Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

• DOI: 10.1146/annurev-physchem-040412-110006
• Publication Date: 2013-01-09T04:52:48Z
• Authors: Mary A. Rohrdanz; Wenwei Zheng; Cecilia Clementi
• Keywords: 0103 physical sciences; 01 natural sciences

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.