Energy landscapes and persistent minima.


Change log
Authors
Carr, Joanne M 
Mazauric, Dorian 
Cazals, Frédéric 
Wales, David J 
Abstract

We consider a coarse-graining of high-dimensional potential energy landscapes based upon persistences, which correspond to lowest barrier heights to lower-energy minima. Persistences can be calculated efficiently for local minima in kinetic transition networks that are based on stationary points of the prevailing energy landscape. The networks studied here represent peptides, proteins, nucleic acids, an atomic cluster, and a glassy system. Minima with high persistence values are likely to represent some form of alternative structural morphology, which, if appreciably populated at the prevailing temperature, could compete with the global minimum (defined as infinitely persistent). Threshold values on persistences (and in some cases equilibrium occupation probabilities) have therefore been used in this work to select subsets of minima, which were then analysed to see how well they can represent features of the full network. Simplified disconnectivity graphs showing only the selected minima can convey the funnelling (including any multiple-funnel) characteristics of the corresponding full graphs. The effect of the choice of persistence threshold on the reduced disconnectivity graphs was considered for a system with a hierarchical, glassy landscape. Sets of persistent minima were also found to be useful in comparing networks for the same system sampled under different conditions, using minimum oriented spanning forests.

Description
Keywords
0501 Ecological Applications
Journal Title
J Chem Phys
Conference Name
Journal ISSN
0021-9606
1089-7690
Volume Title
144
Publisher
AIP Publishing
Sponsorship
European Research Council (267369)
Engineering and Physical Sciences Research Council (EP/N035003/1)
D.J.W and J.M.C gratefully acknowledge funding from the European Research Council [267369].