• 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, in press (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, in press (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, 1084-1091 (2018). DOI: 10.1016/j.apsusc.2017.08.123


  • Seishi Shimizu, Steven Abbott, Nobuyuki Matubayasi, A Molecular Thermodynamics Approach to Capture Non-specific Flavour-Macromolecule Interactions, Encyclopedia of Food Chemistry, XX. DOI: 10.1016/B978-0-12-814026-0.22424-4
  • 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 XXX-XXX, 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 XXX-XXX, 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 XXX-XXX, 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


  • 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).


  • 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, 6269 (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


  • 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), 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


  • 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


  • 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


  • 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