Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning. Issue 6 (12th August 2015)

• Record Type: Journal Article
• Authors: Bello‐Rivas, Juan M.; Elber, Ron
• Is Part Of: Journal of computational chemistry. Volume 37:Issue 6(2016)
• Page Start: 602
• Page End: 613
• Publication Date: 2015-08-12
• Subjects: molecular dynamics -- ergodicity -- glasses -- milestoning -- first passage times; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.24039
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract : We investigated by computational means the kinetics and stationary behavior of stochastic dynamics on an ensemble of rough two‐dimensional energy landscapes. There are no obvious separations of temporal scales in these systems, which constitute a simple model for the behavior of glasses and some biomaterials. Even though there are significant computational challenges present in these systems due to the large number of metastable states, the Milestoning method is able to compute their kinetic and thermodynamic properties exactly. We observe two clearly distinguished regimes in the overall kinetics: one in which diffusive behavior dominates and another that follows an Arrhenius law (despite the absence of a dominant barrier). We compare our results with those obtained with an exactly‐solvable one‐dimensional model, and with the results from the rough one‐dimensional energy model introduced by Zwanzig. © 2015 Wiley Periodicals, Inc. Abstract : We compute, using the Milestoning method, the stationary flux (shown), the mean first passage time of Brownian trajectories, and the free energy (not shown) on a large ensemble of random energy landscapes with varying degrees of roughness and at a wide range of temperatures. We find two different behaviors: a diffusive regime for high temperatures and an Arrhenius‐like regime for low temperatures.