光武 亜代理（ミツタケ　アヨリ）

光武 亜代理
学位
理学博士
所属・職位
慶應義塾大学 理工学部 物理学科
専任講師
URL
http://www.phys.keio.ac.jp/faculty/ayori/syousai/
研究分野
生物物理、計算物理、化学物理

論文・プロシーディングス･総説（査読有り）

  1. Naoyuki Karasawa, Ayori Mitsutake, Hiroshi Takano Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation Phys Rev E. 2017 Dec;96(6-1):062408. doi: 10.1103/PhysRevE.96.062408. Epub 2017 Dec 15
  2. Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenji Mochizuki, Kenichiro Koga Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy J. Compt. Chem. Vol 39, Issue 4, 202-217 (2018)
  3. Yutaka Maruyama, Ayori Mitsukake Stability of Unfolded and Folded Protein Structures Using a 3D-RISM with the RMDFT J. Phys. Chem. B, 121 (42), 9881-9885 (2017)
  4. Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, and Kenichiro Koga A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution J. Chem. Phys. 144, 224104 (2016)
  5. Mitsutake A, Takano H.:Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature. J Chem Phys. 2015 Sep 28;143(12):124111. doi: 10.1063/1.4931813
  6. Sumi T, Mitsutake A, Maruyama Y.:A solvation-free-energy functional: a reference-modified density functional formulation. J Comput Chem. 2015 Jul 5;36(18):1359-69. doi: 10.1002/jcc.23942. Epub 2015 May 31
  7. Ayori Mitsutake, Hiroshi Takano「生体系のシミュレーションのサンプリング手法及び解析方法の開発」日本物理学会学会誌、70(3), 194 (2015)
  8. Kaneko T, Bai J, Yasuoka K, Mitsutake A, Zeng XC. Liquid-solid and solid-solid phase transition of monolayer water: high-density rhombic monolayer ice. J Chem Phys. 2014 May 14;140(18):184507. doi: 10.1063/1.4874696.
  9. 光武亜代理、学術賞受賞寄稿「多次元焼き戻し法の開発及び緩和モード解析とWHAM法の一般化による構造解析法の開発」分子シミュレーション研究会会誌"アンサンブル" 16(1)1(2014)
  10. T. Kaneko, J. Bai, K. Yasuoka, A. Mitsutake, and X.C. Zeng, A new computational apporach to determine liquid-solid phase equilibria of water confined to slit nanopores, J. Chem. Theory Comput., 9, 3299-3310 (2013).
  11. T. Nagai, A. Mitsutake, and H. Takano, Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of Human Lysozyme, J. Phys. Soc. Jpn., 82, 023803 (2013).
  12. A. Mitsutake, Effective sampling algorithms and analysis method for biomolecular simulations, AIP Conference Proceedings Volume 1518: 4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku, edited by M. Tokuyama and I. Oppenheim 598-601 (2013) .
  13. T. Kaneko, A. Mitsutake, and K. Yasuoka, Multibaric-multithermal ensemble study of liquid-solid phase transition in Lennard-Jones particles, J. Phys. Soc. Jpn, 81, SA014 (2012).
  14. T. Kaneko, T. Akiyama, K. Yasuoka, A. Mitsutake, and X.C. Zeng, Size dependent phase changes in water clusters, J. Chem. Theo. and Comput.7, 3083-3087 (2011).
  15. A. Mitsutake, H. Iijima, and H. Takano, Relaxation mode analysis of a peptide system, J. Chem. Phys.135, 164102 (2011). (Vir. J. Bio. Phys. Res. 22(9) Protein Conformational Dynamics/Folding に掲載）
  16. T. Kaneko, K. Yasuoka, A. Mitsutake, and X.C. Zeng, Multicanonical molecular dynamics simulation study of the liquid-solid and solid-solid transitions in Lennard-Jones clusters, Proc. of the 8th ASME/JSME thermal Enginnering Joint Conference, T30089 (Hawai, March, 2011).
  17. A. Mitsutake, Y. Mori, and Y. Okamoto, Multi-dimensional multicanonical algorithm, simulated tempering, replica-exchange method, and all that, Physics Procedia/Recent Developments in Computer Simulation Studies in Condensed Matter Physics, 4 (2), 89-105 (2010).
  18. A. Mitsutake, Simulated-tempering replica-exchange method for the multidimensional version, J. Chem. Phys. 131, 094105 (2009). (Vir. J. Bio. Phys. Res. 18(6) Quantum Mechanical Dynamics に掲載）
  19. A. Mitsutake and Y. Okamoto, Multidimensional generalized-ensemble algorithms for complex systems, J. Chem. Phys. 130, 214105 (2009).
  20. A. Mitsutake and Y. Okamoto, From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering, Phys. Rev. E 79, 047701 (2009). (Vir. J. Bio. Phys. Res. 17(8) Statistical and Nonlinear Physics に掲載）
