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	Sampling saddle points on a free energy surface
	Samanta, Amit ; Chen, Ming ; Yu, Tang-Qing ; Tuckerman, Mark ; Weinan, E.
	2014
关键词	MOLECULAR-DYNAMICS POTENTIAL SURFACES PATHWAYS
英文摘要	Many problems in biology, chemistry, and materials science require knowledge of saddle points on free energy surfaces. These saddle points act as transition states and are the bottlenecks for transitions of the system between different metastable states. For simple systems in which the free energy depends on a few variables, the free energy surface can be precomputed, and saddle points can then be found using existing techniques. For complex systems, where the free energy depends on many degrees of freedom, this is not feasible. In this paper, we develop an algorithm for finding the saddle points on a high-dimensional free energy surface "on-the-fly" without requiring a priori knowledge the free energy function itself. This is done by using the general strategy of the heterogeneous multi-scale method by applying a macro-scale solver, here the gentlest ascent dynamics algorithm, with the needed force and Hessian values computed on-the-fly using a micro-scale model such as molecular dynamics. The algorithm is capable of dealing with problems involving many coarse-grained variables. The utility of the algorithm is illustrated by studying the saddle points associated with (a) the isomerization transition of the alanine dipeptide using two coarse-grained variables, specifically the Ramachandran dihedral angles, and (b) the beta-hairpin structure of the alanine decamer using 20 coarse-grained variables, specifically the full set of Ramachandran angle pairs associated with each residue. For the alanine decamer, we obtain a detailed network showing the connectivity of the minima obtained and the saddle-point structures that connect them, which provides a way to visualize the gross features of the high-dimensional surface. (C) 2014 AIP Publishing LLC.; http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000336047700016&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701 ; Physics, Atomic, Molecular & Chemical; SCI(E); EI; PubMed; 4; ARTICLE; asamanta@math.princeton.edu; 16; 164109; 140
语种	英语
出处	PubMed ; SCI ; EI
出版者	journal of chemical physics
内容类型	其他
源URL	[http://hdl.handle.net/20.500.11897/189717]
专题	数学科学学院
推荐引用方式 GB/T 7714	Samanta, Amit,Chen, Ming,Yu, Tang-Qing,et al. Sampling saddle points on a free energy surface. 2014-01-01.

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