Stefan Hervø-Hansen, Kazuya Okita, Kento Kasahara, Nobuyuki Matubayasi, Solvent-Environment Dependence of the Excess Chemical Potential and Its Computation Scheme Formulated through Error Minimization, J. Chem. Theory Comput., 21, in press (2025). DOI: 10.1021/acs.jctc.4c01000
Shunsuke Ogita, Yoshiki Ishii, Go Watanabe, Hitoshi Washizu, Kang Kim, Nobuyuki Matubayasi, Atomistic analysis of nematic phase transition in 4-cyano-4'-n-alkyl biphenyl liquid crystals: Sampling for the first-order phase transition and the free-energy decomposition, J. Chem. Phys., 162, 054905 (9 pages) (2025). DOI: 10.1063/5.0242416
Kazuya Okita, Yusei Maruyama, Kento Kasahara, Nobuyuki Matubayasi, Flexible framework of computing binding free energy using the energy representation theory of solution, J. Chem. Phys., 162, 034103 (12 pages) (2025). DOI: 10.1063/5.0242641
Seishi Shimizu, Nobuyuki Matubayasi, Gas and Liquid Isotherms: The Need for A Common Foundation, Langmuir, 41, 2103-2110 (2025). DOI: 10.1021/acs.langmuir.4c04324
2024
Seishi Shimizu, Nobuyuki Matubayasi, Temperature Dependence of Hydrotropy, J. Phys. Chem. B, 128, 10915-10924 (2024). DOI: 10.1021/acs.jpcb.4c04619
Takuma Yagasaki, Nobuyuki Matubayasi, High Antifouling Performance of Weakly Hydrophilic Polymer Brushes: A Molecular Dynamics Study, Langmuir, 40, 15046-15058 (2024). DOI: 10.1021/acs.langmuir.4c01365
Yuya Matsubara, Ryo Okabe, Ren Masayama, Nozomi Morishita Watanabe, Hiroshi Umakoshi, Kento Kasahara, and Nobuyuki Matubayasi, A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation, J. Chem. Phys., 161, 024108 (15 pages) (2024). DOI: 10.1063/5.0214401
Kokoro Shikata, Kento Kasahara, Nozomi Morishita Watanabe, Hiroshi Umakoshi, Kang Kim, and Nobuyuki Matubayasi, Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures, J. Chem. Phys., 161, 015102 (10 pages) (2024). DOI: 10.1063/5.0208008. Press release at
Seishi Shimizu, Nobuyuki Matubayasi, Synergistic Solvation as the Enhancement of Local Mixing, J. Phys. Chem. B, 128, 5713-5726 (2024). DOI: 10.1021/acs.jpcb.4c01582
Tuan Minh Do, Dominik Horinek, Nobuyuki Matubayasi, How ATP suppresses the fibrillation of amyloid peptides: analysis of the free-energy contributions, Phys. Chem. Chem. Phys., 26, 11880-11892 (2024). DOI: 10.1039/d4cp00179f
Yumi Yakiyama, Minghong Li, Dongyi Zhou, Tsuyoshi Abe, Chisato Sato, Kohei Sambe, Tomoyuki Akutagawa, Teppei Matsumura, Nobuyuki Matubayasi, and Hidehiro Sakurai, Biased Bowl-Direction of Monofluorosumanene in the Solid State, J. Am. Chem. Soc., 146, 5224-5231 (2024). DOI: 10.1021/jacs.3c11311. Press release at
Seishi Shimizu, Nobuyuki Matubayasi, Actual Amount Adsorbed as Estimated from the Surface Excess Isotherm, Langmuir, 40, 1666-1673 (2024). DOI: 10.1021/acs.langmuir.3c02597
Stefan Hervø-Hansen, Daoyang Lin, Kento Kasahara, Nobuyuki Matubayasi, Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects, Chem. Sci., 15, 477-489 (2024). DOI: 10.1039/d3sc04617f. Selected as the back cover for Volume 15, Issue 2 (2024)
Seishi Shimizu, Nobuyuki Matubayasi, Replacing the Langmuir Isotherm with the Statistical Thermodynamic Fluctuation Theory, J. Phys. Chem. Lett., 15, 3683-3689 (2024). DOI: 10.1021/acs.jpclett.4c00281
2023
Shota Goto, Kang Kim, Nobuyuki Matubayasi, Unraveling the Glass-like Dynamic Heterogeneity in Ring Polymer Melts: From Semiflexible to Stiff Chain, ACS Polym. Au, 3, 437-446 (2023). DOI: 10.1021/acspolymersau.3c00013. Press release at
Kokoro Shikata, Takuma Kikutsuji, Nobuhiro Yasoshima, Kang Kim, Nobuyuki Matubayasi, Revealing the hidden dynamics of confined water in acrylate polymers: Insights from hydrogen-bond lifetime analysis, J. Chem. Phys., 158, 174901 (10 pages) (2023). DOI: 10.1063/5.0148753. Press release at
Makoto Suzuki, Akira Tsuchiko, Yoshiyuki Tanaka, Nobuyuki Matubayasi, George Mogami, Nobuyuki Uozumi, Satoshi Takahashi, 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, J. Phys. Chem. B, 127, 285-299 (2023). DOI: 10.1021/acs.jpcb.2c06952
Ryo Kawada, Katsuhiro Endo, Kenji Yasuoka, Hidekazu Kojima, Nobuyuki Matubayasi, Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models, J. Chem. Inf. Model., 63, 76-86 (2023). DOI: 10.1021/acs.jcim.2c01316
Kazuya Okita, Kento Kasahara, Nobuyuki Matubayasi, Diffusion theory of molecular liquids in the energy representation and application to solvation dynamics, J. Chem. Phys., 157, 244505 (14 pages) (2022). DOI: 10.1063/5.0125432. Selected as an Editor’s Pick
