Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 112, Issue 11, Pages 3235-3240Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1418241112
Keywords
free energy surface; stochastic optimization; activation-relaxation; machine learning; network representation
Categories
Funding
- National Science Foundation [CHE-1301314]
- Margaret and Herman Sokol Doctoral Fellowship in the Sciences
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [1301314] Funding Source: National Science Foundation
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Coarse graining of complex systems possessing many degrees of freedom can often be a useful approach for analyzing and understanding key features of these systems in terms of just a few variables. The relevant energy landscape in a coarse-grained description is the free energy surface as a function of the coarse-grained variables, which, despite the dimensional reduction, can still be an object of high dimension. Consequently, navigating and exploring this high-dimensional free energy surface is a nontrivial task. In this paper, we use techniques from multiscale modeling, stochastic optimization, and machine learning to devise a strategy for locating minima and saddle points (termed landmarks) on a high-dimensional free energy surface on the fly and without requiring prior knowledge of or an explicit form for the surface. In addition, we propose a compact graph representation of the landmarks and connections between them, and we show that the graph nodes can be subsequently analyzed and clustered based on key attributes that elucidate important properties of the system. Finally, we show that knowledge of landmark locations allows for the efficient determination of their relative free energies via enhanced sampling techniques.
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