Discovering mountain passes via torchlight: Methods for the definition of reaction coordinates and pathways in complex macromolecular reactions

Mary A. Rohrdanz, Wenwei Zheng, Cecilia Clementi

Research output: Contribution to journalReview article

125 Scopus citations

Abstract

The long-timescale dynamics of macromolecular systems can be oftentimes viewed as a reaction connecting metastable states of the system. In the past decade, various approaches have been developed to discover the collective motions associated with this dynamics. The corresponding collective variables are used in many applications, e.g., to understand the reaction mechanism, to quantify the system's free energy landscape, to enhance the sampling of the reaction path, and to determine the reaction rate. In this review we focus on a number of key developments in this field, providing an overview of several methods along with their relative regimes of applicability.

Original languageEnglish (US)
Pages (from-to)295-316
Number of pages22
JournalAnnual Review of Physical Chemistry
Volume64
DOIs
StatePublished - Apr 1 2013
Externally publishedYes

Keywords

  • Machine learning
  • Molecular dynamics
  • Path sampling
  • Reaction rate

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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