Toward identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method

Dimitri Antoniou, Steven D. Schwartz

Research output: Contribution to journalArticlepeer-review

30 Scopus citations

Abstract

We propose a new method for analyzing an ensemble of transition states to extract components of the reaction coordinate. We use the kernel principal component analysis (kPCA), which is a generalization of the ordinary PCA that does not make a linearization approximation We applied this method to a TPS study of human LDH we had previously published [Quaytman, S.; Schwartz, S. D. Proc. Natl. Acad. Sci. U.S.A.2007, 104, 12253] and extracted a reasonable representation for the reaction coordinate.

Original languageEnglish (US)
Pages (from-to)2465-2469
Number of pages5
JournalJournal of Physical Chemistry B
Volume115
Issue number10
DOIs
StatePublished - Mar 17 2011
Externally publishedYes

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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