Eur. Phys. J. B 63, 387-391 (2008)
https://doi.org/10.1140/epjb/e2008-00136-7

Funnels in energy landscapes

¹ Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
² Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
³ RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
⁴ Santa Fe Institute, Santa Fe, New Mexico, USA

Corresponding author: ^a klemm@bioinf.uni-leipzig.de

Received: 29 August 2007
Revised: 13 February 2008
Published online: 2 April 2008

Abstract

Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a “folding funnel” that is concisely defined in terms of energy minima and saddle points, while at the same time conforming to a notion of a “folding funnel” as it is discussed in the protein folding literature.