Mt. Fuji's web site (Japanese/English)

  • メカノバイオリジーに向けた細胞ダイナミクスのモデル化・シミュレーション
  • 生体分子の構造変化経路サンプリング
  • 分子の量子ダイナミクス計算


最近のものは google citationresearchmapを参照。

Molecular mechanism of inhibition for xanthine oxidoreductase (XOR)

  1. H. Kikuchi, H. Fujisaki, T. Furuta, K. Okamoto, S. Leimkuhler, and T. Nishino,
    Different inhibitory potency of febuxostat towards mammalian and bacterial xanthine oxidoreductases: insight from molecular dynamics,
    Scientific Reports, 2:331: DOI: 10.1038/srep00331 (2012) (8 pages).

String methods and beyond to calculate the reaction coordinates in biomolecular systems

  1. H. Fujisaki, M. Shiga, and A. Kidera,
    OnsagerMachlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways,
    J. Chem. Phys. 132, 134101 (2010) (8 pages); arXiv:1003.0971.

  2. Y. Matsunaga, H. Fujisaki, T. Terada, T. Furuta, K. Moritsugu, and A. Kidera,
    Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase,
    PLoS Comput. Biol. 8, e1002555 (2012) (12 pages).

  3. M. Shiga and H. Fujisaki,
    A quantum generalization of intrinsic reaction coordinate using path integral centroid coordinate,
    J. Chem. Phys. 136, 184103 (2012) (11 pages).

  4. H. Fujisaki, M. Shiga, K. Moritsugu, and A. Kidera,
    Multiscale enhanced path sampling based on the Onsager-Machlup action: Application to a model polymer,
    J. Chem. Phys. 139, 054117 (2013) (9 pages).

Vibrational energy relaxation in protein dynamics

  1. H. Fujisaki and J.E. Straub,
    Vibrational energy relaxation in proteins,
    PNAS 102, 6726-6731 (2005); e-print q-bio.BM/0412048.

  2. H. Fujisaki, Y. Zhang, and J.E. Straub,
    Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins,
    J. Chem. Phys. 124, 144910 (2006) (11 pages); e-print arXiv:q-bio/0601034.

  3. M. Cremeens, H. Fujisaki, Y. Zhang, J. Zimmermann, L.B. Sagle, S. Matsuda, P.E. Dawson, J.E. Straub, and F.E.Romesberg,
    Efforts Toward Developing Direct Probes of Protein Dynamics,
    J. Am. Chem. Soc. 128, 6028-6029 (2006).

  4. Y. Zhang, H. Fujisaki, and J.E. Straub,
    Molecular Dynamics Study on the Solvent Dependent Heme Cooling Following Ligand Photolysis in Carbonmonoxy Myoglobin,
    J. Phys. Chem. B 111, 3243-3250 (2007).

  5. H. Fujisaki, K. Yagi, K. Hirao, and J.E. Straub,
    Quantum dynamics of N-methylacetamide studied by vibrational configuration interaction method,
    Chem. Phys. Lett. 443, 6-11 (2007); e-print q-bio arXiv:0706.1905.

  6. H. Fujisaki and J.E. Straub,
    Vibrational energy relaxation (VER) of isotopically labelled amide I modes in cytochrome c: Theoretical investigation of VER rates and pathways,
    J. Phys. Chem. B 111, 12017-12023 (2007); e-print q-bio arXiv:0707.2300.

  7. Hiroshi Fujisaki, Kiyoshi Yagi, John E. Straub, and Gerhard Stock,
    Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces,
    Int. J. Quant. Chem. 109 (2009) 2047-2057; arXiv:0807.1368.

  8. Hiroshi Fujisaki and Gerhard Stock,
    Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment,
    J. Chem. Phys. 129, 134110 (2008) (10 pages) (Top 20 Most downloaded articles in Oct. 2008); e-print arXiv:0807.1369.

  9. Yong Zhang, Hiroshi Fujisaki, and John E. Straub,
    Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model,
    J. Chem. Phys. 130, 025102 (2009) (10 pages).

  10. Yong Zhang, Hiroshi Fujisaki, and John E. Straub,
    Mode Specific Vibrational Energy Relaxation of Amide I and II Modes in N-Methylacetamide/Water Clusters: The Intra- and Inter-Molecular Energy Transfer Mechanisms,
    J. Phys. Chem. A. 113 (2009) 3051-3060.

  11. Hiroshi Fujisaki, Kiyoshi Yagi, Hiroto Kikuchi, Toshiya Takami, and Gerhard Stock,
    Vibrational quantum dynamics using ab initio tier model: Application to acetylbenzonitrile,
    in preparation.

  12. Hiroshi Fujisaki, Kiyoshi Yagi, Yong Zhang, and John E. Straub,
    Molecular tier model calculation of energy transfer: Application to porphyrin and its derivatives,
    in preparation.

Controlling molecular dynamics

  1. H. Fujisaki, Y. Teranishi, and H. Nakamura,
    Control of photodissociation branching using the complete reflection phenomenon: Application to HI molecule,
    J. Theor. Comp. Chem. 1, 245 (2002) (9 pages); e-print quant-ph/0211142.
  2. T. Takami and H. Fujisaki,
    Coarse-Grained Picture for Controlling "Complex" Quantum Systems,
    J. Phys. Soc. Jpn. 73, 3215 (2004) (2 pages); e-print nlin.CD/0402003.
  3. T. Takami and H. Fujisaki,
    Analytic approach for controlling quantum states in complex systems,
    Phys. Rev. E 75, 036219 (2007) (10 pages); e-print arXiv:nlin/0701056.
  4. T. Takami and H. Fujisaki,
    Resonant Analytic Fields Applied to Generic Multi-state Systems,
    arXiv:0806.4217; J. Mod. Opt. 56 (2009) 822-830.

