Hiroshi Kuratsuji and Ayaka Yoshida, Spinor Representation of Hydrogen Bonds and Dynamics of DNA Morphology, Memoirs of the Research Institute of Science & Engineering, Ritumeikan University 68, 91-100 (2009). Yves-Henri Sanejouand, Empiri…

Akiyuki Ishikawa, Atushi Tanaka, and Akira Shudo, Dynamical Tunneling in Many-Dimensional Chaotic Systems, Phys. Rev. Lett. 104, 224102 (2010).

Akihito, Akishinonomiya Fumihito, Yuji Ikeda, Masahiro Aizawa, Takashi Makino, Yumi Umehara, Yoshiaki Kai, Yuriko Nishimoto, Masami Hasegawa, Tetsuji Nakabo and Takashi Gojobori, Evolution of Pacific Ocean and the Sea of Japan populations …

E. Vanden-Eijnden, Some Recent Techniques for Free Energy Calculations, J. Comp. Chem. 30 (2009) 1737-1747. Elber の milestoning が簡単に理解できるのがいい。

C. Micheletti, G. Bussi, and A. Laio, Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations, J. Chem. Phys. 129, 074105 (2008).

Hiroshi Fujisaki, Motoyuki Shiga, and Akinori Kidera, Onsager–Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways, J. Chem. Phys. 132, 134101 (2010) (8 pages).

W. E, W. Ren, and E. Vanden-Eijnden, A general strategy for designing seamless multiscale methods, J. Comp. Phys. 228, 5437 (2009).

Hiroshi Fujisaki, Yong Zhang, and John E. Straub, Non-Markovian theory of vibrational energy relaxation and its applications to biomolecular systems, arXiv:1003.4796 (to be published in Adv. Chem. Phys.).

P. Eastman, N. Gronbech-Jensen, and S. Doniach, Simulation of protein folding by reaction path annealing, J. Chem. Phys. 114, 3823 (2001).

S. a Beccara, G. Garberoglio, P. Faccioli, and F. Pederiva, Ab initio dynamics of rare thermally activated reactions, J. Chem. Phys. 132, 111102 (2010). 先にやられた。。

D.J. Wales, Discrete path sampling, Mol. Phys. 100, 3285 (2002). まあ、量子論で言ったら、フェルミの黄金則をそのまま計算しているような印象を受けるなあ。

Hiroshi Fujisaki, Motoyuki Shiga, Akinori Kidera, Onsager-Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways, http://arxiv.org/abs/1003.0971

A. Heyden and D.G. Truhlar, Conservative Algorithms for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations, J. Chem. Theo. Comp. 4, 217-221 (2008). Growing string method もやっている人。しかし、自信た…

H. Kagawa, H. Kikuchi, Q. Gao, and T. Ogihara, Molecular Orbital Study of the Interaction between MgATP and the Myosin Motor domain Using the PM6 method, J. Comp. Chem. Jpn. 9 (2010) 37-42.

Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent, Sang-Min Park, Phuong H. Nguyen, and Gerhard Stock, J. Chem. Phys. 131 184503 (2009).

A. Blondel and M. Karplus, New Formulation for Derivatives of Torsion Angles and Improper Torsion Angles in Molecular Mechanics: Elimination of Singularities, J. Comp. Chem. 17 (1996) 1132-1141.

T.F. Miller III and C. Predescu, Sampling diffusive transition paths, J. Chem. Phys. 126, 144102 (2007).

Hanbin Liu, Yemin Shi, Xiaojiang S. Chen, and Arieh Warshel, Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases, PNAS 106 (2009) 7449. Warshel 研もいまは中国人ばかりなのだなあ。

Jordan Pelc, Jiangbin Gong, and Paul Brumer, Chaos and correspondence in classical and quantum Hamiltonian ratchets: A Heisenberg approach, Phys. Rev. E 79, 066207 (2009).

H. Martinez-Seara, T. Rog, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen, and R. Reigada, Effect of Double Bond Position on Lipid Bilayer Properties: Insight through Atomistic Simulations, J. Phys. Chem. B 111, 11162 (2007).

S. Fuchigami, S. Omori, M. Ikeguchi, and A. Kidera, Normal mode analysis of protein dynamics in a non-Eckart frame, preprint.

Changbong Hyeon, Patricia A. Jennings, Joseph A. Adams and Jose N. Onuchic, Ligand-induced global transitions in the catalytic domain of protein kinase A, Proc. Natl. Acad. Sci. USA 106, 3023 (2009).

M. Gruebele and P.G. Wolynes, Quantizing Ulam's Control Conjecture, Phys. Rev. Lett. 99, 060201 (2007). 高見さんの論文が refer されている。しかし、Gruebele 研にいたあの中国人学生は元気かなあ。

Y.S. Kim and R.M. Hochstrasser, Applications of 2D IR Spectroscopy to Peptides, Proteins, and Hydrogen-Bond Dynamics, J. Phys. Chem. B 113, 8231 (2009).

W. Li and S. Takada, Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously, J. Chem. Phys. 130, 214101 (2009).

D. Li, M.S. Liu, B. Ji, K. Hwang, and Y. Huang, Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors, J. Chem. Phys. 130, 215102 (2009). gating とドラッグデザインが何か結びつかないかねえ。

Agung Budiyono and Ken Umeno, Madelung fluid model for the most likely wave function of a single free particle in a two-dimensional space with a given average energy, Phys. Rev. A 79, 042104 (2009). 前に教えてもらったアグンさんの論文。

Z. Yang, P. Majek, and I. Bahar, Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL, PLOS 5, e1000360 (2009). とにかく長い！

Karunesh Arora and Charles L. Brooks III, Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations, J. Am. Chem. Soc. 131 (2009) 5642-5647. 確かに Transition state theory…

D. Tobi and I. Bahar, Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state, PNAS 102 (2005) 18908-13. しかし、目の付けどころはいい。