研究業績

Papers
総説・解説
書籍

Papers

  1. 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, 283, 126276 (2023).
  2. 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., 158, 194803 (2023).
  3. Kazushi Fujimoto, “Fracture and Toughening Mechanisms of Glassy Polymer at the Molecular Level”, Nihon Reoroji Gakkaishi, 50, 37-41 (2022).  [Invited Reveiw]
  4. Tetsuro Nagai, Kazushi Fujimoto, and Susumu Okazaki, “Three-dimensional free-energy landscape of hydrogen and oxygen molecules in polymer electrolyte membranes: Insight into diffusion paths”, J. Chem. Phys., 156, 044507 (2022). 
  5. Kazushi Fujimoto, Youhei Yamaguchi, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, and Susumu Okazaki, “All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution”, J. Chem. Phys., 155, 145101 (2021).  [J. Chem. Phys. Featured Article]
  6. Kazushi Fujimoto, Tetsuro Nagai, Tsuyoshi Yamaguchi, “Momentum removal to obtain the position-dependent diffusion constant in constrained molecular dynamics simulation”, J. Comput. Chem., 42 (30), 2136-2144 (2021). 
  7. Zhiye Tang, Kazushi Fujimoto, Susumu Okazaki, “A comparison of the brittle PMMA with the ductile PC on the elasticity and yielding from a molecular dynamics perspective”, Polymer 226, 123809 (2021). 
  8. Tetsuro Nagai, Syuhei Tsurumaki, Ryo Urano, Kazushi Fujimoto, Wataru Shinoda, Susumu Okazaki, S. “Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement.” J Chem Theory Comput, 16 (12), 7239–7254 (2020).
  9. Zhiye Tang, Kazushi Fujimoto, Susumu Okazaki, “All-atom molecular dynamics study of impact fracture of glassy polymers. II: Microscopic origins of stresses in elasticity, yielding, and strain hardening”, Polymer, 207 (20), 12298 (2020) 
  10. Kazushi Fujimoto, Motohiro Fukai, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki, “Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation”, Pure. Appl. Chem., 92 (10), 1585-1594 (2020). 
  11. Kosuke Takeda, Kazushi Fujimoto, Noriyuki Yoshii, Susumu Okazaki, “Molecular dynamics study of solubilization of cyclohexane, benzene, and phenol into mixed micelles composed of sodium dodecyl sulfate and octaethylene glycol monododecyl ether”, J. Comput. Chem., 40, 2722-2729 (2019) 
  12. Kazushi Fujimoto, Rajdeep Singh Payal, Tomonori Hattori, Wataru Shinoda, Masayuki Nakagaki, Sigeyoshi Sakaki, Susumu Okazaki, “Development of dissociative force field for all‐atomistic molecular dynamics calculation of fracture of polymers”, J. Comput. Chem. 40, 2571–2576 (2019). 
  13. Kazushi Fujimoto, Zhiye Tang, Wataru Shinoda, Susumu Okazaki, “All-atom molecular dynamics study of impact fracture of glassy polymers. I: Molecular mechanism of brittleness of PMMA and ductility of PC”, Polymer, 178 (12), 121570 (2019). 
  14. Yusuke Yasuda, Yuta Hidaka, Koichi Mayumi, Takeshi Yamada, Kazushi Fujimoto, Susumu Okazaki, Hideaki Yokoyama, Kohzo Ito, “Molecular Dynamics of Polyrotaxane in Solution Investigated by Quasi-Elastic Neutron Scattering and Molecular Dynamics Simulation: Sliding Motion of Rings on Polymer”, J. Am. Chem. Soc. 141, 9655−9663 (2019). 
  15. Rajdeep Singh Payal, Kazushi Fujimoto, Changwoon Jang, Wataru Shinoda, Yuki Takei, Hiroshi Shima, Katsuhiko Tsunoda, Susumu Okazaki, “Molecular mechanism of material deformation and failure in butadiene rubber: Insight from all-atom molecular dynamics simulation using a bond breaking potential model”, Polymer, 170, 113-119 (2019). 
  16. Noriyuki Yoshii, Mika Komori, Shinji Kawada, Hiroaki Takabayashi, Kazushi Fujimoto, Susumu Okazaki, “Free 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”, Acta Physico-Chimica Sinica, 34 (10), 1163–1170 (2018).
  17. Shinji Kawada, Kazushi Fujimoto, Noriyuki Yoshii, Susumu Okazaki, “Molecular dynamics study of the potential of mean force of SDS aggregates”, J. Chem. Phys., 147, 084903 (2017).
  18. Kazushi Fujimoto, Yousuke Kubo, Shinji Kawada, Noriyuki Yoshii, Susumu Okazaki, “Molecular dynamics study of the aggregation rate for zwitterionic dodecyldimethylamine oxide and cationic dodecyltrimethylammonium chloride micelles”, Molecular Simulation, 43, 1331-1337 (2017). 
  19. Noriyuki Yoshii, Yuki Nimura, Kazushi Fujimoto, and Susumu Okazaki “Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study”, J. Phys. Chem., 47, 034906-1-10 (2017).
  20. Go Hamasaka, Tsubasa Muto, Yoshimichi Andoh, Kazushi Fujimoto, Kenichi Kato, Masaki Tanaka, Susumu Okazaki and Yasuhiro Uozumi, “Detailed Structural Analysis of a Self-Assembled Vesicular Amphiphilic NCN-Pincer Palladium Complex by Wide-Angle X-Ray Scattering and Molecular Dynamics Calculations”, Chemistry – A European Journal, 23, 1291-1298 (2017). 
  21. Osamu Ichikawa, Kazushi Fujimoto, Atsushi Yamada, Susumu Okazaki, Kazuto Yamazaki, “G-Protein/β-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation”, Plos One, 0155816 (2016).
  22. Lin Wang, Kazushi Fujimoto, Noriyuki Yoshii, and Susumu Okazaki, “A molecular dynamics study of the breathing and deforming modes of the spherical ionic SDS and nonionic C12E8 micelles”, J. Chem. Phys., 144, 034903-1-7 (2016). 
  23. Masahiro Kitabata, Kazushi Fujimoto, Noriyuki Yoshii, and Susumu Okazaki, “A molecular dynamics study of local pressures and interfacial tensions of SDS micelles and dodecane droplets in water”, J. Chem. Phys. 144, 224701 1-9 (2016). 
  24. Shinji Kawada, Mika Komori, Kazushi Fujimoto, Noriyuki Yoshii, and Susumu Okazaki, “Molecular dynamics study of the formation mechanisms of ionic SDS and nonionic C12E8 micelles and n-dodecane droplets”, Chem. Phys. Lett., 217, 36-40 (2016). 
  25. Noriyuki Yoshii, Kazushi Fujimoto, and Susumu Okazaki, “Molecular dynamics study of the structure of anionic SDS, cationic DTAC, zwitterionic DDAO, and nonionic C12E8 spherical micelles in solution”, J. Mol. Liq., 646, 99-102 (2015).  
  26. Noriyuki Yoshii, Yoshimichi Andoh, Kazushi Fujimoto, Hidekazu Kojima, Atsushi Yamada, and Susumu Okazaki, “MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program”, Int. J. Quantum Chem., 115, 342-348 (2015). 
  27. Ryouichi Wada, Kazushi Fujimoto, and Minoru Kato, “Why 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.”, J. Phys. Chem., B, 118, 12223-12231 (2014). 
  28. Y Andoh, N Yoshii, A Yamada; K Fujimoto, H Kojima, K Mizutani, A Nakagawa, A Nomoto, and S Okazaki, “All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution”, J. Chem. Phys., 141, 16501 1-11(2014). 
  29. 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, “MODYLAS: 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”, J. Chem. Theory Comput., 9, 3201-3209 (2013). 
  30. K. Fujimoto, N. Yoshii, and S. Okazaki, “Molecular dynamics study of free energy of transfer of alcohol and amine from water phase to the micelle by thermodynamic integration method”, J. Chem. Phys., 137, 094902 1-6(2012). 
  31. K. Fujimoto, N. Yoshii, and S. Okazaki, “Enthalpy and Entropy of transfer of alkanes from water phase to the micelle core”, Mol. Simul., 38, 342-345 (2012). 
  32. K. Fujimoto, N. Yoshii, and S. Okazaki, “Free 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”, J. Chem. Phys., 136, 014511, 1-9 (2012). 
  33. K. Fujimoto, N. Yoshii, and S. Okazaki, “Molecular 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”, J. Chem. Phys, 133, 074511 1-6 (2010). 