Multimode effects in nonadiabatic molecular systems

  1. H. Fujisaki and K. Takatsuka,
    Chaos induced by quantum effect due to breakdown of the Born-Oppenheimer adiabaticity,
    Phys. Rev. E 63, 066221 (2001) (10 pages).

  2. H. Fujisaki and K. Takatsuka,
    Highly excited vibronic eigenfunctions in a multimode nonadiabatic system with Duschinsky rotation,
    J. Chem. Phys. 114, 3497 (2001) (11 pages).

  3. H. Fujisaki,
    Quantum-"classical" correspondence in a nonadiabatic transition system,
    Phys. Rev. E 69, 037201 (2004) (4 pages); e-print quant-ph/0401136.

  4. H. Fujisaki,
    Entanglement induced by nonadiabatic chaos,
    Phys. Rev. A 70, 012313 (2004) (4 pages); e-print quant-ph/0402036.

Quantum chaos and entanglement

  1. A. Tanaka, H. Fujisaki, and T. Miyadera,
    Saturation of the production of quantum entanglement between weakly coupled mapping systems in strongly chaotic region,
    Phys. Rev. E. 66, 045201(R) (2002) (4 pages); e-print quant-ph/0209086.

  2. H. Fujisaki, T. Miyadera, and A. Tanaka,
    Dynamical aspects of quantum entanglement for weakly coupled kicked tops,
    Phys. Rev. E. 67, 066201 (2003) (9 pages); e-print quant-ph/0211110.

  3. H. Fujisaki, A. Tanaka, and T. Miyadera,
    Dynamical aspects of quantum entanglement for coupled mapping systems,
    J. Phys. Soc. Jpn. Suppl. C 72, 111 (2003) (4 pages); e-print quant-ph/0302015.

Quantum optics for semiconductor LEDs

  1. H. Fujisaki and A. Shimizu,
    Quantum Noise in Semiconductor Light-Emitting Devices at a Low-Injection Level,
    J. Phys. Soc. Jpn. 66, 34 (1997) (4 pages).

  2. H. Fujisaki and A. Shimizu,
    Quantum Langevin equations for semiconductor light-emitting devices and the photon statistics at a low-injection level,
    Phys. Rev. A 57, 3074 (1998) (10 pages).

  • 藤崎弘士,
    統計数理 in preparation.
  • 藤崎弘士,
    分子シミュレーション研究会会誌アンサンブル in preparation.
  • 藤崎弘士,
    日本医科大学医学会誌 in press (2013).
  • 藤崎弘士,
    日本医科大学医学会誌 9(2), 135 (2013) (5 pages).
  • 高見利也, 藤崎弘士,
    日本医科大学基礎科学紀要 41, 27-56 (2012).
  • 藤崎弘士, 古田忠臣, 岡本研, 菊地浩人,
    理論生物物理と生化学を組み合わせた薬効研究 -- キサンチン酸化還元酵素と阻害剤フェブキソスタットの結合機序 --,
    日本医科大学医学会誌 8(3), 222 (2012).
  • Hiroshi Fujisaki, Yong Zhang, and John E. Straub,
    Non-Markovian theory of vibrational energy relaxation and its applications to biomolecular systems,
    Adv. Chem. Phys. 145, 1-33 (2011); arXiv:1003.4796.
  • S. Fuchigami, H. Fujisaki, Y. Matsunaga, and A. Kidera,
    Protein Functional Motion: Basic Concepts and Computational Methodologies,
    Adv. Chem. Phys. 145, 35-82 (2011)
  • 藤崎弘士,
    国士舘大学情報科学センター紀要 32, 62-67 (2011).
  • 藤崎弘士,
    日本医科大学基礎科学紀要 40, 83-98 (2011).
  • A. Kidera, K. Moritsugu, Y. Matsunaga, and H. Fujisaki,
    Molecular Dynamics Simulation of Proteins: Two Models of Anharmonic Dynamics,
    in Proteins: Energy, Heat and Signal Flow (Computation in Chemistry),
    edited by D.M. Leitner and J.E. Straub, Taylor and Francis/CRC Press, London (2009).
  • T. Takami and H. Fujisaki,
    Analytic approach for controlling realistic quantum chaos systems,
    arXiv:0707.2624; AIP Conf. Proc. 963, 821-824 (2007).
  • T. Takami, H. Fujisaki, and T. Miyadera,
    Coarse Grained Picture for Controlling Quantum Chaos,
    Adv. Chem. Phys. 130, part A: 435-458 (2005); e-print nlin.CD/0402005.
  • H. Fujisaki, L. Bu, and J.E. Straub,
    Vibrational energy relaxation of a CD stretching mode in cytochrome c,
    Adv. Chem. Phys. 130, part B, 179-203 (2005); e-print q-bio.BM/0403019.
  • H. Fujisaki, L. Bu, and J.E. Straub,
    Probing vibrational energy relaxation in proteins using normal modes,
    in "Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems" edited by Q. Cui and I. Bahar, Chapman and Hall/CRC Press, Boca Raton, Florida (2005); e-print q-bio.BM/0408023.
  • H. Fujisaki, Y. Teranishi, A. Kondorskiy, and H. Nakamura,
    Semiclassical approaches to controlling chemical reaction dynamics,
    e-print quant-ph/0302025.

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