Olivia P. L. Dalby, Steven Abbott, Nobuyuki Matubayasi, Seishi Shimizu, Cooperative Sorption on Heterogeneous Surfaces, Langmuir, 38, 13084-13092 (2022). DOI: 10.1021/acs.langmuir.2c01750
Takuma Yagasaki, Nobuyuki Matubayasi, Molecular dynamics study of the interactions between a hydrophilic polymer brush on graphene and amino acid side chain analogues in water, Phys. Chem. Chem. Phys., 24, 22877-22888 (2022). DOI: 10.1039/d2cp03112d
Kento Kasahara, Ren Masayama, Yuya Matsubara, Nobuyuki Matubayasi, Constructing a Memory Kernel of the Returning Probability to Efficiently Describe Molecular Binding Processes, Chem. Lett., 51, 823-827 (2022). DOI: 10.1246/cl.220236
Senri Tanaka, Naoki Yamamoto, Kento Kasahara, Yoshiki Ishii, Nobuyuki Matubayasi, Crystal Growth of Urea and Its Modulation by Additives as Analyzed by All-Atom MD Simulation and Solution Theory, J. Phys. Chem. B, 126, 5274-5290 (2022). DOI: 10.1021/acs.jpcb.2c01764
Seishi Shimizu, Nobuyuki Matubayasi, Surface Area Estimation: Replacing the Brunauer-Emmett-Teller Model with the Statistical Thermodynamic Fluctuation Theory, Langmuir, 38, 7989-8002 (2022). DOI: 10.1021/acs.langmuir.2c00753
Yoshiki Ishii, Nobuyuki Matubayasi, Hitoshi Washizu, Nonpolarizable Force Fields through the Self-Consistent Modeling Scheme with MD and DFT Methods: From Ionic Liquids to Self-Assembled Ionic Liquid Crystals, J. Phys. Chem. B, 126, 4611-4622 (2022). DOI: 10.1021/acs.jpcb.2c02782
Nobuhiro Yasoshima, Tatsuya Ishiyama, Nobuyuki Matubayasi, Adsorption Energetics of Amino Acid Analogs on Polymer/Water Interfaces Studied by All-Atom Molecular Dynamics Simulation and a Theory of Solutions, J. Phys. Chem. B, 126, 4389-4400 (2022). DOI: 10.1021/acs.jpcb.2c01297. Selected as the front cover for Volume 126, Issue 23 (2022)
Ryota Matsuba, Hiroyuki Kubota, Nobuyuki Matubayasi, All‑atom molecular simulation study of cellulose acetate: amorphous structure and the dissolution of small molecule, Cellulose, 29, 5463-5478 (2022). DOI: 10.1007/s10570-022-04616-4
Takuma Kikutsuji, Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi, Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI), J. Chem. Phys., 156, 154108 (8 pages) (2022). DOI: 10.1063/5.0087310. Selected for a most-read article in The Journal of Chemical Physics in 2022. Press release at
Stefan Hervø-Hansen, Jan Heyda, Mikael Lund, Nobuyuki Matubayasi, Anion-cation contrast of small molecule solvation in salt solutions, Phys. Chem. Chem. Phys., 24, 3238-3249 (2022). DOI: 10.1039/d1cp04129k
Kengo Takemoto, Yoshiki Ishii, Hitoshi Washizu, Kang Kim, Nobuyuki Matubayasi, Simulating the nematic-isotropic phase transition of liquid crystal model via generalized replica-exchange method, J. Chem. Phys., 156, 014901 (8 pages) (2022). DOI: 10.1063/5.0073105
Seishi Shimizu, Nobuyuki Matubayasi, Ensemble transformation in the fluctuation theory, Physica A, 585, 126430 (14 pages) (2022). DOI: 10.1016/j.physa.2021.126430; Physica A, 605, 127987 (1 pages) (2022) (Corrigendum). DOI: 10.1016/j.physa.2022.127987
Nobuhiro Yasoshima, Tatsuya Ishiyama, Makoto Gemmei-Ide, Nobuyuki Matubayasi, Molecular Structure and Vibrational Spectra of Water Molecules Sorbed in Poly(2-methoxyethylacrylate) Revealed by Molecular Dynamics Simulation, J. Phys. Chem. B, 125, 12095-12103 (2021). DOI: 10.1021/acs.jpcb.1c07342
Kento Kasahara, Ren Masayama, Kazuya Okita, Nobuyuki Matubayasi, Atomistic description of molecular binding processes based on returning probability theory, J. Chem. Phys., 155, 204503 (15 pages) (2021). DOI: 10.1063/5.0070308
Takuma Yagasaki, Nobuyuki Matubayasi, Crystallization of Polyethylene Brushes and Its Effect on Interactions with Water, Macromolecules, 54, 8303-8313 (2021). DOI: 10.1021/acs.macromol.1c01145
Shota Goto, Kang Kim, Nobuyuki Matubayasi, Effects of chain length on Rouse modes and non-Gaussianity in linear and ring polymer melts, J. Chem. Phys., 155, 124901 (10 pages) (2021). DOI: 10.1063/5.0061281
Seishi Shimizu, Nobuyuki Matubayasi, Temperature Dependence of Sorption, Langmuir, 37, 11008-11017 (2021). DOI: 10.1021/acs.langmuir.1c01576
Raffaele Pastore, Takuma Kikutsuji, Francesco Rusciano, Nobuyuki Matubayasi, Kang Kim, Francesco Greco, Breakdown of the Stokes-Einstein relation in supercooled liquids: A cage-jump perspective, J. Chem. Phys., 155, 114503 (7 pages) (2021). DOI: 10.1063/5.0059622
Hidekazu Kojima, Kazuya Handa, Kazuo Yamada, Nobuyuki Matubayasi, Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions, J. Phys. Chem. B, 125, 9357-9371 (2021). DOI: 10.1021/acs.jpcb.1c04818.
