Mesoporous Materials.

Sorption: A Statistical Thermodynamic Fluctuation Theory

N. Matubayasi, S. Shimizu, 2021, Langmuir : the ACS journal of surfaces and colloids.

Cooperativity in micellar solubilization.

N. Matubayasi, S. Shimizu, 2021, Physical chemistry chemical physics : PCCP.

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

N. Matubayasi, S. Shimizu, Richard Stenner, 2017 .

Gelation of carrageenan: Effects of sugars and polyols

N. Matubayasi, S. Shimizu, Richard Stenner, 2016 .

Preferential solvation: dividing surface vs excess numbers.

N. Matubayasi, S. Shimizu, 2014, The journal of physical chemistry. B.

Preferential hydration of proteins: A Kirkwood-Buff approach

Seishi Shimizu, Nobuyuki Matubayasi, N. Matubayasi, 2006 .

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

F. Hirata, N. Matubayasi, Hirofumi Sato, 2000 .

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

N. Matubayasi, H. Washizu, Y. Ishii, 2021, The Journal of Chemical Physics.

Water activity in liquid food systems: A molecular scale interpretation

J. Clark, A. Matharu, N. Matubayasi, 2017, Food chemistry.

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

H. Deguchi, N. Watari, N. Matubayasi, 2013 .

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

H. Deguchi, N. Watari, Yamazaki Noriko, 2011 .

Free-energy and structural analysis of ion solvation and contact ion-pair formation of Li(+) with BF4(-) and PF6(-) in water and carbonate solvents.

N. Matubayasi, B. Minofar, Y. Kameda, 2012, The journal of physical chemistry. B.

Effect of Concentration, Acid, Temperature, and Metal on Competitive Reaction Pathways for Decarbonylation and Decarboxylation of Formic Acid in Hot Water

N. Matubayasi, M. Nakahara, C. Wakai, 2004 .

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

J. Clark, N. Matubayasi, S. Shimizu, 2019, Food Hydrocolloids.

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

N. Matubayasi, M. Nakahara, Hideaki Takahashi, 2007 .

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

N. Matubayasi, M. Nakahara, H. Kimura, 2013, The journal of physical chemistry. A.

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

M. Ikeguchi, N. Matubayasi, Toru Ekimoto, 2015, The Journal of chemical physics.

Structural characteristics of yeast F1-ATPase before and after 16-degree rotation of the γ subunit: theoretical analysis focused on the water-entropy effect.

N. Matubayasi, M. Kinoshita, Takashi Yoshidome, 2012, The Journal of chemical physics.

NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics.

N. Matubayasi, S. Sakuraba, M. Nakahara, 2011, The journal of physical chemistry. B.

Nuclear magnetic resonance and molecular dynamics simulation study on the reorientational relaxation of solutes in supercritical methanol

N. Matubayasi, M. Nakahara, T. Yamaguchi, 2005 .

Tumbling and spinning diffusions of acetonitrile in water and organic solvents

N. Matubayasi, M. Nakahara, C. Wakai, 2000 .

Jump in the Rotational Mobility of Benzene Induced by the Clathrate Hydrate Formation (INTERFACE SCIENCE - Solutions and Interfaces)

N. Matubayasi, M. Nakahara, C. Wakai, 1995 .

High-Sensitivity Raman Spectroscopy of Supercritical Water and Methanol over a Wide Range of Density

