Literature DB >> 30028174

Unfolding Hidden Barriers by Active Enhanced Sampling.

Jing Zhang1, Ming Chen2.   

Abstract

Collective variable (CV) or order parameter based enhanced sampling algorithms have achieved great success due to their ability to efficiently explore the rough potential energy landscapes of complex systems. However, the degeneracy of microscopic configurations, originating from the orthogonal space perpendicular to the CVs, is likely to shadow "hidden barriers" and greatly reduce the efficiency of CV-based sampling. Here we demonstrate that systematic machine learning CV, through enhanced sampling, can iteratively lift such degeneracies on the fly. We introduce an active learning scheme that consists of a parametric CV learner based on deep neural network and a CV-based enhanced sampler. Our active enhanced sampling algorithm is capable of identifying the least informative regions based on a historical sample, forming a positive feedback loop between the CV learner and sampler. This approach is able to globally preserve kinetic characteristics by incrementally enhancing both sample completeness and CV quality.

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Year:  2018        PMID: 30028174     DOI: 10.1103/PhysRevLett.121.010601

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  6 in total

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Authors:  Rebecca J Howard; Vincenzo Carnevale; Lucie Delemotte; Ute A Hellmich; Brad S Rothberg
Journal:  Biochim Biophys Acta Biomembr       Date:  2017-12-16       Impact factor: 4.019

3.  A survey of multiscale modeling: Foundations, historical milestones, current status, and future prospects.

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Review 4.  Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.

Authors:  Xiping Gong; Yumeng Zhang; Jianhan Chen
Journal:  Biomolecules       Date:  2021-09-28

5.  Molecular Insights from Conformational Ensembles via Machine Learning.

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Journal:  Biophys J       Date:  2019-12-21       Impact factor: 4.033

Review 6.  Collective variable-based enhanced sampling and machine learning.

Authors:  Ming Chen
Journal:  Eur Phys J B       Date:  2021-10-20       Impact factor: 1.500

  6 in total

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