Published as part of The Journal of Physical Chemistry virtual special issue "Dor Ben-Amotz Festschrift"
Yoshiki Ishii, Nobuyuki Matubayasi, Go Watanabe, Takashi Kato, Hitoshi Washizu, Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal, Sci. Adv., 7, eabf0669 (2021). DOI: 10.1126/sciadv.abf0669. Selected as the Cover for Volume 7, Issue 31 (2021).
Yuto Suzuki, Mario Gutiérrez, Senri Tanaka, Eduardo Gomez, Norimitsu Tohnai, Nobuhiro Yasuda, Nobuyuki Matubayasi, Abderrazzak Douhal, Ichiro Hisaki, Construction of isostructural hydrogen-bonded organic frameworks: limitations and possibilities of pore expansion, Chem. Sci., 12, 9607-9618 (2021). DOI: 10.1039/d1sc02690a. Chem. Sci., 13, 14410-14410 (2022)(correction). DOI: 10.1039/d2sc90241a. Selected as the Front Cover for Volume 12, Issue 28 (2021), compiled in the themed collection: 2021 ChemSci Pick of the Week Collection, compiled in the themed collection: 2021 Chemical Science HOT Article Collection, and placed in the 10% of highly cited articles from the Royal Society of Chemistry in 2022
Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi, Transition pathway of hydrogen bond switching in supercooled water analyzed by the Markov state model, J. Chem. Phys., 154, 234501 (7 pages) (2021). DOI: 10.1063/5.0055531
Naoya Tomoshige, Shota Goto, Hideyuki Mizuno, Tatsuya Mori, Kang Kim, Nobuyuki Matubayasi, Understanding the scaling of boson peak through insensitivity of elastic heterogeneity to bending rigidity in polymer glasses, J. Phys.: Condens. Matter, 33, 274002 (7 pages) (2021). DOI: 10.1088/1361-648X/abfd51
Lukman Hakim, Yoshiki Ishii, Nobuyuki Matubayasi, Spatial-Decomposition Analysis of Electrical Conductivity in Mixtures of Ionic Liquid and Sodium Salt for Sodium-Ion Battery Electrolytes, J. Phys. Chem. B, 125, 3374-3385 (2021). DOI: 10.1021/acs.jpcb.1c00372
Seishi Shimizu, Nobuyuki Matubayasi, Implicit function theorem and Jacobians in solvation and adsorption, Physica A, 570, 125801 (11 pages) (2021). DOI: 10.1016/j.physa.2021.125801
Seishi Shimizu, Nobuyuki Matubayasi, Phase stability condition and liquid-liquid phase separation under mesoscale confinement, Physica A, 563, 125385 (13 pages) (2021). DOI: 10.1016/j.physa.2020.125385
Nobuyuki Matubayasi, Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation, Chem. Commun., 57, 9968-9978 (2021). DOI: 10.1039/d1cc03395f
Seishi Shimizu, Nobuyuki Matubayasi, Fluctuation adsorption theory: quantifying adsorbate-adsorbate interaction and interfacial phase transition from an isotherm, Phys. Chem. Chem. Phys., 22, 28304-28316 (2020). DOI: 10.1039/d0cp05122e
Sebastian Schöttl, Nobuyuki Matubayasi, Dominik Horinek, Solubilization Power of Surfactant-Free Microemulsions, Phys. Chem. Chem. Phys., 22, 22185-22189 (2020). DOI: 10.1039/d0cp02933e. Selected as the Inside front cover for Volume 22, Issue 39 (2020) and as a 2020 PCCP HOT Article
Seishi Shimizu, Nobuyuki Matubayasi, Intensive nature of fluctuations: Reconceptualizing Kirkwood-Buff theory via elementary algebra, J. Mol. Liq., 318, 114225 (8 pages) (2020). DOI: 10.1016/j.molliq.2020.114225
Lukman Hakim, Yoshiki Ishii, Kazuhiko Matsumoto, Rika Hagiwara, Koji Ohara, Yasuhiro Umebayashi, Nobuyuki Matubayasi, 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, J. Phys. Chem. B, 124, 7291-7305 (2020). DOI: 10.1021/acs.jpcb.0c04078
Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi, Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide, J. Chem. Phys., 153, 054115 (8 pages) (2020). DOI: 10.1063/5.0009066
Bin W. Zhang, Nobuyuki Matubayasi, Ronald M. Levy, Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals, J. Phys. Chem. B, 124, 5220-5237 (2020). DOI: 10.1021/acs.jpcb.0c02721. Published as part of The Journal of Physical Chemistry virtual special issue "Peter J. Rossky Festschrift"
Seishi Shimizu, Nobuyuki Matubayasi, Thermodynamic stability condition can judge whether a nanoparticle dispersion can be considered a solution in a single phase, J. Colloid Interface Sci., 575, 472-479 (2020). DOI: 10.1016/j.jcis.2020.04.101
Kazuo Yamada, Nobuyuki Matubayasi, Chain-Increment Method for Free-Energy Computation of a Polymer with All-Atom Molecular Simulations, Macromolecules, 53, 775-788 (2020). DOI: 10.1021/acs.macromol.9b01952
Yoshiki Ishii, Nobuyuki Matubayasi, Self-Consistent Scheme Combining MD and Order‑N DFT Methods: An Improved Set of Nonpolarizable Force Fields for Ionic Liquids, J. Chem. Theory Comput., 16, 651-665 (2020). DOI: 10.1021/acs.jctc.9b00793
Ronald M. Levy, Nobuyuki Matubayasi, Bin W. Zhang, Solvation Thermodynamics from the Perspective of Endpoints DFT, J. Phys. Chem. B, 124, 11771-11782 (2020). DOI: 10.1021/acs.jpcb.0c08988