N. Matubayasi, M. Nakahara, Y. Yasaka, 2007 .

NMR Study on the Reorientational Relaxation in Supercritical Alcohols

N. Matubayasi, M. Nakahara, T. Yamaguchi, 2004 .

Structural study of supercritical water. III. Rotational dynamics

N. Matubayasi, M. Nakahara, N. Nakao, 2001 .

Pressure Effect on Hydrophobic Hydration: Rotational Dynamics of Benzene

N. Matubayasi, M. Nakahara, C. Wakai, 1999 .

Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo

N. Matubayasi, M. Nakahara, 1999 .

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

N. Matubayasi, M. Nakahara, C. Wakai, 2005, The Journal of chemical physics.

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

N. Matubayasi, M. Nakahara, 2000 .

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

N. Matubayasi, Y. Karino, 2013, Physical chemistry chemical physics : PCCP.

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

N. Matubayasi, T. Kawakami, Isamu Shigemoto, 2018, The Journal of chemical physics.

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

N. Matubayasi, Kang-Sahn Kim, Shota Goto, 2021, The Journal of chemical physics.

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

N. Matubayasi, M. Nakahara, Ken Yoshida, 2014, Journal of Solution Chemistry.

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

N. Matubayasi, M. Nakahara, Saiko Morooka, 2007, The journal of physical chemistry. A.

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

N. Matubayasi, M. Nakahara, C. Wakai, 2005, The journal of physical chemistry. A.

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

N. Matubayasi, M. Nakahara, Yasuharu Nagai, 2005, The journal of physical chemistry. A.

Mechanisms and Kinetics of Acetaldehyde Reaction in Supercritical Water: Noncatalytic Disproportionation, Condensation, and Decarbonylation

N. Matubayasi, M. Nakahara, Yasuharu Nagai, 2004 .

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

Nobuyuki Matubayasi, N. Matubayasi, M. Nakahara, 1997 .

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

N. Matubayasi, E. Okamura, M. Nakahara, 2006, The journal of physical chemistry. B.

Statistical thermodynamics of regular solutions and solubility parameters

N. Matubayasi, S. Shimizu, 2019, Journal of Molecular Liquids.

Statistical thermodynamic foundation for mesoscale aggregation in ternary mixtures.

N. Matubayasi, S. Shimizu, 2018, Physical chemistry chemical physics : PCCP.

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

Nobuyuki Matubayasi, N. Matubayasi, M. Nakahara, 2003 .

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

Nobuyuki Matubayasi, Ken Yoshida, N. Matubayasi, 2008, The Journal of chemical physics.

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

N. Matubayasi, M. Nakahara, Ken Yoshida, 2006, The Journal of chemical physics.

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

N. Matubayasi, M. Nakahara, C. Wakai, 2004 .

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

N. Matubayasi, Tatsuya Mori, Naoya Tomoshige, 2019, Scientific Reports.

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

N. Matubayasi, R. Ishizuka, 2016, Journal of chemical theory and computation.

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

N. Matubayasi, Takashi Kato, Go Watanabe, 2021, Science Advances.

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

Nobuyuki Matubayasi, Akio Kitao, Kazuhiro Takemura, 2018, The Journal of chemical physics.

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

Nobuyuki Matubayasi, Akio Kitao, Kazuhiro Takemura, 2012, The Journal of chemical physics.

Hot Water Induces an Acid-Catalyzed Reaction in Its Undissociated Form

N. Matubayasi, M. Nakahara, Yasuharu Nagai, 2004 .

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

N. Matubayasi, Hodaka Mori, 2019, The Journal of chemical physics.

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

N. Matubayasi, Hodaka Mori, 2018, Polymer.

Physical driving force of actomyosin motility based on the hydration effect

N. Matubayasi, Makoto Suzuki, Takahiro Watanabe, 2017, Cytoskeleton.

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

F. Greco, N. Matubayasi, Kang-Sahn Kim, 2021, The Journal of chemical physics.

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

N. Matubayasi, Kang-Sahn Kim, Takuma Kikutsuji, 2018, The Journal of chemical physics.

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.

N. Matubayasi, M. Nakano, R. Kishi, 2008, The Journal of chemical physics.

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

N. Matubayasi, M. Nakano, R. Kishi, 2008 .

Effective charges of ionic liquid determined self‐consistently through combination of molecular dynamics simulation and density‐functional theory

Nobuyuki Matubayasi, Ryosuke Ishizuka, N. Matubayasi, 2017, J. Comput. Chem..

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

N. Matubayasi, S. Maeda, A. Morita, 2017, The journal of physical chemistry. B.

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.

N. Matubayasi, K. Ohara, R. Hagiwara, 2020, The journal of physical chemistry. B.

Spatial-Decomposition Analysis of Electrical Conductivity.

N. Matubayasi, 2018, Chemical record.

Spatial-decomposition analysis of electrical conductivity in ionic liquid.

N. Matubayasi, R. Ishizuka, K. Tu, 2014, The Journal of chemical physics.

Spatial-decomposition analysis of electrical conductivity in concentrated electrolyte solution.

