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Collective coordinates and the mechanism for conformational transitions of complex molecules

Yanao, Tomohiro and Koon, Wang S. and Marsden, Jerrold E. and Kevrekidis, Ioannis G. (2007) Collective coordinates and the mechanism for conformational transitions of complex molecules. Proceedings in Applied Mathematics and Mechanics, 7 (1). pp. 1080503-1080504. ISSN 1617-7061. http://resolver.caltech.edu/CaltechAUTHORS:20101026-074214900

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Abstract

Reduction of dimensionality is crucial for the deeper understanding of the mechanism for large-amplitude conformational transitions of complex molecules. By taking up a six-atomcluster as an illustrative example, we present a general methodology to understand conformational transitions of molecules in terms of the low-dimensional dynamics of molecular gyration radii. The dynamics of gyration radii is generally governed by the interplay between the ordinary potential force and a dynamical force called the internal centrifugal force. We show that the internal centrifugal force can be more important than the original potential barrier and gives rise to a new dynamical barrier that truly dominates the conformational transitions of the system. This kind of dynamical effect should be crucially important in a wide class of molecular reaction dynamics.


Item Type:Article
Related URLs:
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http://dx.doi.org/10.1002/pamm.200700486DOIUNSPECIFIED
http://onlinelibrary.wiley.com/doi/10.1002/pamm.200700486/abstractPublisherUNSPECIFIED
http://www.cds.caltech.edu/~marsden/bib/2007/13-YaKoMaKe2007/AuthorUNSPECIFIED
Additional Information:© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Article first published online: 7 SEP 2008.
Record Number:CaltechAUTHORS:20101026-074214900
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20101026-074214900
Official Citation:Yanao, T., W. S. Koon, et al. (2007). "Collective coordinates and the mechanism for conformational transitions of complex molecules." PAMM 7(1): 1080503-1080504.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:20518
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:30 Nov 2010 23:03
Last Modified:26 Dec 2012 12:33

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