Local and global perspectives on diffusion maps in the analysis of molecular systems

DOI10.1098/RSPA.2019.0036zbMATH Open1472.82029arXiv1901.06936OpenAlexW3106423384WikidataQ89819503 ScholiaQ89819503MaRDI QIDQ5160841FDOQ5160841

Authors: Zofia Trstanova, Tony Lelièvre, Benedict Leimkuhler 

Publication date: 29 October 2021

Published in: Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences (Search for Journal in Brave)

Abstract: Diffusion maps approximate the generator of Langevin dynamics from simulation data. They afford a means of identifying the slowly-evolving principal modes of high-dimensional molecular systems. When combined with a biasing mechanism, diffusion maps can accelerate the sampling of the stationary Boltzmann-Gibbs distribution. In this work, we contrast the local and global perspectives on diffusion maps, based on whether or not the data distribution has been fully explored. In the global setting, we use diffusion maps to identify metastable sets and to approximate the corresponding committor functions of transitions between them. We also discuss the use of diffusion maps within the metastable sets, formalising the locality via the concept of the quasi-stationary distribution and justifying the convergence of diffusion maps within a local equilibrium. This perspective allows us to propose an enhanced sampling algorithm. We demonstrate the practical relevance of these approaches both for simple models and for molecular dynamics problems (alanine dipeptide and deca-alanine).

Full work available at URL: https://arxiv.org/abs/1901.06936

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zbMATH Keywords

diffusion mapsmetastabilitymolecular dynamicsapplied mathematicscomputational chemistryatomic and molecular physicscommittors

Mathematics Subject Classification ID

Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31)

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Cited In (3)

• Title not available (Why is that?)
• Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems
• Computing committors in collective variables via Mahalanobis diffusion maps

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