Kinetics of model energy landscapes: an approach to complex systems.
An idealized potential energy surface (PES), simply a PES-like network of stationary points, is demonstrated to be a useful tool to study kinetic relaxation of complex energy landscapes. Combined with a master equation, we show that if constructed with proper regularity, the kinetics of the PES is easy to predict and understand by carefully examining the eigenmodes of the master equation. By modifying the idealized PES model to make it more and more complicated, we demonstrate a systematic method to study the complex kinetics on large PES. The idealized PES model is used to explore the feasibility and the robustness of statistical sampling of large PES. We develop several sampling strategies, such as the "rough topography sampling" and the "low barrier saddle sampling" in the idealized PES model and find they are also applicable to a realistic PES of the 13-atom Morse cluster with range parameter rho= 6. To measure the robustness of the sampling methods, we compare the eigenvalue spectra, the eigenvector similarity and the relaxation times of the total energy of the full and sample PESs.
Lu
Jun
J
Department of Chemistry and The James Franck Institute, The University of Chicago, USA.
Zhang
Chi
C
Stephen Berry
R
R
D000465:Algorithms; D003198:Computer Simulation; D004735:Energy Transfer; D019277:Entropy; D007700:Kinetics; D008956:Models, Chemical; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins