{"id":324,"date":"2023-05-15T14:06:12","date_gmt":"2023-05-15T05:06:12","guid":{"rendered":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc\/?page_id=324"},"modified":"2026-04-09T14:39:17","modified_gmt":"2026-04-09T05:39:17","slug":"publications","status":"publish","type":"page","link":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc\/publications\/","title":{"rendered":"\u7814\u7a76\u696d\u7e3e"},"content":{"rendered":"\n
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  1. Takafumi Ishii, Takashi Kojima*<\/sup>, Yusuke Yasuda, Kazushi Fujimoto, “An analysis method of local entropy changes from atomic fluctuations”, PLOS One<\/em>,\u00a0Accepted<\/strong>.<\/a><\/li>\n\n\n\n
  2. Kodai Kikuchi, Kazushi Fujimoto, Kazuyoshi Kaneko, Akio Shimizu, Tatsushi Matsuyama, Junichi Ida, “Prediction and Elucidation of Cellulose Solubility in Ionic Liquids under High Pressure using All-Atom Molecular Dynamics Simulations”, RSC Adv<\/em>., 16<\/strong>, 2710-2722 (2026).\"\"<\/a><\/li>\n\n\n\n
  3. Yuki Ito, Yusuke Yasuda, Yukako Konishi, Taiki Shiba, Kaoru Dokko, Kazushi Fujimoto*, “Composition-Dependent Structure and Dynamics of Lithium-Sulfur Battery Electrolytes Revealed by Molecular Dynamics Simulations”, J. Phys. Chem. C, <\/em> 130<\/strong>, 1327\u20131337 (2026).\"\"<\/a>[Cover]<\/a><\/li>\n\n\n\n
  4. Yuki Kitamura, Yusuke Yasuda, Junya Metoki, Shogo Tsujino, Kazuma Yoshimura, Takahide Watanabe, and Kazushi Fujimoto*, “Locally Ordered Junctions Govern Diffusion in Triglycerides: Insights from Molecular Dynamics Simulations”, RSC Adv<\/em>., 15<\/strong>, 45514-45523 (2025).\"\"<\/a><\/li>\n\n\n\n
  5. Taketoshi Kitagawa, Yusuke Yasuda, Tetsuro Nagai, and Kazushi Fujimoto*, “Hierarchical Dynamics of Hydronium Ions in Polymer Electrolyte Membranes Revealed by All-Atom Molecular Dynamics Simulations”, J. Chem. Phys.<\/em>, 163<\/strong>, 161102 (2025).\"\"<\/a><\/li>\n\n\n\n
  6. Takuma Kureha*, Yuma Sasaki, Yusuke Shinozaki, Yuka Wakayama, Keita Namba, Yuichiro Nishizawa, Haruka Minato, Natsuki Watanabe, Takayuki Uchihashi, Kazushi Fujimoto, Daisuke Suzuki*, “Controlled Disassembly of Poly(methyl acrylate) Microparticle-based Polymers using Ethanol-water Mixtures”, Langmuir<\/em>, 41<\/strong>, 36, 24225\u201324235 (2025).\"\"<\/a><\/li>\n\n\n\n
  7. Kodai Kikuchi*, Kazushi Fujimoto, Akio Shimizu, Kazuyoshi Kaneko, Tatsushi Matsuyama, and Junichi Ida, “Prediction and Elucidation of Cellulose Dissolution Rate in Ionic LiquidsUnder High Pressure Using All-Atom Molecular Dynamics Simulations”, J. Mol. Liq.,<\/em> 437<\/strong>, part A, 128344 (2025).\"\"<\/a><\/li>\n\n\n\n
  8. Yuta Akagi, Kazushi Fujimoto <\/sup>and, Yusuke Yasuda*, “Coarse-grained molecular dynamics simulations and structural analysis of end-linked polymer networks under different cross-linking protocols”, Polym. J.<\/em> 57<\/strong>, 1183-1194 (2025).\"\"<\/a><\/li>\n\n\n\n
  9. Ikki Takahashi, Yoshiki Hieda, Minoru Kato, Yusuke Yasuda, Kazushi Fujimoto*, “Mechanistic Insights into Yielding and Fracture of Polymer Nanoparticles under Compression via All-Atom Molecular Dynamics Simulations for Applications in Anisotropic Conductive Adhesives”, ACS Appl. Nano Mater.<\/em>, 8<\/strong> (18), 9276\u20139285 (2025)\"\"<\/a> [Cover]<\/a>[Article on Request]<\/a><\/li>\n\n\n\n
