文章基本信息

标题：Systematic determination of order parameters for chain dynamics using diffusion maps
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作者：Andrew L. Ferguson ; Athanassios Z. Panagiotopoulos ; Pablo G. Debenedetti 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2010
卷号：107
期号：31
页码：13597-13602
DOI：10.1073/pnas.1003293107
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：We employ the diffusion map approach as a nonlinear dimensionality reduction technique to extract a dynamically relevant, low-dimensional description of n-alkane chains in the ideal-gas phase and in aqueous solution. In the case of C8 we find the dynamics to be governed by torsional motions. For C16 and C24 we extract three global order parameters with which we characterize the fundamental dynamics, and determine that the low free-energy pathway of globular collapse proceeds by a "kink and slide" mechanism, whereby a bend near the end of the linear chain migrates toward the middle to form a hairpin and, ultimately, a coiled helix. The low-dimensional representation is subtly perturbed in the solvated phase relative to the ideal gas, and its geometric structure is conserved between C16 and C24. The methodology is directly extensible to biomolecular self-assembly processes, such as protein folding.
关键词：hydrophobicity ; data mining ; solvation ; hydrocarbon ; folding pathways