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Dynamic pathways to mediate reactions buried in thermal fluctuations. II. Numerical illustrations using a model system
| Title: | Dynamic pathways to mediate reactions buried in thermal fluctuations. II. Numerical illustrations using a model system |
| Authors: | Kawai, Shinnosuke Browse this author | | Komatsuzaki, Tamiki Browse this author |
| Keywords: | fluctuations | | friction | | numerical analysis | | potential energy surfaces | | random processes | | reaction kinetics theory | | solvent effects | | statistical distributions |
| Issue Date: | 14-Dec-2009 |
| Publisher: | American Institute of Physics |
| Journal Title: | Journal of Chemical Physics |
| Volume: | 131 |
| Issue: | 22 |
| Start Page: | 224506 |
| Publisher DOI: | 10.1063/1.3268622 |
| PMID: | 20001056 |
| Abstract: | The framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in thermal fluctuation is examined with a model system. Numerical simulations are carried out for an underdamped Langevin equation with the Müller-Brown potential surface, which contains three wells and two saddles, and are compared to the prediction by the theory. Reaction probabilities for specific initial conditions of the system as well as their average over the Boltzmann distribution are investigated in the position space and in a space spanned by the position coordinates and the velocities of the system. The nonlinear couplings between the reactive and the nonreactive modes are shown to have significant effects on the reactivity in the model system. The magnitude and the direction of the nonlinear effect are different for the two saddles, which is found to be correctly reproduced by our theory. The whole position-velocity space of the model system is found to be divided into the two distinct regions: One is of mainly reactive (with reaction probability more than half) initial conditions and the other, the mainly nonreactive (with reaction probability less than half) ones. Our theory can actually assign their boundaries as the zero of the statistical average of the new reaction coordinate as an analytical functional of both the original position coordinates and velocities of the system (solute), as well as of the random force and the friction constants from the environment (solvent). The result validates the statement in the previous paper that the sign of the reaction coordinate thus extracted determines the fate of the reaction. Physical interpretation of the reactivity under thermal fluctuation that is naturally derived, thanks to the analyticity of the theoretical framework, is also exemplified for the model system. |
| Rights: | Copyright 2009 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in J. Chem. Phys. 131, 224506 (2009) and may be found at https://dx.doi.org/10.1063/1.3268622 |
| Type: | article |
| URI: | http://hdl.handle.net/2115/42521 |
| Appears in Collections: | 電子科学研究所 (Research Institute for Electronic Science) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 河合 信之輔
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