Naoya Tomoshige, Hideyuki Mizuno, Tatsuya Mori, Kang Kim, Nobuyuki Matubayasi, Boson peak, elasticity, and glass transition temperature in polymer glasses: Effects of the rigidity of chain bending, Sci. Rep., 9, 19514 (13 pages) (2019). DOI: 10.1038/s41598-019-55564-2
Hodaka Mori, Nobuyuki Matubayasi, Local viscoelasticity at resin-metal interface analyzed with spatial-decomposition formula for relaxation modulus, J. Chem. Phys., 151, 114904 (14 pages) (2019). DOI: 10.1063/1.5109599
Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi, 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, J. Mol. Liq., 294, 111603 (6 pages) (2019). DOI: 10.1016/j.molliq.2019.111603
Keisuke Mizuta, Yoshiki Ishii, Kang Kim, Nobuyuki Matubayasi, Bridging the gap between molecular dynamics and hydrodynamics in nanoscale Brownian motions, Soft Matter, 15, 4380-4390 (2019). DOI: 10.1039/c9sm00246d
Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi, Diffusion dynamics of supercooled water modeled with the cage-jump motion and hydrogen-bond rearrangement, J. Chem. Phys., 150, 204502 (6 pages) (2019). DOI: 10.1063/1.5095978. Invited article for the special-topic issue on Chemical Physics of Supercooled Water
Yoshiki Ishii, Naoki Yamamoto, Nobuyuki Matubayasi, Bin W. Zhang, Di Cui, Ronald M. Levy, Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method, J. Chem. Theory Comput., 15, 2896-2912 (2019). DOI: 10.1021/acs.jctc.8b01309
Keiichi Masutani, Yu Yamamori, Kang Kim, Nobuyuki Matubayasi, Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation, J. Chem. Phys., 150, 145101 (14 pages) (2019). DOI: 10.1063/1.5088395
Eva Pluhařová, Pavel Jungwirth, Nobuyuki Matubayasi, Ondrej Marsalek, Structure and Dynamics of the Hydration Shell: Spatially Decomposed Time Correlation Approach, J. Chem. Theory Comput., 15, 803-812 (2019). DOI: 10.1021/acs.jctc.8b00111
Seishi Shimizu, Nobuyuki Matubayasi, Statistical thermodynamics of regular solutions and solubility parameters, J. Mol. Liq., 273, 626-633 (2019). DOI: 10.1016/j.molliq.2018.10.024
Thomas W. J. Nicol, Noriyuki Isobe, James H. Clark, Nobuyuki Matubayasi, Seishi Shimizu, The mechanism of salt effects on starch gelatinization from a statistical thermodynamic perspective, Food Hydrocolloids, 87, 593-601 (2019). DOI: 10.1016/j.foodhyd.2018.08.042
Nobuyuki Matubayasi, Keiichi Masutani, Energetics of cosolvent effect on peptide aggregation, Biophysics and Physicobiology, 16, 185-195 (2019). DOI: 10.2142/biophysico.16.0_185. Invited article for the special issue "Progress of Theoretical and Computational Biophysics" in honor of Professor Nobuhiro Go's outstanding contribution on the occasion of his 80th birthday
Nobuyuki Matubayasi, Energy-Representation Theory of Solutions: Its Formulation and Application to Soft, Molecular Aggregates, Bull. Chem. Soc. Jpn., 92, 1910-1927 (2019). DOI: 10.1246/bcsj.20190246. Award Account: The Chemical Society of Japan Award for Creative Work for 2018. Selected as Inside Cover for Vol. 92, No. 11
Seishi Shimizu, Steven Abbott, Nobuyuki Matubayasi, A Molecular Thermodynamics Approach to Capture Non-specific Flavour-Macromolecule Interactions, Encyclopedia of Food Chemistry, vol. 2, page 522-527, edited by L. Melton, F. Shahidi, and P. Varelis, Elsevier (2019); ISBN: 9780128140260. DOI: 10.1016/B978-0-08-100596-5.22424-4
2018
Ai Shinobu, Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao, Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations, J. Chem. Phys., 149, 195101 (10 pages) (2018). DOI: 10.1063/1.5055799
Hodaka Mori, Nobuyuki Matubayasi, Resin filling into nano-sized pore on metal surface analyzed by all-atom molecular dynamics simulation over a variety of resin and pore sizes, Polymer, 150, 360-370 (2018). DOI: 10.1016/j.polymer.2018.06.052
Naoki Yamamoto, Ippei Nakakuki, Nobuyuki Matubayasi, Free-energy analysis of physisorption on solid-liquid interface with the solution theory in the energy representation, J. Chem. Phys., 149, 014504 (10 pages) (2018). DOI: 10.1063/1.5027861
Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi, How do hydrogen bonds break in supercooled water?: Detecting pathways not going through saddle point of two-dimensional potential of mean force, J. Chem. Phys., 148, 244501 (8 pages) (2018). DOI: 10.1063/1.5033419
Tomonori Kawakami, Isamu Shigemoto, Nobuyuki Matubayasi, Structure and permeability of ionomers studied by atomistic molecular simulation combined with the theory of solutions in the energy representation, J. Chem. Phys., 148, 214903 (14 pages) (2018). DOI: 10.1063/1.5018884