N. Matubayasi, R. Ishizuka, K. Tu, 2014, The Journal of chemical physics.

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

N. Matubayasi, Y. Ishii, 2019, Journal of chemical theory and computation.

Understanding Sorption Mechanisms Directly from Isotherms

N. Matubayasi, S. Shimizu, 2023, Langmuir : the ACS journal of surfaces and colloids.

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

K. Okazaki, Toshifumi Mori, N. Matubayasi, 2022, The Journal of chemical physics.

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

N. Matubayasi, S. Shimizu, 2018, Physical chemistry chemical physics : PCCP.

Recent Advances in Studies on Organic Reactions in Water at High Temperatures and High Pressures

N. Matubayasi, M. Nakahara, Y. Yasaka, 2010 .

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

N. Matubayasi, Y. Kameda, M. Nakahara, 2010 .

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

N. Matubayasi, M. Nakahara, C. Wakai, 2004, The Journal of chemical physics.

Unifying hydrotropy under Gibbs phase rule.

N. Matubayasi, S. Shimizu, 2017, Physical chemistry chemical physics : PCCP.

Enthalpy and Entropy Decomposition of Free-Energy Changes for Side-Chain Conformations of Aspartic Acid and Asparagine in Acidic, Neutral, and Basic Aqueous Solutions

F. Hirata, N. Matubayasi, Hirofumi Sato, 2002 .

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

N. Matubayasi, H. Nagao, K. Nishikawa, 2010 .

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

N. Matubayasi, S. Shimizu, 2020, Journal of colloid and interface science.

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

N. Matubayasi, S. Shimizu, 2017, Physical chemistry chemical physics : PCCP.

Cooperative Sorption on Porous Materials

N. Matubayasi, S. Shimizu, 2021, Langmuir : the ACS journal of surfaces and colloids.

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

N. Matubayasi, S. Shimizu, 2021 .

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

N. Matubayasi, S. Shimizu, 2017, Biophysical chemistry.

Conferences and Meetings

N. Matubayasi, S. Shimizu, 1969 .

Implicit function theorem and Jacobians in solvation and adsorption

Seishi Shimizu, Nobuyuki Matubayasi, N. Matubayasi, 2021 .

NMR Study of the Structure and Dynamics of Supercritical Water

N. Matubayasi, M. Nakahara, 2003 .

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

N. Matubayasi, Hodaka Mori, 2018 .

Development of a Massively Parallel QM/MM Approach Combined with a Theory of Solutions

N. Matubayasi, Hideaki Takahashi, 2015 .

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.

N. Matubayasi, M. Nakahara, Y. Yasaka, 2007, The journal of physical chemistry. A.

Energetic contributions from the cation and anion to the stability of carbon dioxide dissolved in imidazolium-based ionic liquids.

N. Matubayasi, Y. Umebayashi, R. Ishizuka, 2015, The journal of physical chemistry. B.

Temperature Dependence of Sorption.

N. Matubayasi, S. Shimizu, 2021, Langmuir : the ACS journal of surfaces and colloids.

Noncatalytic Disproportionation and Decarbonylation Reactions of Benzaldehyde in Supercritical Water

N. Matubayasi, M. Nakahara, Yasuharu Nagai, 2004 .

Life Sun CO 2 Fossile Fuels breathing photosynthesis Artificial Fuels in Future fossilization

N. Matubayasi, M. Nakahara, Y. Yasaka, 2008 .

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

N. Matubayasi, Kang-Min Kim, Nobuhiro Yasoshima, 2023, The Journal of chemical physics.

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

N. Matubayasi, Makoto Gemmei-Ide, T. Ishiyama, 2021, The journal of physical chemistry. B.

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

N. Matubayasi, Kang-Sahn Kim, Takuma Kikutsuji, 2019, Journal of Molecular Liquids.

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

N. Matubayasi, Kang-Sahn Kim, Takuma Kikutsuji, 2019, The Journal of chemical physics.

Frequency-domain investigation of the ionic mobility of triflate salts in tetrahydrofuran.

N. Matubayasi, Y. Yasaka, S. Koda, 2011, The journal of physical chemistry. B.

Energetic origin of proton affinity to the air/water interface.

N. Matubayasi, M. Nakano, P. Jungwirth, 2011, The journal of physical chemistry. B.

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.

N. Matubayasi, M. Nakano, R. Kishi, 2008, The Journal of chemical physics.

A novel quantum mechanical/molecular mechanical approach to the free energy calculation for isomerization of glycine in aqueous solution.