  21. A. Mitsutake, M. Kinoshita, F. Hirata, Y. Okamoto, Combination of generalized-ensemble algorithms and one-dimensional reference interaction site model theory, Condensed Matter Physics, 10(4), 495-508 (2007).
  22. A. Mitsutake, Generalized-ensemble simulations of biomolecular system, Biophysical J. 88 (1) , 513A-513A Part 2 Suppl.(2005).
  23. A. Mitsutake, Y. Sugita, and Y. Okamoto, Generalized-ensemble Monte Carlo algorithms for simulations of proteins, AIP Conference Proceedings Volume 708: Slow Dynamics in Complex Systems, edited by M. Tokuyama and I. Oppenheim (American Institute of Physics, Melville, 2004) pp. 350-351.
  24. A. Mitsutake, M. Kinoshita, Y. Okamoto, and F. Hirata, Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution, J. Phys. Chem. B 108, 19002-19012 (2004).
  25. A. Mitsutake and Y. Okamoto, Replica-exchange extensions of simulated tempering method, J. Chem. Phys. 121, 2491-2504 (2004). (Vir. J. Bio. Phys. Res. 8(3) Protein Conformational Dynamics/Folding に掲載）
  26. G. La Penna, A. Mitsutake, M. Masuya, and Y. Okamoto, Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory, Chem. Phys. Lett. 380, 609-619 (2003).
  27. A. Mitsutake, Y. Sugita, and Y. Okamoto, Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of small peptides. II. Application to a more complex system, J. Chem. Phys. 118, 6676-6688 (2003). (Vir. J. Bio. Phys. Res. 5(7) Fundamental Polymer Statics/Dynamics に掲載）
  28. A. Mitsutake, Y. Sugita, and Y. Okamoto, Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of small peptides. I. Formulation and benchmark test, J. Chem. Phys. 118, 6664-6675 (2003). (Vir. J. Bio. Phys. Res. 5(7) Fundamental Polymer Statics/Dynamics に掲載）
  29. T. Nakazawa, S. Ban, Y. Okuda, M. Masuya, A. Mitsutake, and Y. Okamoto, A pH-dependent variation in α-helix structure of the S-peptide of ribonuclease studied by Monte Carlo simulated annealing, Biopolymers 63, 273-279 (2002).
  30. T. Nagasima, Y. Sugita, A. Mitsutake, and Y. Okamoto, Generalized-ensemble simulations of spin systems and protein systems, Comput. Phys. Commun. 146, 69-76 (2002).
  31. A. Mitsutake, Y. Sugita, and Y. Okamoto, Generalized-ensemble algorithms for molecular simulations of biopolymers, Biopolymers (Peptide Science) 60, 96-123 (2001).
  32. A. Mitsutake and Y. Okamoto, Replica-exchange simulated tempering method for simulations of frustrated systems, Chem. Phys. Lett. 332, 131-138 (2000).
  33. A. Mitsutake, M. Kinoshita, Y. Okamoto, and F. Hirata, Multicanonical algorithm combined with the RISM theory for simulating peptides in aqueous solution, Chem. Phys. Lett. 329, 295-303 (2000) .
  34. A. Mitsutake and Y. Okamoto, Helix-coil transitions of amino-acid homo-oligomers in aqueous solution studied by multicanonical simulations, J. Chem. Phys. 112, 10638-10647 (2000). (Vir. J. Bio. Phys. Res. 1(6) Protein Conformational Dunamics/Folding に掲載）
  35. A. Mitsutake and Y. Okamoto, α-Helix propensities of homo-oligomers in aqueous solution studied by multicanonical algorithm, Chem. Phys. Lett. 309, 95-100 (1999).
  36. A. Mitsutake, M. Irisa, Y. Okamoto, and F. Hirata, Classi cation of low-energy conformations of Met-enkephalin in the gas phase and in a model solvent based on the extended scaled particle theory, and F. Hirata, Bull. Chem. Soc. Jpn. 72, 1717-1729 (1999).
  37. A. Mitsutake, U.H.E. Hansmann, and Y. Okamoto, Temperature dependence of distributions of conformations of a small peptide, J. Mol. Graph. Model. 16, 226-238; 262-263 (1998).
  38. A. Mitsutake, T. Iitaka, and Y. Okamoto, A method for calculating the eigenvalues of large Hermitian matrices by second-order recursion formulae, Comput. Phys. Commun. 96, 217-231 (1996)
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