2024

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
  • Kento Kasahara, Ren Masayama, Kazuya Okita, Nobuyuki Matubayasi, Elucidating protein-ligand binding kinetics based on returning probability theory, J. Chem. Phys., 159, 134103 (15 pages) (2023). DOI: 10.1063/5.0165692
  • Seishi Shimizu, Nobuyuki Matubayasi, Cooperativity in Sorption Isotherms, Langmuir, 39, 13820-13829 (2023). DOI: 10.1021/acs.langmuir.3c01243
  • Takuma Yagasaki, Nobuyuki Matubayasi, Molecular Dynamics Study of the Antifouling Mechanism of Hydrophilic Polymer Brushes, Langmuir, 39, 13158-13168 (2023). DOI: 10.1021/acs.langmuir.3c01552
  • Seishi Shimizu, Nobuyuki Matubayasi, Sorption from Solution: A Statistical Thermodynamic Fluctuation Theory, Langmuir, 39, 12987-12998 (2023). DOI: 10.1021/acs.langmuir.3c00804
  • Kazuo Yamada, Nobuyuki Matubayasi, Chain-Increment Approach to the Mutual Miscibility of Polymers with All-Atom Molecular Simulation, Macromolecules, 56, 3857-3872 (2023). DOI: 10.1021/acs.macromol.2c02304
  • Seishi Shimizu, Nobuyuki Matubayasi, Understanding Sorption Mechanisms Directly from Isotherms, Langmuir, 39, 6113-6125 (2023). DOI: 10.1021/acs.langmuir.3c00256
  • 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
  • Himadri S. Sarkar, Takato Mashita, Toshiyuki Kowada, Satoshi Hamaguchi, Toshizo Sato, Kento Kasahara, Nobuyuki Matubayasi, Toshitaka Matsui, Shin Mizukami, Arylazopyrazole-Based Photoswitchable Inhibitors Selective for Escherichia coli Dihydrofolate Reductase, ACS Chem. Biol., 18, 340-346 (2023). DOI: 10.1021/acschembio.2c00749
  • 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

  • 松林 伸幸, タンパク質の構造解析手法とIn silicoスクリーニングへの応用事例, 第4章6節 分子動力学シミュレーションと溶液統計力学理論を用いたペプチド凝集の解析, page 263-270, 株式会社技術情報協会 (2023). ISBN 978-4-86104-971-2
  • 笠原 健人, 沖田 和也, 松林 伸幸, 凝縮系のダイナミクスを解析するためのエネルギー表示理論の開発, フロンティア (ISSN 2758-4496), 5, No.2, 90-98 (2023).
  • 松林 伸幸, 金 鋼, 矢ケ崎 琢磨, 笠原 健人, 研究室紹介「大阪大学基礎工学研究科 分子集合系化学工学グループ」, フロンティア (ISSN 2758-4496), 5, No.1, 44-56 (2023).

2022

  • 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). DOI: 10.1016/j.physa.2022.127987

  • 松林 伸幸, 石山 達也, 泰岡 顕治, 尾形 修司, 藤本 和士,「富岳」成果創出加速プログラム「環境適合型機能性化学品」, アンサンブル (ISSN 1884-6750), 24, No.1, 22-31 (2022).

2021

  • 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
  • Seishi Shimizu, Nobuyuki Matubayasi, Cooperative Sorption on Porous Materials, Langmuir, 37, 10279-10290 (2021). DOI: 10.1021/acs.langmuir.1c01236
  • 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. B125, 9357-9371 (2021). DOI: 10.1021/acs.jpcb.1c04818. 
    Repository for datasets at https://zenodo.org/record/8210506
    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
  • Seishi Shimizu, Nobuyuki Matubayasi, Adsorbate-adsorbate interactions on microporous materials, Micropor. Mesopor. Mater., 323, 111254 (8 pages) (2021). DOI: 10.1016/j.micromeso.2021.111254
  • Seishi Shimizu, Nobuyuki Matubayasi, Sorption: A Statistical Thermodynamic Fluctuation Theory, Langmuir, 37, 7380-7391 (2021). DOI: 10.1021/acs.langmuir.1c00742
  • 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
  • Seishi Shimizu, Nobuyuki Matubayasi, Cooperativity in micellar solubilization, Phys. Chem. Chem. Phys., 23, 8705-8716 (2021). DOI: 10.1039/d0cp06479c
  • 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
  • 松林 伸幸, 溶媒和概念の普遍化に基づくソフト分子集合系の物質分配機能の全原子解析, 生産と技術, Vol.73, No.3 (2021年 夏号), pages 61-64 (2021).
  • 山田 一雄, 松林 伸幸, 高分子系における化学ポテンシャルのChain-Increment法による全原子計算, 大阪大学サイバーメディアHPCジャーナル, No.10, 3-8 (2021).