総説・解説

  1. 藤本和士「全原子分子動力学計算法による高分子破壊シミュレーション」2020年10月 アンサンブル(22巻4号289-293頁)
  2. 藤本和士「全原子分子動力学計算によるガラス状高分子衝撃破壊の分子論」2019 年12月 日本化学会情報化学部会誌 (37 巻 4 号 99-103頁) 
  3. 藤本和士、岡崎 進 「生体高分子－タンパク質－の分子動力学シミュレーション」2017年9月 高分子（66巻10月号552-554頁）
  4. 藤本和士 「GPUマシンでシミュレーション タンパク質のフォールディング計算がより手軽に」2015年6月 化学（Vol.70 No.6 2015　６６−６７頁）
  5. 藤本和士「ミセル水溶液中の溶質の可溶化に関する計算機シミュレーション」2013年7月 熱測定(40巻3号114-119頁)
  6. 藤本和士「分子動力学法に基づいた自由エネルギー計算によるSDSミセル可溶化の理論的研究」 2013年1月 アンサンブル(15巻1号57-60頁)

書籍

  1. 藤本和士、湯之也、岡崎　進　「第1章　第1節　延性と脆性の分子論的起源－全原子分子動力学計算からのアプローチ」　ポリマーの強靭化技術最前線　破壊機構、分子結合制御、しなやかタフポリマーの開発　株式会社エヌ・ティー・エス　(2020)