Logo

Japanese Page

Personal Information

Naohito Urakami
Department of Physics and Informatics,
Faculty of Science, Yamaguchi University
1677-1 Yoshida, Yamaguchi, 753-8512, JAPAN
Tel:+81-839-33-5690, Fax:+81-839-33-5273

Research Interest

Molecular simulations, such as molecular dynamics simulation and Monte Carlo simulation, are one of the most powerful tools in order to investigate microscopic state of materials, and are applied to wide variety of research field. The research interests are to study the behaviors of soft matter like polymer chains, surfactant, and liquid crystal. The self-organization and the molecular recognition which are observed in biomolecular systems are the research key words, and are mainly investigated by carrying out the molecular simulations.

My papers and Proceedings

  1. N. Urakami, T. Jimbo, Y. Sakuma, and M. Imai
    Molecular mechanism of vesicle division induced by coupling between lipid geometry and membrane curvatures
    Soft Matter, in print
  2. T. Jimbo, Y. Sakuma, N. Urakami, P. Ziherl,c, and M. Imai
    Role of Inverse-Cone-Shape Lipids in Temperature-Controlled Self-Reproduction of Binary Vesicles
    Biophys. J., 110 (2016) 1551-1562.
  3. N. Urakami, A. Takaki, M. Imai, and T. Yamamoto
    Molecular dynamics simulation for shape change of water-in-oil droplets
    Molecular Simulation, 41 (2015) 986-992.
  4. Y. Oofuji, N. Urakami, M. Imai, and T. Yamamoto
    Dissipative Particle Dynamics Simulation for Vesicle Shape Change
    Proceeding of International Conference on Artificial Life and Robotics (ICAROB) (2014) 308-311.
  5. A. Sakashita, N. Urakami, P. Ziherl, and M. Imai
    Three-dimensional analysis of lipid vesicle transformations
    Soft Matter, 7 (2012) 8569-8581.
  6. 浦上直人，山本隆
    高分子科学と生物物理の計算科学的融合，高分子，60，807-809 (2011).
  7. T. Kurokawa, N. Urakami, K. N. Yaegashi, A. Sakashita, M. Imai and T. Yamamoto
    Molecular dynamics simulation for morphological change of water-in-oil microemulsion droplets induced by addition of polymer chains
    Soft matter, 7 (2011) 7504-7510.
  8. Y. Sakuma, N. Urakami, T. Taniguchi, and M. Imai
    Asymmetric distribution of cone-shaped lipids in a highly curved bilayer revealed by a small angle neutron scattering technique
    J. Phys.: Condens. Matter, 23 (2011) 284104(1-6).
  9. N. Urakami, J. Imada, and T. Yamamoto
    Simulation of Chain Length Recognition Observed in Formation of Inclusion Complex
    Comput. Phys. Comm., 182 (2011) 240-242.
  10. Y. Sakuma,N. Urakami, Y. Ogata, M. Nagao, S. Komura, T. Kawakatsu and M.Imai
    Diffusion of domains on nanometer sized vesicle
    Journal of Physics:Conference Series, 251 (2010) 012036.
  11. 野口威照，浦上直人，今井正幸，山本隆
    余剰面積の違いによるベシクルの形態変化シミュレーション
    高分子論文，67(10), (2010) 605-610.
  12. 浦上直人
    シクロデキストリンの包接化合物形成と分子認識−粗視化モデルを用いたシミュレーション−
    分子シミュレーション研究会会誌「アンサンブル」12(3) (2010) 34-37.
  13. 三根雅生, 浦上直人, 野崎浩二, 山本隆,
    n-アルカン薄膜の構造形成における基板構造の効果
    高分子論文集, 67(3) (2010) 198-202.
  14. N. Urakami, J. Imada, and T. Yamamoto
    Simulation of Pseudopolyrotaxane Formation and Orientailnal Order between Pseudopolyrotaxanes
    J. Chem. Phys., 132 (2010) 054901(1-7).
  15. T. Masui, N. Urakami, and M. Imai
    Nano-meter-sized domain formation in lipid membranes observed by small angle neutron scattering
    Eur. Phys. J. E, 27 (2008) 379-389.