  10. Fujimoto, Kazushi*, Ishikawa, Hiroaki, Shimooka, Minoru, Kaneko, Toshihiro, Okazaki, Susumu*, “Molecular Mechanistic Analysis of Liquid-Crystalline Polymers Composed of p-Hydroxybenzoic Acid I: Thermal Properties”, J. Phys. Chem., B<\/em>, 129<\/strong>, 1, 524\u2013531 (2025).\"\"<\/a> [Cover]<\/a>[Article on Request]<\/a><\/li>\n\n\n\n
  11. Shota Mino, Kosuke Matsui, Masahide Goto, Akiyuki Ryoki, Takeyuki Suzuki, Kazushi Fujimoto, Hiromitsu Sogawa, Hiroto Kudo and Fumio Sanda*, “Star-Shaped Polymers with Helical Polyacetylene Arms. Comparison of Solution- and Solid-State Properties with Linear Helical Polyacetylenes”, Macromolecules<\/em>, 57<\/strong>, 22, 10824\u201310834 (2024).\"\"<\/a><\/li>\n\n\n\n
  12. Keita Namba, Yuma Sasaki, Yuto Kawamura, Shotaro Yoshida, Yoshiki Hieda, Kazushi Fujimoto, Natsuki Watanabe, Yuichiro Nishizawa, Takayuki Uchihashi
    Daisuke Suzuki*, and, Takuma Kureha*, “Nanoscale Structures of Tough Microparticle-Based Films Investigated by Synchrotron X-Ray Scattering and All-Atom Molecular-Dynamics Simulation”, Langmuir<\/em>, 40<\/strong>, 43, 22614\u201322626 (2024).    \"\"<\/a><\/li>\n\n\n\n
  13. Kazushi Fujimoto*, Hiroaki Ishikawa, Zhiye Tang, and Susumu Okazaki*, “All-atom molecular dynamics study of the impact fracture of glassy polymers. III: Compressive fracture of PC and PMMA”, Polymer<\/em>, 283<\/strong>, 126276 (2023).\"\"<\/a><\/li>\n\n\n\n
  14. Yoshimichi Andoh, Shin-ichi Ichikawa, Tatsuya Sakashita, Kazushi Fujimoto, Noriyuki Yoshii, Tetsuro Nagai, Zhiye Tang, Susumu Okazaki*, “An exa-scale high-performance molecular dynamics simulation program: MODYLAS”, J. Chem. Phys.<\/em>, 158<\/strong>, 194803 (2023).\"\"<\/a><\/li>\n\n\n\n
  15. Kazushi Fujimoto*, \u201cFracture and Toughening Mechanisms of Glassy Polymer at the Molecular Level\u201d, Nihon Reoroji Gakkaishi<\/em>, 50<\/strong>, 37-41 (2022). \"\"<\/a><\/a> [Invited Reveiw]<\/strong><\/li>\n\n\n\n
  16. Tetsuro Nagai, Kazushi Fujimoto, and Susumu Okazaki*, \u201cThree-dimensional free-energy landscape of hydrogen and oxygen molecules in polymer electrolyte membranes: Insight into diffusion paths\u201d, J. Chem. Phys.<\/em>, 156<\/strong>, 044507 (2022). \"\"<\/a><\/a><\/li>\n\n\n\n
  17. Kazushi Fujimoto, <\/strong>Youhei Yamaguchi, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, and Susumu Okazaki*, \u201cAll-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution\u201d, J. Chem. Phys.<\/em>, 155<\/strong>, 145101 (2021). \"\"<\/a><\/a> [J. Chem. Phys. Featured Article]<\/strong><\/li>\n\n\n\n
  18. Kazushi Fujimoto, Tetsuro Nagai, Tsuyoshi Yamaguchi*, \u201cMomentum removal to obtain the position-dependent diffusion constant in constrained molecular dynamics simulation\u201d, J. Comput. Chem.<\/em>, 42<\/strong> (30), 2136-2144 (2021). \"\"<\/a><\/a><\/li>\n\n\n\n
  19. Zhiye Tang, Kazushi Fujimoto, Susumu Okazaki*, \u201cA comparison of the brittle PMMA with the ductile PC on the elasticity and yielding from a molecular dynamics perspective\u201d, Polymer<\/em> 226<\/strong>, 123809 (2021). \"\"<\/a><\/a><\/li>\n\n\n\n
