1. Systematic determination of order parameters for chain dynamics using diffusion maps.
- Author
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Ferguson, Andrew L., Panagiotopoulos, Athanassios Z., Debenedetti, Pablo G., and Kevrekidis, loannis G.
- Subjects
DIMENSION reduction (Statistics) ,SALTWATER solutions ,HELICES (Algebraic topology) ,PROTEIN folding ,NITROALKANES ,ADDITION polymerization - Abstract
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 C
16 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. [ABSTRACT FROM AUTHOR]- Published
- 2010
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