Seishi Shimizu, Nobuyuki Matubayasi, Statistical thermodynamic foundation for mesoscale aggregation in ternary mixtures, Phys. Chem. Chem. Phys., 20, 13777-13784 (2018). DOI: 10.1039/c8cp01207e. Selected as a 2018 PCCP HOT Article
Bin W. Zhang, Di Cui, Nobuyuki Matubayasi, Ronald M. Levy, The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations, J. Phys.Chem. B 122, 4700-4707 (2018). DOI: 10.1021/acs.jpcb.8b02666
Tomoko Mizuguchi, Nobuyuki Matubayasi, Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions, J. Phys.Chem. B 122, 3219-3229 (2018). DOI: 10.1021/acs.jpcb.7b08241. Invited article for Festschrift issue in honor of the 90th birthday of Benjamin Widom
Yoshihiko Tokunaga, Yu Yamamori, Nobuyuki Matubayasi, Probabilistic analysis for identifying the driving force of protein folding, J. Chem. Phys., 148, 125101 (9 pages) (2018). DOI: 10.1063/1.5019410
Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao, Binding free energy analysis of protein-protein docking model structures by evERdock, J. Chem. Phys., 148, 105101 (10 pages) (2018). DOI: 10.1063/1.5019864
Kai-Min Tu, Kang Kim, Nobuyuki Matubayasi, Spatial-decomposition analysis of viscosity with application to Lennard-Jones fluid, J. Chem. Phys., 148, 094501 (10 pages) (2018). DOI: 10.1063/1.5018483
Seishi Shimizu, Nobuyuki Matubayasi, Ion hydration: linking self-diffusion and reorientational motion to water structure, Phys. Chem. Chem. Phys., 20, 5909-5917 (2018). DOI: 10.1039/c7cp07309g
Di Cui, Bin W. Zhang, Nobuyuki Matubayasi, Ronald M. Levy, The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force, J. Chem. Theory Comput., 14, 512–526 (2018). DOI: 10.1021/acs.jctc.7b01076
Seishi Shimizu, Nobuyuki Matubayasi, A unified perspective on preferential solvation and adsorption based on inhomogeneous solvation theory, Physica A, 492, 1988-1996 (2018). DOI: 10.1016/j.physa.2017.11.113
Hodaka Mori, Nobuyuki Matubayasi, MD simulation analysis of resin filling into nano-sized pore formed on metal surface, Appl. Surf. Sci., 427, Part A, 1084-1091 (2018). DOI: 10.1016/j.apsusc.2017.08.123
George Mogami, Makoto Suzuki, Nobuyuki Matubayasi, Spatial Distribution of Ionic Hydration Energy and Hyper-Mobile Water, The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery, Chapter 3, page 33-52, edited by M. Suzuki, Springer Nature Singapore Pte Ltd. (2018); ISBN: 978-981-10-8458-4. DOI: 10.1007/978-981-10-8459-1_3
Nobuyuki Matubayasi, All-Atom Analysis of Free Energy of Protein Solvation Through Molecular Simulation and Solution Theory, The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery, Chapter 10, page 141-155, edited by M. Suzuki, Springer Nature Singapore Pte Ltd. (2018); ISBN: 978-981-10-8458-4. DOI: 10.1007/978-981-10-8459-1_10
Makoto Suzuki, George Mogami, Takahiro Watanabe, Nobuyuki Matubayasi, Novel Intermolecular Surface Force Unveils the Driving Force of the Actomyosin System, The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery, Chapter 16, page 257-274, edited by M. Suzuki, Springer Nature Singapore Pte Ltd. (2018); ISBN: 978-981-10-8458-4. DOI: 10.1007/978-981-10-8459-1_16
Makoto Suzuki, George Mogami, Hideyuki Ohsugi, Takahiro Watanabe, Nobuyuki Matubayasi, Physical driving force of actomyosin motility based on the hydration effect, Cytoskeleton, 74, 512-527 (2017). DOI: 10.1002/cm.21417. Special Issue: Actin biophysics in the tradition of Fumio Oosawa. Press release at
Seishi Shimizu, Nobuyuki Matubayasi, Osmolyte depletion viewed in terms of the dividing membrane and its work of expansion against osmotic pressure, Biophysical Chemistry, 231, 111-115 (2017). DOI: 10.1016/j.bpc.2017.02.003. Invited article for the special issue for HPBB2016(9th International Conference on High Pressure Bioscience and Biotechnology)
Seishi Shimizu, Nobuyuki Matubayasi, Hydrotropy and scattering: pre-ouzo as an extended near-spinodal region, Phys. Chem. Chem. Phys., 19, 26734-26742 (2017). DOI: 10.1039/c7cp04990k
Ryosuke Ishizuka, Nobuyuki Matubayasi, Effective Charges of Ionic Liquid Determined Self-Consistently through Combination of Molecular Dynamics Simulation and Density-Functional Theory, J. Comput. Chem.38, 2559-2569 (2017). DOI: 10.1002/jcc.24880. Selected as the front cover for Volume 38, Issue 30 (2017)
Seishi Shimizu, Nobuyuki Matubayasi, Unifying hydrotropy under Gibbs phase rule, Phys. Chem. Chem. Phys., 19, 23597-23605 (2017). DOI: 10.1039/c7cp02132a. Perspective article for themed collections: Surface chemistry and interface science and 2017 PCCP HOT Articles
