論文
Graeme Henkelman, Andri Arnaldsson, and Hannes Jónsson, Theoretical calculations of CH4 and H2 associative desorption from Ni(111): Could subsurface hydrogen play an important role? J. Chem. Phys. 124, 044706 (2006). Harmonic TST について…
無時間の思想。
Hiroto Kikuchi, Hiroshi Fujisaki, Tadaomi Furuta, Ken Okamoto, Silke Leimkühler, and Takeshi Nishino, Different inhibitory potency of febuxostat towards mammalian and bacterial xanthine oxidoreductases: insight from molecular dynamics, Sci…
Po-hung Wang, R.B. Best, and J. Blumberger, Multiscale Simulation Reveals Multiple Pathways for H2 and O2 Transport in a [NiFe]-Hydrogenase, J. Am. Chem. Soc. 133, 3548 (2011).
C. Brif, R. Chakrabarti, and H. Rabitz, Control of Quantum Phenomena, Adv. Chem. Phys. 148, 1-76 (2012).
H. Kokubo, T. Tanaka, and Y. Okamoto, Ab Initio Prediction of Protein–Ligand Binding Structures by Replica-Exchange Umbrella Sampling Simulations, J. Comp. Chem., DOI: 10.1002/jcc.21860.
R. D. Astumian, Stochastic Conformational Pumping: A Mechanism for Free-Energy Transduction by Molecules, Annu. Rev. Biophys. 40, 289-313 (2011).
U. von Toussaint, Bayesian inference in physics, Rev. Mod. Phys. 83, 943-999 (2011).
Naoki Fujii, Misao Mizuno, and Yasuhisa Mizutani, Direct Observation of Vibrational Energy Flow in Cytochrome c, J. Phys. Chem. B, Article ASAP DOI: 10.1021/jp207500b.
F.X. Vazquez, I. Navrotskaya, and E. Geva, Vibrational energy relaxation rates via the linearized semiclassical method without force derivatives, J. Phys. Chem. A 114, 5682 (2010).
V. Ovchinnikov, M. Karplus, and E. Vanden-Eijnden, Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI, J. Chem. Phys. 134, 085103 (2011); M. Miyazaki and T. Harada, Bayesian e…
Yusuke Naritomi and Sotaro Fuchigami, Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions, J. Chem. Phys. 134, 065101 (2011) (8 pages). ICA の論文。
M. Kamada, M. Toda, M. Sekijima, M. Takata, and K. Joe, Analysis of motion features for molecular dynamics simulation of proteins, Chem. Phys. Lett. 502 (2011) 241–247.
J.R. Drugowich de Felicio and V.L. Libero, Updating Monte Carlo algorithms, Am. J. Phys. 64 (1996) 1281.
Shina C.L. Kamerlin, Spyridon Vicatos, Anatoly Dryga, and Arieh Warshel, Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems, Annu. Rev. Phys. Chem. 62:41–64 (2011). Warshel 節炸裂。
K. Moritsugu, T. Terada, and A. Kidera, Scalable free energy calculation of proteins via multiscale essential sampling, J. Chem. Phys. (in press).
Alan S. Perelson and Gérard Weisbuch, Immunology for physicists, Rev. Mod. Phys. 69, 1219-1268 (1997).
David E. Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, and Willy Wriggers, "Atomic-Level Characterization of the Structural Dyna…
K. Harada and T. Ikegami, Evolution of Specificity in an Immune Network, J. Theor. Biol. 203, 439-449 (2000).
小島 和雄, 太田 正光, 木材における液体の移動速度に及ぼす物理的諸因子の影響とその次元解析, 木材学会誌 Vol. 56 (2010), No. 5, 307-316. 立高時代の恩師、小島先生の論文。71歳でD3とは格好いい！
N. Dorsaz, C. De Michele, F. Piazza, P. De Los Rios, and G. Foffi, Diffusion-Limited Reactions in Crowded Environments, Phys. Rev. Lett. 105, 120601 (2010).
A. G. Dijkstra and Y. Tanimura, Non-Markovian entanglement dynamics in the presence of system-bath coherence, Phys. Rev. Lett 104, 250401 (2010). Arend はとにかくやることが早い。
A.K. Chakraborty and A. Kosmrlj, Statistical Mechanical Concepts in Immunology, Annu. Rev. Phys. Chem. 61, 283 (2010). 今年の ARPC はいい記事揃い。Vanden-Eijnden の transition path theory や Dinner の nonequilibrium umbrella sampling など。
Kaito Takahashi, Kathryn L. Plath, Rex T. Skodje, and Veronica Vaida, Dynamics of Vibrational Overtone Excited Pyruvic Acid in the Gas Phase: Line Broadening through Hydrogen-Atom Chattering, J. Phys. Chem. A 112, 7321–7331 (2008).
G. Hummer and A. Szabo, Free Energy Surfaces from Single-Molecule Force Spectroscopy, Acc. Chem. Res. 38, 504-513 (2005).
A. Bastida, M.A. Soler, J. Zúñiga, A. Requena, A. Kalstein, and S. Fernández-Alberti, Instantaneous normal modes, resonances, and decay channels in the vibrational relaxation of the amide I mode of N-methylacetamide-D in liquid deuterated …
Takefumi Yamashita and Gregory A. Voth, Properties of Hydrated Excess Protons near Phospholipid Bilayers, J. Phys. Chem. B 114, 592-603 (2010). やっと出ました。
Hiroaki S. Yamada, Kensuke S. Ikeda, Universal Irreversibility of Normal Quantum Diffusion, arXiv:1006.0363.
ポール・デイヴィス、生命の量子論、パリティ、p.4, Vol.25, No.6 (2010); マーク・ブキャナン、ブラック・スワンを探せ、パリティ、p.34, Vol.25, No.2 (2010); ジョン・ホイーラーと相対論と量子情報、パリティ、p.4, Vol.25, No.2 (2010).
Günter Schwarz, Ralf R. Mendel & Markus W. Ribbe, Molybdenum cofactors, enzymes and pathways, Nature 460, 839-847 (13 August 2009).
