| 概 要 |
Path search and path sampling algorithms are powerful methods to scrutinize rare chemical events (reactions) in molecular systems in condensed phase or in biomolecules. We have applied the "string method" due to Eric Vanden-Eijnden, a simple and powerful method of path search for free energy landscape, to conformational change of an enzymatic reaction [1] and proton transfer reactions in small molecules including quantum effects [2].
To further obtain some kinetic aspects of chemical reactions, we are pursuing to use the Onsager-Machlup (OM) action principle as a variation of transition path sampling methods [3].
In this talk, we introduce the basic ideas behind the path search and path sampling methods and discuss some connections to multiscale modeling and statistical inference for complex and dynamic phenomena.
[1] 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).
[2] M. Shiga and H. Fujisaki, A quantum generalization of intrinsic reaction coordinate using path integral centroid coordinate, J. Chem. Phys. 136, 184103 (2012).
[3] 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. (in press).
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