Minoru Sayou, Ryosuke Ishizuka, Nobuyuki Matubayasi, Energetic Analysis of Adsorption and Absorption of Small Molecule to Nanodroplet of Water, J. Phys.Chem. B 121, 5995-6001 (2017). DOI: 10.1021/acs.jpcb.7b01554
Andrew J. Maneffa, Richard Stenner, Avtar S. Matharu, James H. Clark, Nobuyuki Matubayasi, Seishi Shimizu, Water activity in liquid food systems: A molecular scale interpretation, Food Chemistry, 237, 1133-1138 (2017). DOI: 10.1016/j.foodchem.2017.06.046
Yu Yamamori, Nobuyuki Matubayasi, Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme, J. Chem. Phys., 146, 225103 (13 pages) (2017). DOI: 10.1063/1.4985222
Shinya Kobayashi, Sotaro Fujii, Aya Koga, Satoshi Wakai, Nobuyuki Matubayasi, Yoshihiro Sambongi, Pseudomonas aeruginosa cytochrome c551 denaturation by five systematic urea derivatives that differ in the alkyl chain length, Bioscience, Biotechnology, and Biochemistry, 81, 1274-1278 (2017). DOI: 10.1080/09168451.2017.1303361
Ronald M. Levy, Di Cui, Bin W. Zhang, Nobuyuki Matubayasi, Relationship between Solvation Thermodynamics from IST and DFT Perspectives, J. Phys.Chem. B 121, 3825-3841 (2017). DOI: 10.1021/acs.jpcb.6b12889. Invited article for Klaus Schulten Memorial Issue
Robert C. Harris, Nanjie Deng, Ronald M. Levy, Ryosuke Ishizuka, Nobuyuki Matubayasi, 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, J. Comput. Chem.,38, 1198-1208 (2017). DOI: 10.1002/jcc.24668. Invited article for Special Issue: Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III
Nobuyuki Matubayasi, Energy Representation Approach, Elsevier Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, edited by J. Reedijk, Waltham, MA, 28-Aug-2017 (2017). DOI: 10.1016/B978-0-12-409547-2.11485-4
Seishi Shimizu, Steven Abbott, Nobuyuki Matubayasi, Quantifying non-specific interactions between flavour and food biomolecules, Food Funct., 8, 2999-3009 (2017). DOI: 10.1039/c7fo00313g. Selected as the front cover for Volume 8, Issue 9 (2017). Featured in the themed collection: Recent HOT articles
Nobuyuki Matubayasi, Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions, Current Opinion in Structural Biology, 43, 45-54 (2017). DOI: 10.1016/j.sbi.2016.10.005. On a themed issue on Theory and simulation edited by Carol Post and Ronald Levy
Seishi Shimizu, Richard Stenner, Nobuyuki Matubayasi, Gastrophysics: Statistical thermodynamics of biomolecular denaturation and gelation from the Kirkwood-Buff theory towards the understanding of tofu, Food Hydrocolloids, 62, 128-139 (2017). DOI: 10.1016/j.foodhyd.2016.07.022
Seishi Shimizu, Nobuyuki Matubayasi, The origin of cooperative solubilisation by hydrotropes, Phys. Chem. Chem. Phys., 18, 25621-25628 (2016). DOI: 10.1039/c6cp04823d
Thomas W. J. Nicol, Nobuyuki Matubayasi, Seishi Shimizu, Origin of nonlinearity in phase solubility: solubilisation by cyclodextrin beyond stoichiometric complexation, Phys. Chem. Chem. Phys., 18, 15205-15217 (2016). DOI: 10.1039/c6cp01582d
Atsushi Date, Ryosuke Ishizuka, Nobuyuki Matubayasi, 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, Phys. Chem. Chem. Phys., 18, 13223-13231 (2016). DOI: 10.1039/c6cp01834c
Megumi Shintani, Nobuyuki Matubayasi, Morphology study of DMPC/DHPC mixtures by solution-state 1H, 31P NMR, and NOE measurements, J. Mol. Liq., 217, 62-69 (2016). DOI: 10.1016/j.molliq.2015.10.003. Invited article for special issue in honor of Prof. Arakawa
George Mogami, Makoto Suzuki, and Nobuyuki Matubayasi, Spatial-Decomposition Analysis of Energetics of Ionic Hydration, J. Phys. Chem. B, 120, 1813-1821 (2016). DOI: 10.1021/acs.jpcb.5b09481. Invited article for Bruce C. Garrett Festschrift Special Issue
Yu Yamamori, Ryosuke Ishizuka, Yasuhito Karino, Shun Sakuraba, Nobuyuki Matubayasi, Interaction-component analysis of the hydration and urea effects on cytochrome c, J. Chem. Phys., 144, 085102 (14 pages) (2016). DOI: 10.1063/1.4941945
Ryosuke Ishizuka, Nobuyuki Matubayasi, Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory, J. Chem. Theory Comput., 12, 804-811 (2016). DOI: 10.1021/acs.jctc.5b00885
Richard Stenner, Nobuyuki Matubayasi, Seishi Shimizu, Gelation of carrageenan: Effects of sugars and polyols, Food Hydrocolloids, 54, 284-292 (2016). DOI: 10.1016/j.foodhyd.2015.10.007
Fumitaka Kamo, Ryosuke Ishizuka, Nobuyuki Matubayasi, Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent, Protein Sci., 25, 56-66 (2016). DOI: 10.1002/pro.2754. Invited article for Festschrift issue in celebration of the 65th birthday of Ronald M. Levy
Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi, An accurate and efficient computation method of the hydration free energy of a large, complex molecule, J. Chem. Phys., 142, 175101 (11 pages) (2015). DOI: 10.1063/1.4919636
