Systematic determination of order parameters for chain dynamics using diffusion maps

Andrew L. Ferguson, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti, Ioannis G. Kevrekidis

Research output: Contribution to journalArticlepeer-review

132 Scopus citations


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 whichwe 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.

Original languageEnglish (US)
Pages (from-to)13597-13602
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number31
StatePublished - Aug 3 2010

All Science Journal Classification (ASJC) codes

  • General


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