2020

  • 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. B124, 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. B124, 11771-11782 (2020). DOI: 10.1021/acs.jpcb.0c08988
  • 山田 一雄, 松林 伸幸, 高分子系における化学ポテンシャルのchain-increment法による全原子計算, アンサンブル (ISSN 1884-6750), 22, No.4, 294-303 (2020).
  • 石井 良樹, 松林 伸幸, 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, アンサンブル (ISSN 1884-6750), 22, No.2, 142-150 (2020).

2019

  • 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 Matter15, 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 Hydrocolloids87, 593-601 (2019). DOI: 10.1016/j.foodhyd.2018.08.042
  • Nobuyuki Matubayasi, Keiichi Masutani, Energetics of cosolvent effect on peptide aggregation, Biophysics and Physicobiology16, 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
  • Nobuyuki Matubayasi, Spatial-Decomposition Analysis of Electrical Conductivity, Chem. Rec.19, 723-734 (2019). DOI: 10.1002/tcr.201800116
  • 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, Polymer150, 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.148214903 (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

 

  • 松林 伸幸, 計算科学によるポリマー材料の解析と設計, デンソーテクニカルレビュー(ISSN 1342-4114), 23, 7-14 (2018). https://www.denso.com/jp/ja/innovation/technology/dtr/v23/
  • 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
  • 松林 伸幸, ポストリチウムに向けた革新的二次電池の材料開発, 第1章3節 MDシミュレーションと空間分割表式による電気伝導度の全原子解析, page 35-43, 境 哲男監修,株式会社エヌ・ティー・エス (2018). ISBN 978-4-86043-523-3

2017

  • 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 Biology43, 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 Hydrocolloids62, 128-139 (2017). DOI: 10.1016/j.foodhyd.2016.07.022
  • 山守 優, 松林 伸幸,  シトクロムcに対する水および尿素の溶媒和効果の相互作用成分解析, アンサンブル (ISSN 1884-6750), 19, No.2, 88-93 (2017).

2016

  • 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 HydrationJ. Phys. Chem. B120, 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 Hydrocolloids54, 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

  • 水口 朋子, 松林 伸幸, ミセル内の小分子に対するミセル界面の揺らぎの影響, 繊維学会誌 (ISSN 0037-9875), 72, No.5, 266-269 (2016).
  • 吉田 健松林 伸幸中原 勝魚崎 泰弘超臨界水の振動スペクトルに対する回転運動の影響:密度効果および水素の同位体効果による解析, 高圧力の科学と技術 (ISSN 0917-639X), 26, No.4, 323-332 (2016). DOI: 10.4131/jshpreview.26.323

2015

  • 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 moleculeJ. 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 solubilizationChem. 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 LiquidsJ. Phys. Chem. B119, 1579-1587 (2015). DOI: 10.1021/jp5101957
  • Toru Ekimoto, Nobuyuki Matubayasi, Mitsunori IkeguchiFinite-Size Effect on the Charging Free Energy of Protein in Explicit SolventJ. Chem. Theory Comput.11, 215-223 (2015). DOI:  10.1021/ct5008394

  • 松林 伸幸, 溶媒和概念の拡張に基づくソフト分子集合系の物質分配機能の解析, 分析化学 (ISSN 0525-1931), 64, No. 3, 185-188 (2015).
  • 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. B118, 1321013216 (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: MonomerMicelle Equilibrium and Minimum Hydrotrope Concentration, J. Phys. Chem. B118, 10515–10524 (2014). DOI: 10.1021/jp505869m
  • Kai-Min Tu , Ryosuke Ishizuka, Nobuyuki Matubayasi, Spatial-decomposition analysis of electrical conductivity in concentrated electrolyte solutionJ. Chem. Phys.141044126 (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. B118, 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 DataJ. Phys. Chem. A118, 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. B118, 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, 32983307 (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, 21022113 (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. Japan 86, 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, 64766487 (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. Japan 85, 124­132 (2012). DOI: 10.1246/bcsj.20110334

  • 松林 伸幸, 巨大分子系の計算化学 超大型計算機時代の理論化学の新展開, 11章 超臨界水と脂質膜, page 123-128, 日本化学会編,CSJカレントレビュー, 化学同人 (2012). ISBN 978-4-7598-1368-5

pre-2012: Under construction