Tomoko Mizuguchi, Ryosuke Ishizuka, Nobuyuki Matubayasi, Effect of diffuseness of micelle boundary on the solute distribution upon solubilization, Chem. Phys. Lett., 624, 19-23 (2015). DOI: 10.1016/j.cplett.2015.02.001
Ryosuke Ishizuka, Nobuyuki Matubayasi, Kai-Min Tu, Yasuhiro Umebayashi, Energetic Contributions from the Cation and Anion to the Stability of Carbon Dioxide Dissolved in Imidazolium-Based Ionic Liquids, J. Phys. Chem. B, 119, 1579-1587 (2015). DOI: 10.1021/jp5101957
Toru Ekimoto, Nobuyuki Matubayasi, Mitsunori Ikeguchi, Finite-Size Effect on the Charging Free Energy of Protein in Explicit Solvent, J. Chem. Theory Comput., 11, 215-223 (2015). DOI: 10.1021/ct5008394
Hideaki Takahashi, Nobuyuki Matubayasi, Development of a Massively Parallel QM/MM Approach Combined with a Theory of Solutions, Quantum Modeling of Complex Molecular Systems (Challenges and Advances in Computational Chemistry and Physics 21), Chapter 6, page 153-196, edited by J.-L.Rivail, M. Ruiz-Lopez, and X. Assfeld, Springer (2015); ISBN: 978-3-319-21626-3. DOI: 10.1007/978-3-319-21626-3
2014
Kai-Min Tu , Ryosuke Ishizuka, Nobuyuki Matubayasi, Spatial-decomposition analysis of electrical conductivity in ionic liquid, J. Chem. Phys., 141, 244507 (11 pages) (2014). DOI: 10.1063/1.4904382
Seishi Shimizu, Nobuyuki Matubayasi, Gelation: The Role of Sugars and Polyols on Gelatin and Agarose, J. Phys. Chem. B, 118, 13210−13216 (2014). DOI: 10.1021/jp509099h
Ken Yoshida, Nobuyuki Matubayasi, Yasuhiro Uosaki, Masaru Nakahara, Effect of Rotational Couplings on Vibrational Spectrum Line Shape of the Bending Mode in Low-Density Supercritical Water: Density and Hydrogen Isotopes Dependencies, J Solution Chem., 43, 1499–1508 (2014). DOI: 10.1007/s10953-014-0220-1
Seishi Shimizu, Nobuyuki Matubayasi, Hydrotropy: Monomer−Micelle Equilibrium and Minimum Hydrotrope Concentration, J. Phys. Chem. B, 118, 10515–10524 (2014). DOI: 10.1021/jp505869m
Kai-Min Tu , Ryosuke Ishizuka, Nobuyuki Matubayasi, Spatial-decomposition analysis of electrical conductivity in concentrated electrolyte solution, J. Chem. Phys., 141, 044126 (9 pages) (2014). DOI: 10.1063/1.4890741
Shun Sakuraba, Nobuyuki Matubayasi, ERmod: Fast and Versatile Computation Software for Solvation Free Energy with Approximate Theory of Solutions, J. Comput. Chem.35, 1592–1608 (2014). DOI: 10.1002/jcc.23651
Seishi Shimizu, Nobuyuki Matubayasi, Preferential Solvation: Dividing Surface vs Excess Numbers, J. Phys. Chem. B, 118, 3922−3930 (2014). DOI: 10.1021/jp410567c. Included in “B” is for Biophysics, a Virtual Issue of The Journal of Physical Chemistry B in February, 2017. This virtual issue is compiled by Senior Editors Pavel Jungwirth and Martin T. Zanni and consists of 25 papers highlighting the most exciting biophysical research papers published in the biomolecules and biomaterials sections of the Journal of Physical Chemistry B since 2014.
Yuichiro Okazaki,Tetsuo Taniuchi,George Mogami,Nobuyuki Matubayasi,and Makoto Suzuki, Comparative Study on the Properties of Hydration Water of Na- and K-Halide Ions by Raman OH/OD-stretching Spectroscopy and Dielectric Relaxation Data, J. Phys. Chem. A, 118, 2922−2930 (2014). DOI: 10.1021/jp412804d
Yasuo Kameda,Hiroshi Deguchi,Hirotoshi Furukawa,Yoshiyuki Kubota,Yasuyuki Yagi, Yoshihiro Imai,Noriko Yamazaki,Noriko Watari,Takuya Hirata, Nobuyuki Matubayasi, Hydration Structure of CO2-Absorbed 2-Aminoethanol Studied by Neutron Diffraction with the 14N/15N Isotopic Substitution Method, J. Phys. Chem. B, 118, 1403−1410 (2014). DOI: 10.1021/jp411780d
2013
G. Mogami, T. Miyazaki, T. Wazawa, N. Matubayasi, and M. Suzuki, Anion-Dependence of Fast Relaxation Component in Na-, K-Halide Solutions at Low Concentrations Measured by High-Resolution Microwave Dielectric Spectroscopy, J. Phys.Chem. A 117, 4851-4862 (2013). DOI: 10.1021/jp4012119
K. Yoshida, N. Matubayasi, Y. Uosaki, and M. Nakahara, Effect of heavy hydrogen isotopes on the vibrational line shape for supercritical water through rotational couplings, J. Chem. Phys., 138, 134508 (12 pages) (2013). DOI: 10.1063/1.4798933
Y. Ito, T. Yoshidome, N. Matubayasi, M. Kinoshita, and M. Ikeguchi, Molecular Dynamics Simulations of Yeast F1-ATPase before and after 16° Rotation of the γ Subunit, J. Phys.Chem. B 117, 3298−3307 (2013). DOI: 10.1021/jp312499u
H. Kimura, M. Nakahara, and N. Matubayasi, Solvent Effect on Pathways and Mechanisms for D-Fructose Conversion to 5-Hydroxymethyl-2-furaldehyde: In Situ 13C NMR Study, J. Phys.Chem. A 117, 2102−2113 (2013). DOI: 10.1021/jp312002h
