論文

Adrien Nicolaï, Patrice Delarue, Patrick Senet, Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70, PLoS Comput Biol 9(12): e1003379 (2013).

Hye Yun Kim, Hyunjin Vincent Kim, Seonmi Jo, C. Justin Lee, Seon Young Choi, Dong Jin Kim & Young Soo Kim, EPPS rescues hippocampus-dependent cognitive deficits in APP/PS1 mice by disaggregation of amyloid-β oligomers and plaques, Nature C…

J.Q. You and F. Nori, Atomic physics and quantum optics using superconducting circuits, Nature 474, 589-597 (2011).

P.C. Bresslof and J.M. Newby, Path integrals and large deviations in stochastic hybrid systems, Phys. Rev. E 89 (2014) 042701. D. Wales, Energy landscapes: calculating pathways and rates, Int. Rev. Phys. Chem. 25 (2006) 237-282.

R.M.H. Merks and J.A. Glazier, A cell-centered approach to developmental biology, Physica A 352 (2005) 113-130.

I. Tunon, D. Laage, J.T. Hynes, Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step, Arch. Biochem. Biophys. (2015), http://dx.doi.org/10.1016/j.abb.2015.06.004.

J. Jeon, J.H. Lim, S. Kim, H. Kim, and M. Cho, Simultaneous spectral and temporal analyses of kinetic energies in nonequilibrium systems: Theory and application to vibrational relaxation of O-D stretch mode of HOD in water, J. Phys. Chem. A…

Tiejun Li, Xiaoguang Li, Xiang Zhou, Finding Transition Pathways on Manifolds, arXiv:1408.3602.

Mary A. Rohrdanz, Wenwei Zheng, and Cecilia Clementi, Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions, Annu. Rev. Phys. Chem. 64 (2013) 295-316.

Masayoshi Takayanagi, Ikuo Kurisaki, and Masataka Nagaoka, Oxygen Entry through Multiple Pathways in T-State Human Hemoglobin, J. Phys. Chem. B, 2013, 117 (20), pp 6082–6091.

G. Hultqvist, et al., Energetic Pathway Sampling in a Protein Interaction Domain, Structure 21, 1193-1202 (2013).

Eric Vanden-Eijnden, Jonathan Weare, Rare Event Simulation of Small Noise Diffusions, Communications on Pure and Applied Mathematics, Special Issue: Second Special Issue Commemorating the 75th Anniversary of the Courant Institute, Volume 6…

Hiroshi Fujisaki, Motoyuki Shiga, Kei Moritsugu, and Akinori Kidera, Multiscale enhanced path sampling based on the Onsager-Machlup action: Application to a model polymer, J. Chem. Phys. 139, 054117 (2013).

S. Still, D.A. Sivak, A.J. Bell, and G.E. Crooks, Thermodynamics of Prediction, Phys. Rev. Lett. 109, 120604 (2012).

S. Keshavamurthy, Scaling perspective on intramolecular vibrational energy flow: Analogies, insights, and challenges, Adv. Chem. Phys. 153, 43-110 (2013).

N. Schaudinnus, A. J. Rzepiela, R. Hegger, and G. Stock, Data driven Langevin modeling of biomolecular dynamics, J. Chem. Phys. 138, 204106 (2013).

Jerry B. Abrams and Mark E. Tuckerman, Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations, J. Phys. Chem. B, 2008, 112 (49), pp 15742–15757.

Tao Xie, Yingang Feng, Lu Shan, Jinfeng Wang, Modeling of the [E43S]SNase-ssDNA–Cd2+ complex: Structural insight into the action of nuclease on ssDNA, Archives of Biochemistry and Biophysics 532 (2013) 103-113.

Boon Leong Lan and Mikito Toda, Fluctuations of healthy and unhealthy heartbeat intervals, Europhys. Lett. 102 (2013) 18002.

A. A. Stuchebrukhov and R. A. Marcus, Theoretical study of intramolecular vibrational relaxation of acetylenic CH vibration for v= 1 and 2 in large polyatomic molecules (CX_3)_3 YCCH, where X=H or 0 and Y=C or Si, J. Chem. Phys. 98, 6044 (…

J. Tailleur and J. Kurchan, Probing rare physical trajectories with Lyapunov weighted dynamics, Nature Phys. 3 (2007) 203.

Noah C. Benson, Valerie Daggett. (2012) A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations. The Journal of Physical Chemistry B 116:29, 8722-8731.

Tetsuya Morishita, Satoru G. Itoh, Hisashi Okumura, and Masuhiro Mikami, Free-energy calculation via mean-force dynamics using a logarithmic energy landscape, Phys. Rev. E 85, 066702 (2012) [5 pages]

D. Antoniou and S.D. Schwartz, Toward Identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method, J. Phys. Chem. B 115, 2465 (2011).

Yasuhiro Matsunaga, Hiroshi Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, and Akinori Kidera, Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase, PLoS Comput Biol 8(6): e1002555 (2012).

J. Hu, A. Ma, and A.R. Dinner, Bias Anealing: A method for obtaining transition paths de novo, J. Chem. Phys. 125, 114101 (2006).

D. Antoniou, M.R. Abolfath, and S.D. Schwartz, Transition path sampling study of classical rate-promoting vibrations, J. Chem. Phys. 121, 6442 (2004).

U. von Toussaint, Bayesian inference in physics, Rev. Mod. Phys. 83, 943-999 (2011). なかなかいいレビューです。

C. Horhammer and H. Buttner, Information and entropy in quantum brownian motion: Themodynamic entropy versus von Neumann entropy, J. Stat. Phys. 133, 1161-1174 (2008).

Masuo Suzuki, Irreversibility and entropy production in transport phenomena I, Physica A 390, 1904-1916 (2011); Irreversibility and entropy production in transport phenomena II: Statistical-mechanical theory on steady states including ther…