Rapid Calculation of Molecular Kinetics Using Compressed Sensing

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dc.citation.firstpage2771en_US
dc.citation.issueNumber5en_US
dc.citation.journalTitleJournal of Chemical Theory and Computationen_US
dc.citation.lastpage2783en_US
dc.citation.volumeNumber14en_US
dc.contributor.authorLitzinger, Florianen_US
dc.contributor.authorBoninsegna, Lorenzoen_US
dc.contributor.authorWu, Haoen_US
dc.contributor.authorNüske, Feliksen_US
dc.contributor.authorPatel, Raajenen_US
dc.contributor.authorBaraniuk, Richarden_US
dc.contributor.authorNoé, Franken_US
dc.contributor.authorClementi, Ceciliaen_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2018-06-27T14:39:39Zen_US
dc.date.available2018-06-27T14:39:39Zen_US
dc.date.issued2018en_US
dc.description.abstractRecent methods for the analysis of molecular kinetics from massive molecular dynamics (MD) data rely on the solution of very large eigenvalue problems. Here we build upon recent results from the field of compressed sensing and develop the spectral oASIS method, a highly efficient approach to approximate the leading eigenvalues and eigenvectors of large generalized eigenvalue problems without ever having to evaluate the full matrices. The approach is demonstrated to reduce the dimensionality of the problem by 1 or 2 orders of magnitude, directly leading to corresponding savings in the computation and storage of the necessary matrices and a speedup of 2 to 4 orders of magnitude in solving the eigenvalue problem. We demonstrate the method on extensive data sets of protein conformational changes and protein-ligand binding using the variational approach to conformation dynamics (VAC) and time-lagged independent component analysis (TICA). Our approach can also be applied to kernel formulations of VAC, TICA, and extended dynamic mode decomposition (EDMD).en_US
dc.identifier.citationLitzinger, Florian, Boninsegna, Lorenzo, Wu, Hao, et al.. "Rapid Calculation of Molecular Kinetics Using Compressed Sensing." <i>Journal of Chemical Theory and Computation,</i> 14, no. 5 (2018) American Chemical Society: 2771-2783. https://doi.org/10.1021/acs.jctc.8b00089.en_US
dc.identifier.doihttps://doi.org/10.1021/acs.jctc.8b00089en_US
dc.identifier.urihttps://hdl.handle.net/1911/102295en_US
dc.language.isoengen_US
dc.publisherAmerican Chemical Societyen_US
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.en_US
dc.titleRapid Calculation of Molecular Kinetics Using Compressed Sensingen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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