Y. Karino and N. Matubayasi, Interaction-component analysis of the urea effect on amino acid analogs, Phys. Chem. Chem. Phys., 15, 4377-4391 (2013). DOI: 10.1039/c3cp43346c
T. Ishikawa, R. R. Burri, Y. O. Kamatari, S. Sakuraba, N. Matubayasi, A. Kitao, and K. Kuwata, 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, Phys. Chem. Chem. Phys., 15, 3646–3654 (2013). DOI: 10.1039/c3cp42761g
K. Takemura, R. R. Burri, T. Ishikawa, T. Ishikura, S. Sakuraba, N. Matubayasi, K. Kuwata, and A. Kitao, Free-energy analysis of lysozyme–triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation, Chem. Phys. Lett., 559, 94-98 (2013). DOI: 10.1016/j.cplett.2012.12.063
Y. Kameda, H. Deguchi, Y. Kubota, H. Furukawa, Y. Yagi, Y. Imai, M. Tatsumi, N. Yamazaki, N. Watari, T. Hirata, and N. Matubayasi, High-Energy X-ray Diffraction Study on the Intramolecular Structure of 2-Aminoethanol in the Liquid State, Bull. Chem. Soc. Japan86, 99–103 (2013). DOI: 10.1246/bcsj.20120222
2012
T. Kawakami, I. Shigemoto, and N. Matubayasi, Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation, J. Chem. Phys., 137, 234903 (9 pages) (2012). DOI: 10.1063/1.4770334; J. Chem. Phys.140, 169903 (2 pages) (2014) (erratum). DOI: 10.1063/1.4873166
Y. Kubota, A. Yoshimori, N. Matubayasi, M. Suzuki, and R. Akiyama, Molecular dynamics study of fast dielectric relaxation of water around a molecular-sized ion, J. Chem. Phys., 137, 224502 (4 pages) (2012). DOI : 10.1063/1.4769972
K. Takemura, H. Guo, S. Sakuraba, N. Matubayasi, and A. Kitao, Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation, J. Chem. Phys., 137, 215105 (10 pages) (2012). DOI : 10.1063/1.4768901
K. Yoshida, N. Matubayasi, Y. Uosaki, and M. Nakahara, Density effect on infrared spectrum for supercritical water in the low- and medium-density region studied by molecular dynamics simulation, J. Chem. Phys., 137, 194506 (10 pages) (2012). DOI : 10.1063/1.4767352
H. Kimura, Y. Yasaka, M. Nakahara, and N. Matubayasi, Nuclear magnetic resonance study on rotational dynamics of water and benzene in a series of ionic liquids: Anion and cation effects, J. Chem. Phys., 137, 194503 (10 pages) (2012). DOI : 10.1063/1.4766258
H. Kimura, M. Nakahara, and N. Matubayasi, Noncatalytic Hydrothermal Elimination of the Terminal D-Glucose Unit from Malto- and Cello-Oligosaccharides through Transformation to D-Fructose, J. Phys.Chem. A 116, 10039–10049 (2012). DOI : 10.1021/jp3034165
T. Yoshidome, Y. Ito, N. Matubayasi, M. Ikeguchi, and M. Kinoshita, Structural characteristics of yeast F1-ATPase before and after 16-degree rotation of the γ subunit: Theoretical analysis focused on the water-entropy effect, J. Chem. Phys., 137, 035102 (8 pages) (2012). DOI : 10.1063/1.4734298
M. Shintani, Y. Matsuo, S. Sakuraba, and N. Matubayasi, Interaction of naphthalene derivatives with lipid in membrane studied by 1H-nuclear Overhauser effect and molecular dynamics simulation, Phys. Chem. Chem. Phys., 14, 14049–14060 (2012). DOI : 10.1039/c2cp41984j
K. M. Tu, N. Matubayasi, K. K. Liang, I. T. Todorov, S. L. Chan, and P.-L. Chau, A possible molecular mechanism for the pressure reversal of general anaesthetics: aggregation of halothane in POPC bilayers at high pressure, Chem. Phys. Lett., 543, 148–154 (2012). DOI : 10.1016/j.cplett.2012.06.044
H. Takahashi, A. Omi, A. Morita, and N. Matubayasi, 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, J. Chem. Phys., 136, 214503 (12 pages) (2012). DOI : 10.1063/1.4722347
M. Takeuchi, N. Matubayasi, Y. Kameda, B. Minofar, S. Ishiguro, and Y. Umebayashi, Free-Energy and Structural Analysis of Ion Solvation and Contact Ion-Pair Formation of Li+ with BF4− and PF6− in Water and Carbonate Solvents, J. Phys.Chem. B 116, 6476−6487 (2012). DOI: 10.1021/jp3011487
P.-L. Chau, K. M. Tu, K. K. Liang, I. T. Todorov, S. J. Roser, R. Barker, and N. Matubayasi, The effect of pressure on halothane binding to hydrated DMPC bilayers, Mol. Phys., 110, 1461–1467 (2012). DOI : 10.1080/00268976.2012.659682
Y. Yasaka, M. L. Klein, M. Nakahara, and N. Matubayasi, Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T1 measurements, J. Chem. Phys., 136, 074508 (12 pages) (2012). DOI : 10.1063/1.3685100
N. Matubayasi and H. Takahashi, Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation, J. Chem. Phys., 136, 044505 (10 pages) (2012). DOI: 10.1063/1.3677184
Y. Tsujino, Y. Yasaka, N. Matubayasi, and M. Nakahara, Pathways and Kinetics of Anisole Pyrolysis Studied by NMR and Selective 13C Labeling. Heterolytic Carbon Monoxide Generation, Bull. Chem. Soc. Japan85, 124132 (2012). DOI: 10.1246/bcsj.20110334