N. Matubayasi, Y. Kawashima, Hideaki Takahashi, 2005, The Journal of chemical physics.

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

Nobuyuki Matubayasi, Hideaki Takahashi, Tomoshige Nitta, 2004, The Journal of chemical physics.

Chapter 9 - Development of a Quantum Chemical Method Combined with a Theory of Solutions—Free-Energy Calculation for Chemical Reactions by Condensed Phase Simulations

N. Matubayasi, M. Nakano, Hideaki Takahashi, 2010 .

A Quantum Chemical Approach to Free Energy Calculation for Chemical Reactions in Condensed System: Combination of a Quantum Chemical Method with a Theory of Statistical Mechanics

N. Matubayasi, M. Nakano, Hideaki Takahashi, 2008 .

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

N. Matubayasi, W. Shinoda, M. Nakahara, 2008, The Journal of chemical physics.

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

N. Matubayasi, M. Nakahara, Ken Yoshida, 2009 .

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

N. Matubayasi, M. Nakahara, Ken Yoshida, 2013, The Journal of chemical physics.

Anion-dependence of fast relaxation component in Na-, K-halide solutions at low concentrations measured by high-resolution microwave dielectric spectroscopy.

N. Matubayasi, T. Wazawa, Makoto Suzuki, 2013, The journal of physical chemistry. A.

Novel Intermolecular Surface Force Unveils the Driving Force of the Actomyosin System

N. Matubayasi, Makoto Suzuki, Takahiro Watanabe, 2018 .

Spatial Distribution of Ionic Hydration Energy and Hyper-Mobile Water

N. Matubayasi, Makoto Suzuki, George Mogami, 2018 .

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

K. Okazaki, Toshifumi Mori, N. Matubayasi, 2020, The Journal of chemical physics.

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

Nobuyuki Matubayasi, Ryosuke Ishizuka, Ronald M. Levy, 2017, J. Comput. Chem..

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

N. Matubayasi, H. Kojima, Kazuo Yamada, 2021, The journal of physical chemistry. B.

Unraveling the glass-like dynamic heterogeneity in ring polymer melts: From semi-flexible to stiff chain

N. Matubayasi, Kang-Min Kim, Shota Goto, 2023, 2305.15711.

Unraveling the glass-like dynamic heterogeneity in ring polymer melts: From flexible to rigid chain sti ff ness

N. Matubayasi, Kang-Min Kim, Shota Goto, 2023 .

Chain-Increment Approach to the Mutual Miscibility of Polymers with All-Atom Molecular Simulation

N. Matubayasi, Kazuo Yamada, 2023, Macromolecules.

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

N. Matubayasi, Y. Yamamori, 2017, The Journal of chemical physics.

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.

N. Matubayasi, R. Ishizuka, A. Date, 2016, Physical chemistry chemical physics : PCCP.

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

Nobuyuki Matubayasi, N. Matubayasi, M. Nakahara, 2002 .

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

N. Matubayasi, M. Nakahara, T. Yamaguchi, 2001 .

Theory of solutions in the energetic representation. I. Formulation

Nobuyuki Matubayasi, N. Matubayasi, M. Nakahara, 2000 .

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

N. Matubayasi, 1996 .

Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute

R. Levy, N. Matubayasi, L. H. Reed, 1994 .

Energy Representation Approach

N. Matubayasi, 2013 .

Free-energy analysis of solvation with the method of energy representation.

N. Matubayasi, 2009, Frontiers in bioscience.

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

N. Matubayasi, 2006 .

Hydrothermal Reactions of Formic Acid : Free-Energy Analysis of Equilibrium

N. Matubayasi, M. Nakahara, 2005 .

Intermolecular Proton Transfer from Formaldehyde Intermediate to Anisole in Noncatalytic Pyrolysis: Phenol Produced without Hydrolysis

N. Matubayasi, M. Nakahara, C. Wakai, 2006 .

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

S. L. Chan, N. Matubayasi, I. Todorov, 2012 .

The effect of pressure on halothane binding to hydrated DMPC bilayers

N. Matubayasi, I. Todorov, S. Roser, 2012 .

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

S. L. Chan, N. Matubayasi, K. Liang, 2008 .

Arylazopyrazole-Based Photoswitchable Inhibitors Selective for Escherichia coli Dihydrofolate Reductase.