  20. Tetsuro Nagai, Syuhei Tsurumaki, Ryo Urano, Kazushi Fujimoto, Wataru Shinoda, Susumu Okazaki*. \u201cPosition-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement.\u201d J. Chem. Theory Comput<\/em>., 16<\/strong><\/em> (12), 7239\u20137254 (2020).\"\"<\/a><\/a><\/li>\n\n\n\n
  21. Zhiye Tang, Kazushi Fujimoto, Susumu Okazaki*, \u201cAll-atom molecular dynamics study of impact fracture of glassy polymers. II: Microscopic origins of stresses in elasticity, yielding, and strain hardening\u201d, Polymer<\/em>, 207<\/strong> (20), 12298 (2020) \"\"<\/a><\/a><\/li>\n\n\n\n
  22. Kazushi Fujimoto, Motohiro Fukai, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki*, \u201cFree energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation\u201d, Pure<\/em>. Appl<\/em>. Chem<\/em>., 92<\/strong> (10), 1585-1594 (2020). \"\"<\/a><\/a><\/li>\n\n\n\n
  23. Kosuke Takeda, Kazushi Fujimoto, Noriyuki Yoshii, Susumu Okazaki*, \u201cMolecular dynamics study of solubilization of cyclohexane, benzene, and phenol into mixed micelles composed of sodium dodecyl sulfate and octaethylene glycol monododecyl ether\u201d, J. Comput. Chem.,<\/em> 40<\/strong>, 2722-2729 (2019) <\/strong>\"\"<\/a><\/a><\/li>\n\n\n\n
  24. Kazushi Fujimoto, Rajdeep Singh Payal, Tomonori Hattori, Wataru Shinoda, Masayuki Nakagaki, Sigeyoshi Sakaki*, Susumu Okazaki*, \u201cDevelopment of dissociative force field for all\u2010atomistic molecular dynamics calculation of fracture of polymers\u201d, J. Comput. Chem. <\/em>40<\/strong>, 2571\u20132576 (2019). \"\"<\/a><\/a><\/li>\n\n\n\n
  25. Kazushi Fujimoto, Zhiye Tang, Wataru Shinoda, Susumu Okazaki*, \u201cAll-atom molecular dynamics study of impact fracture of glassy polymers. I: Molecular mechanism of brittleness of PMMA and ductility of PC\u201d, Polymer<\/em>, 178 <\/strong>(12), 121570 (2019). \"\"<\/a><\/a><\/li>\n\n\n\n
  26. Yusuke Yasuda, Yuta Hidaka, Koichi Mayumi*, Takeshi Yamada, Kazushi Fujimoto, Susumu Okazaki, Hideaki Yokoyama, Kohzo Ito*, \u201cMolecular Dynamics of Polyrotaxane in Solution Investigated by Quasi-Elastic Neutron Scattering and Molecular Dynamics Simulation: Sliding Motion of Rings on Polymer\u201d, J. Am. Chem. Soc. <\/em>141<\/strong>, 9655\u22129663 (2019). \"\"<\/a> [Cover]<\/a><\/a><\/li>\n\n\n\n
  27. Rajdeep Singh Payal, Kazushi Fujimoto, Changwoon Jang, Wataru Shinoda, Yuki Takei, Hiroshi Shima, Katsuhiko Tsunoda, Susumu Okazaki*, \u201cMolecular mechanism of material deformation and failure in butadiene rubber: Insight from all-atom molecular dynamics simulation using a bond breaking potential model\u201d, Polymer<\/em>, 170, <\/strong>113-119 (2019). \"\"<\/a><\/a><\/li>\n\n\n\n
  28. Noriyuki Yoshii, Mika Komori, Shinji Kawada, Hiroaki Takabayashi, Kazushi Fujimoto, Susumu Okazaki*, \u201cFree energy of micelle formation for sodium dodecyl sulfate from a dispersed state in solution to complete micelles along its aggregation pathways evaluated by chemical species model combined with molecular dynamics calculations\u201d, Acta Physico-Chimica Sinica<\/em>, 34 <\/strong>(10), 1163\u20131170 (2018).<\/li>\n\n\n\n
