title: Configurational subdiffusion of peptides: a network study.
abstract: Molecular dynamics (MD) simulation of linear peptides reveals configurational subdiffusion at equilibrium extending from 10⁻¹² to 10⁻⁸ s. Rouse chain and continuous-time random walk models of the subdiffusion are critically discussed. Network approaches to analyzing MD simulations are shown to reproduce the time dependence of the subdiffusive mean squared displacement, which is found to arise from the fractal-like geometry of the accessible volume in the configuration space. Convergence properties of the simulation pertaining to the subdiffusive dynamics are characterized and the effect on the subdiffusive properties of representing the solvent explicitly or implicitly is compared. Non-Markovianity and other factors limiting the range of applicability of the network models are examined.
authors.affiliation: Computational Molecular Biophysics, Universität Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Neusius
authors.forename: Isabella
authors.initials: I
authors.lastname: Daidone
authors.forename: Igor M
authors.initials: IM
authors.lastname: Sokolov
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
mesh_terms: D003198:Computer Simulation; D004058:Diffusion; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D010455:Peptides / Q000737:chemistry*
chemical_list: D010455:Peptides