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

Funnels in energy landscapes

K. Klemm¹, C. Flamm² and P.F. Stadler<sup>1, 2, 3, 4

1</sup>  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, Austria
³  RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
⁴  Santa Fe Institute, Santa Fe, New Mexico, USA

klemm@bioinf.uni-leipzig.de

Received 29 August 2007 / Received in final form 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.

PACS
87.10.+e - General theory and mathematical aspects.
87.15.Cc - Folding and sequence analysis.
89.75.Fb - Structures and organization in complex systems .

© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2008