{"id":37,"date":"2023-06-12T15:49:08","date_gmt":"2023-06-12T06:49:08","guid":{"rendered":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/?page_id=37"},"modified":"2026-04-09T14:41:30","modified_gmt":"2026-04-09T05:41:30","slug":"publication","status":"publish","type":"page","link":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/publication\/","title":{"rendered":"Publication"},"content":{"rendered":"\n
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Papers<\/a><\/p>\n<\/div>\n\n\n\n

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Papers<\/h2>\n\n\n\n

* Corresponding author.<\/p>\n\n\n\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>.<\/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><\/li>\n\n\n\n
  4. Yuki Kitamura, Yusuke Yasuda, Junya Metoki, Shogo Tsujino, Kazuma Yoshimura, Takahide Watanabe, and Kazushi Fujimoto*, \u201cLocally Ordered Junctions Govern Diffusion in Triglycerides: Insights from Molecular Dynamics Simulations\u201d, 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><\/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] [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] [Article on Request]<\/a><\/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<\/strong>, Noriyuki Yoshii, Tetsuro Nagai, Zhiye Tang, Susumu Okazaki, \u201cAn exa-scale high-performance molecular dynamics simulation program: MODYLAS\u201d, 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, S. \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, <\/strong>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><\/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).<\/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<\/div>\n<\/div>\n\n\n\n

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    Papers Papers * Corresponding author.<\/p>\n","protected":false},"author":297,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":""},"class_list":["post-37","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/wp-json\/wp\/v2\/pages\/37","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/wp-json\/wp\/v2\/users\/297"}],"replies":[{"embeddable":true,"href":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/wp-json\/wp\/v2\/comments?post=37"}],"version-history":[{"count":32,"href":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/wp-json\/wp\/v2\/pages\/37\/revisions"}],"predecessor-version":[{"id":268,"href":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/wp-json\/wp\/v2\/pages\/37\/revisions\/268"}],"wp:attachment":[{"href":"https:\/\/wps.itc.kansai-u.ac.jp\/tcc-en\/wp-json\/wp\/v2\/media?parent=37"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}