Physics – Condensed Matter – Statistical Mechanics
Scientific paper
2000-06-13
Phys. Rev. E 62, 4025 (2000)
Physics
Condensed Matter
Statistical Mechanics
8 pages, 9 EPS figures, Phys. Rev. E (in press)
Scientific paper
10.1103/PhysRevE.62.4025
The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence. For good folders, on the other hand, two nearby trajectories may initially move apart but eventually they come together. Thus good folders are intrinsically non-chaotic. A choice of a distance of the initial conformation from the native state affects the way in which a separation between the twin trajectories behaves in time. This observation allows one to determine the size of a folding funnel in good folders. We study the energy landscapes of the toy models by determining the power spectra and fractal characteristics of the dependence of the potential energy on time. For good folders, folding and unfolding trajectories have distinctly different correlated behaviors at low frequencies.
Cieplak Marek
Li Mai Suan
Sushko Nazar
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