N. Matubayasi, S. Mizukami, Kento Kasahara, 2023, ACS chemical biology.

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

N. Matubayasi, Kazuo Yamada, 2020 .

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

N. Matubayasi, R. Ishizuka, Fumitaka Kamo, 2016, Protein science : a publication of the Protein Society.

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

N. Matubayasi, Kang-Sahn Kim, K. Tu, 2018 .

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

N. Matubayasi, Naoki Yamamoto, I. Nakakuki, 2018, The Journal of chemical physics.

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

N. Matubayasi, S. Sakuraba, Y. Yamamori, 2016, The Journal of chemical physics.

Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions

Nobuyuki Matubayasi, Shun Sakuraba, N. Matubayasi, 2014, J. Comput. Chem..

Comparative study on the properties of hydration water of Na- and K-halide ions by Raman OH/OD-stretching spectroscopy and dielectric relaxation data.

T. Taniuchi, N. Matubayasi, Makoto Suzuki, 2014, The journal of physical chemistry. A.

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

N. Matubayasi, Makoto Suzuki, R. Akiyama, 2012, The Journal of chemical physics.

Water as an in situ NMR indicator for impurity acids in ionic liquids.

N. Matubayasi, M. Nakahara, Y. Yasaka, 2009, Analytical chemistry.

Elucidating protein-ligand binding kinetics based on returning probability theory.

N. Matubayasi, Kento Kasahara, Kazuya Okita, 2023, The Journal of chemical physics.

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

A. Kitao, N. Matubayasi, Kazuhiro Takemura, 2018, The Journal of chemical physics.

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

Bin W. Zhang, R. Levy, N. Matubayasi, 2018, The journal of physical chemistry. B.

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

N. Matubayasi, M. Nakahara, 2000 .

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.

N. Matubayasi, N. Uozumi, Makoto Suzuki, 2022, The journal of physical chemistry. B.

Energetic origin of proton affinity to the air/water interface.

N. Matubayasi, M. Nakano, P. Jungwirth, 2011, The journal of physical chemistry. B.

Distribution-function approach to free energy computation.

N. Matubayasi, S. Sakuraba, 2011, The Journal of chemical physics.

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

Nobuyuki Matubayasi, Maxim V. Fedorov, N. Matubayasi, 2010 .

Energy-Representation Theory of Solutions: Its Formulation and Application to Soft, Molecular Aggregates

N. Matubayasi, 2019 .

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

N. Matubayasi, Y. Karino, 2013, Physical chemistry chemical physics : PCCP.

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

N. Matubayasi, Y. Karino, 2011, The Journal of chemical physics.

Cooperativity in Sorption Isotherms

N. Matubayasi, S. Shimizu, 2023, Langmuir : the ACS journal of surfaces and colloids.

Sorption from Solution: A Statistical Thermodynamic Fluctuation Theory

N. Matubayasi, S. Shimizu, 2023, Langmuir : the ACS journal of surfaces and colloids.

Actual Amount Adsorbed as Estimated from the Surface Excess Isotherm

N. Matubayasi, S. Shimizu, 2024, Langmuir : the ACS journal of surfaces and colloids.

Preferential solvation: dividing surface vs excess numbers.

N. Matubayasi, S. Shimizu, 2014, Journal of Physical Chemistry B.

Water activity in liquid food systems: A molecular scale interpretation

J. Clark, A. Matharu, N. Matubayasi, 2017, Food chemistry.

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

Takeshi Ishikawa, Nobuyuki Matubayasi, Akio Kitao, 2013 .

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

N. Matubayasi, Kang-Sahn Kim, Takuma Kikutsuji, 2019, The Journal of chemical physics.

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

N. Matubayasi, T. Yagasaki, 2022, Physical chemistry chemical physics : PCCP.

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

N. Matubayasi, Y. Ishii, Keisuke Mizuta, 2019, Soft matter.

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

Bin W. Zhang, R. Levy, N. Matubayasi, 2020, The journal of physical chemistry. B.

Spatial-Decomposition Analysis of Energetics of Ionic Hydration.

N. Matubayasi, Makoto Suzuki, George Mogami, 2016, The journal of physical chemistry. B.

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

N. Matubayasi, Kang-Min Kim, Shota Goto, 2023, ACS polymers Au.

Noncatalytic Cannizzaro-type Reaction of Acetaldehyde in Supercritical Water

N. Matubayasi, M. Nakahara, Yasuharu Nagai, 2003 .