  16. K. Tanaka, K. Ishikawa, K. Nozaki, N. Urakami, and T. Yamamoto
    Structures of Multilayered Thin Films of Long-Chain Molecules: X-ray Scattering Study
    Polymer J., 40 (2008) 1017-1024.
  17. Y. Suganuma, N. Urakami, R. Mawatari, S. Komura, K. N. Yaegashi, and M. Imai
    Lamellar to micelle transition of nonionic surfactant assemblies induced by addition of colloidal particles
    J. Chem. Phys., 129 (2008) 134903(1-10).
  18. Y. Sakuma, N. Urakami, Y. Ogata, M. Nagao, S. Komura, and M. Imai
    Dynamics of Nano-Meter-Sized Domains on a Vesicle
    AIP Conf. Proc., 982 (2008) 717-720.
  19. 浦上直人, 今田絢子, 藤岡千尋, 山本隆,
    シクロデキストリンと高分子鎖の包接化合物形成シミュレーション
    高分子論文集, 64(5) (2007) 280-285.
  20. T. Yamamoto, K. Nozaki, A. Yamaguchi, N. Urakami
    Molecular simulation of crystallization in n-alkane ultrathin films: Effects of film thickness and substrate attraction
    J. Chem. Phys., 127 (2007) 154704(1-10).
  21. T. Masui, M. Imai, and N. Urakami
    Microdomain Formation in Model Biomembranes
    Physica B, 385&386 (2006) 821-823.
  22. K. Nakaya, M. Imai, S. Komura, T. Kawakatsu and N. Urakami
    Polymer-Confinement-Induced Nematic Transition of Microemulsion Droplets
    Europhys. Lett., 71 (2005) 494-500.
  23. T. Yamamoto, N. Orimi, N. Urakami, K. Sawada
    Molecular dynamics modeling of polymer crystallization; from simple polymers to helical ones
    Faraday Discussion, 128 (2005) 75-80.
  24. K. Nakaya, M. Imai, S. Komura, and N. Urakami
    Morphology Transition from Sphere to Rod by Confining the Polymer Chains in a Dilute Microemulsion
    AIP Conf. Proc., 708 (2004) 106-107.
  25. N. Urakami and M. Imai
    Dependence on sphere size of the phase behavior of mixtures of rods and spheres
    J. Chem. Phys., 119 (2003) 2463-2470.
  26. N. Urakami and M. Imai
    The Effect of Sphere Size on the Phase Behaviors in the Rod and Sphere Mixture System
    J. Macromol. Sci. Phys., 42 (2003) 533-543.
  27. M. Imai, N. Urakami, A. Nakamura, R. Takada, R. Oikawa, and Y. Sano
    Polysaccharides Induced Crystallization of Tobacco Mosaic Virus Particles
    Langmuir, 18 (2002) 9918-9923.
  28. M. Okazaki, T. Watanabe, N. Urakami, and T. Yamamoto
    Molecular dynamics simulation of polymer insertion into lipid bilayers
    arXiv:cond-mat/0204546 (2002).
  29. Okajima, T. Kawamura, C. Kongo, Y. Hiwatari, N. Urakami, R. Hayashi, and K. Kato
    Monte Carlo and molecular dynamics studies for the colour rewritable Films
    Cond. Matt. Phys., 4 (2001) 25-35.
  30. N. Urakami, M. Imai, Y. Sano, and M. Takasu
    The effects of chondroitin sulfate on the tobacco mosaic virus configuration
    Prog. Theor. Phys. Supple., 138 (2000) 390-391.
  31. N. Urakami, M. Imai, Y. Sano, and M. Takasu
    The Isotropic-Nematic Transition and the Phase Separation of the TMV particle by Polysaccharide
    J. Chem. Phys., 111 (1999) 2322-2328.
  32. N. Urakami, M. Takasu
    Multicanonical MC Simulation of a Polymer with Stickers - Initial Relaxation and Free Energy Calculations -
    Prog. Theor. Phys. Supple., 126 (1997) 329-332.
  33. N. Urakami, M. Takasu
    Distribution of Gyration Radius of a Model of Ionomer Studied by Multicanonical Monte Carlo Simulation
    Molecular Simulation, 19 (1997) 63-73.
  34. N. Urakami, M. Takasu
    Multicanonical Monte Carlo Simulation of a Polymer with Stickers
    J. Phys. Soc. Jpn., 65 (1996) 2694-2699.
Informatics