Flows in complex networks: theory, algorithms, and application to lennard-Jones cluster rearrangement

DOI10.1007/S10955-014-0997-8zbMATH Open1301.82031arXiv1402.1736OpenAlexW3104017145MaRDI QIDQ741344FDOQ741344

Authors: Eric Vanden-Eijnden, Maria Kourkina Cameron 

Publication date: 11 September 2014

Published in: Journal of Statistical Physics (Search for Journal in Brave)

Abstract: A set of analytical and computational tools based on transition path theory (TPT) is proposed to analyze flows in complex networks. Specifically, TPT is used to study the statistical properties of the reactive trajectories by which transitions occur between specific groups of nodes on the network. Sampling tools are built upon the outputs of TPT that allow to generate these reactive trajectories directly, or even transition paths that travel from one group of nodes to the other without making any detour and carry the same probability current as the reactive trajectories. These objects permit to characterize the mechanism of the transitions, for example by quantifying the width of the tubes by which these transitions occur, the location and distribution of their dynamical bottlenecks, etc. These tools are applied to a network modeling the dynamics of the Lennard-Jones cluster with 38 atoms (LJ38) and used to understand the mechanism by which this cluster rearranges itself between its two most likely states at various temperatures.

Full work available at URL: https://arxiv.org/abs/1402.1736

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zbMATH Keywords

self-assemblytransition path theoryprotein foldingMarkov state modelsglassy dynamics

Mathematics Subject Classification ID

Numerical analysis or methods applied to Markov chains (65C40) Continuous-time Markov processes on discrete state spaces (60J27) Dynamic lattice systems (kinetic Ising, etc.) and systems on graphs in time-dependent statistical mechanics (82C20) Classical dynamic and nonequilibrium statistical mechanics (general) (82C05)

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Cited In (17)

• Metastability of reversible random walks in potential fields
• Invertibility of graph translation and support of Laplacian Fiedler vectors
• Interface dynamics of a metastable mass-conserving spatially extended diffusion
• A convergent discretization method for transition path theory for diffusion processes
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• Point cloud discretization of Fokker-Planck operators for committor functions

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