Uncovering the topology of configuration space networks
Abstract
The configuration space network (CSN) of a dynamical system is an effective approach to represent the ensemble of configurations sampled during a simulation and their dynamic connectivity. To elucidate the connection between the CSN topology and the underlying free-energy landscape governing the system dynamics and thermodynamics, an analytical soluti on is provided to explain the heavy tail of the degree distribution, neighbor co nnectivity and clustering coefficient. This derivation allows to understand the universal CSN network topology observed in systems ranging from a simple quadratic well to the native state of the beta3s peptide and a 2D lattice heteropolymer. Moreover CSN are shown to fall in the general class of complex networks describe d by the fitness model.
Keywords
Cite
@article{arxiv.0704.2699,
title = {Uncovering the topology of configuration space networks},
author = {David Gfeller and Paolo De Los Rios and David Morton de Lachapelle and Guido Caldarelli and Francesco Rao},
journal= {arXiv preprint arXiv:0704.2699},
year = {2009}
}
Comments
6 figures