  29. Shinji Kawada, Kazushi Fujimoto, Noriyuki Yoshii, Susumu Okazaki*, \u201cMolecular dynamics study of the potential of mean force of SDS aggregates\u201d, J. Chem. Phys.<\/em>, 147<\/strong>, 084903 (2017).<\/li>\n\n\n\n
  30. Kazushi Fujimoto, Yousuke Kubo, Shinji Kawada, Noriyuki Yoshii, Susumu Okazaki*, \u201cMolecular dynamics study of the aggregation rate for zwitterionic dodecyldimethylamine oxide and cationic dodecyltrimethylammonium chloride micelles\u201d, Mol. Simul<\/em>., 43<\/strong>, 1331-1337 (2017). \"\"<\/a><\/a><\/li>\n\n\n\n
  31. Noriyuki Yoshii, Yuki Nimura, Kazushi Fujimoto, and Susumu Okazaki* \u201cSpherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study\u201d, J. Phys. Chem.<\/em>, 47<\/strong>, 034906-1-10 (2017).\"\"<\/a><\/a><\/li>\n\n\n\n
  32. Go Hamasaka, Tsubasa Muto, Yoshimichi Andoh, Kazushi Fujimoto, Kenichi Kato, Masaki Tanaka, Susumu Okazaki and Yasuhiro Uozumi*, \u201cDetailed Structural Analysis of a Self-Assembled Vesicular Amphiphilic NCN-Pincer Palladium Complex by Wide-Angle X-Ray Scattering and Molecular Dynamics Calculations\u201d, Chemistry \u2013 A European Journal<\/em>, 23<\/strong>, 1291-1298 (2017). \"\"<\/a><\/a><\/li>\n\n\n\n
  33. Osamu Ichikawa, Kazushi Fujimoto, Atsushi Yamada, Susumu Okazaki, Kazuto Yamazaki*, \u201cG-Protein\/\u03b2-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation\u201d, Plos One, <\/em>0155816 (2016).\"\"<\/a><\/li>\n\n\n\n
  34. Lin Wang, Kazushi Fujimoto, Noriyuki Yoshii, and Susumu Okazaki*, \u201cA molecular dynamics study of the breathing and deforming modes of the spherical ionic SDS and nonionic C12E8 micelles\u201d, J. Chem. Phys.<\/em>, 144<\/strong>, 034903-1-7 (2016). \"\"<\/a><\/a><\/li>\n\n\n\n
  35. Masahiro Kitabata, Kazushi Fujimoto, Noriyuki Yoshii, and Susumu Okazaki*, \u201cA molecular dynamics study of local pressures and interfacial tensions of SDS micelles and dodecane droplets in water\u201d, J. Chem. Phys.<\/em> 144<\/strong>, 224701 1-9 (2016). \"\"<\/a><\/a><\/li>\n\n\n\n
  36. Shinji Kawada, Mika Komori, Kazushi Fujimoto, Noriyuki Yoshii, and Susumu Okazaki*, \u201cMolecular dynamics study of the formation mechanisms of ionic SDS and nonionic C12E8 micelles and n-dodecane droplets\u201d, Chem. Phys. Lett.<\/em>, 217<\/strong>, 36-40 (2016). \"\"<\/a><\/a><\/li>\n\n\n\n
  37. Noriyuki Yoshii, Kazushi Fujimoto, and Susumu Okazaki*, \u201cMolecular dynamics study of the structure of anionic SDS, cationic DTAC, zwitterionic DDAO, and nonionic C12E8 spherical micelles in solution\u201d, J. Mol. Liq.<\/em>, 646<\/strong>, 99-102 (2015).  \"\"<\/a><\/a><\/li>\n\n\n\n
  38. Noriyuki Yoshii, Yoshimichi Andoh, Kazushi Fujimoto, Hidekazu Kojima, Atsushi Yamada, and Susumu Okazaki*, \u201cMODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program\u201d, Int. J. Quantum Chem.<\/em>, 115<\/strong>, 342-348 (2015). \"\"<\/a><\/a><\/li>\n\n\n\n
  39. Ryouichi Wada, Kazushi Fujimoto, and Minoru Kato*, \u201cWhy Is Poly(oxyethylene) Soluble in Water? Evidence from the Thermodynamic Profile of the Conformational Equilibria of 1,2-Dimethoxyethane and Dimethoxymethane Revealed by Raman Spectroscopy.\u201d, J. Phys. Chem., B<\/em>, 118<\/strong>, 12223-12231 (2014). \"\"<\/a><\/a><\/li>\n\n\n\n
  40. Y. Andoh, N. Yoshii, A. Yamada; K. Fujimoto, H. Kojima, K. Mizutani, A. Nakagawa, A. Nomoto, and S. Okazaki*, \u201cAll-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution\u201d, J. Chem. Phys.<\/em>, 141<\/strong>, 16501 1-11(2014). \"\"<\/a><\/a><\/li>\n\n\n\n
  41. Yoshimichi Andoh, Noriyuki Yoshii, Kazushi Fujimoto, Keisuke Mizutani, Hidekazu Kojima, Atsushi Yamada, Susumu Okazaki*, Kazutomo Kawaguchi, Hidemi Nagao, Kensuke Iwahashi, Fumiyasu Mizutani, Kazuo Minami, Shin-ichi Ichikawa, Hidemi Komatsu, Shigeru Ishizuki, Yasuhiro Takeda, and Masao Fukushima, \u201cMODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithm\u201d, J. Chem. Theory Comput.<\/em>, 9<\/strong>, 3201-3209 (2013). \"\"<\/a><\/a><\/li>\n\n\n\n
  42. K. Fujimoto, N. Yoshii, and S. Okazaki*, \u201cMolecular dynamics study of free energy of transfer of alcohol and amine from water phase to the micelle by thermodynamic integration method\u201d, J. Chem. Phys.<\/em>, 137<\/strong>, 094902 1-6(2012)\"\"<\/a>. <\/a><\/li>\n\n\n\n
  43. K. Fujimoto, N. Yoshii, and S. Okazaki*, \u201cEnthalpy and Entropy of transfer of alkanes from water phase to the micelle core\u201d, Mol. Simul.<\/em>, 38<\/strong>, 342-345 (2012). \"\"<\/a><\/a><\/li>\n\n\n\n
  44. K. Fujimoto, N. Yoshii, and S. Okazaki*, \u201cFree energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations\u201d, J. Chem. Phys.<\/em>, 136<\/strong>, 014511, 1-9 (2012). \"\"<\/a><\/a><\/li>\n\n\n\n
  45. K. Fujimoto, N. Yoshii, and S. Okazaki*, \u201cMolecular dynamics study of solubilization of immiscible solutes by a micelle: Free energy of transfer of alkanes from water to the micelle core by thermodynamic integration method\u201d, J. Chem. Phys<\/em>, 133<\/strong>, 074511 1-6 (2010). \"\"<\/a><\/a><\/li>\n<\/ol>\n\n\n\n
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      1. \u85e4\u672c \u548c\u58eb\uff0e\u300c\u7b2c12\u7ae0\u3000\u9ad8\u5206\u5b50\u300d\uff0c\u677e\u6797 \u4f38\u5e78 \u7de8\u300e\u5206\u5b50\u52d5\u529b\u5b66\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u57fa\u790e\u7406\u8ad6\u300f\uff0c\u8b1b\u8ac7\u793e\uff0c2025\u5e74<\/li>\n\n\n\n
      2. \u85e4\u672c\u548c\u58eb\u3001\u6e6f\u4e4b\u4e5f\u3001\u5ca1\u5d0e\u3000\u9032\u3000\u300c\u7b2c1\u7ae0\u3000\u7b2c1\u7bc0\u3000\u5ef6\u6027\u3068\u8106\u6027\u306e\u5206\u5b50\u8ad6\u7684\u8d77\u6e90\uff0d\u5168\u539f\u5b50\u5206\u5b50\u52d5\u529b\u5b66\u8a08\u7b97\u304b\u3089\u306e\u30a2\u30d7\u30ed\u30fc\u30c1\u300d\u3000\u30dd\u30ea\u30de\u30fc\u306e\u5f37\u976d\u5316\u6280\u8853\u6700\u524d\u7dda\u3000\u7834\u58ca\u6a5f\u69cb\u3001\u5206\u5b50\u7d50\u5408\u5236\u5fa1\u3001\u3057\u306a\u3084\u304b\u30bf\u30d5\u30dd\u30ea\u30de\u30fc\u306e\u958b\u767a<\/strong>\u3000\u682a\u5f0f\u4f1a\u793e\u30a8\u30cc\u30fb\u30c6\u30a3\u30fc\u30fb\u30a8\u30b9\u3000(2020)<\/li>\n<\/ol>\n<\/div>\n\n\n\n
        <\/div>\n\n\n\n
        <\/div>\n\n\n\n
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