dc.contributor.author
Wu, Hao
dc.contributor.author
Nüske, Feliks
dc.contributor.author
Paul, Fabian
dc.contributor.author
Klus, Stefan
dc.contributor.author
Koltai, Péter
dc.contributor.author
Noe, Frank
dc.date.accessioned
2018-06-08T11:12:06Z
dc.date.available
2017-05-31T12:48:07.236Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/21798
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-25086
dc.description.abstract
Markov state models (MSMs) and master equation models are popular approaches
to approximate molecular kinetics, equilibria, metastable states, and reaction
coordinates in terms of a state space discretization usually obtained by
clustering. Recently, a powerful generalization of MSMs has been introduced,
the variational approach conformation dynamics/molecular kinetics (VAC) and
its special case the time-lagged independent component analysis (TICA), which
allow us to approximate slow collective variables and molecular kinetics by
linear combinations of smooth basis functions or order parameters. While it is
known how to estimate MSMs from trajectories whose starting points are not
sampled from an equilibrium ensemble, this has not yet been the case for TICA
and the VAC. Previous estimates from short trajectories have been strongly
biased and thus not variationally optimal. Here, we employ the Koopman
operator theory and the ideas from dynamic mode decomposition to extend the
VAC and TICA to non-equilibrium data. The main insight is that the VAC and
TICA provide a coefficient matrix that we call Koopman model, as it
approximates the underlying dynamical (Koopman) operator in conjunction with
the basis set used. This Koopman model can be used to compute a stationary
vector to reweight the data to equilibrium. From such a Koopman-reweighted
sample, equilibrium expectation values and variationally optimal reversible
Koopman models can be constructed even with short simulations. The Koopman
model can be used to propagate densities, and its eigenvalue decomposition
provides estimates of relaxation time scales and slow collective variables for
dimension reduction. Koopman models are generalizations of Markov state
models, TICA, and the linear VAC and allow molecular kinetics to be described
without a cluster discretization.
en
dc.rights.uri
http://publishing.aip.org/authors/web-posting-guidelines
dc.subject
Relaxation times
dc.subject
Markov processes
dc.subject
Conformational dynamics
dc.subject.ddc
500 Naturwissenschaften und Mathematik::530 Physik
dc.title
Variational Koopman models
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation
Journal of Chemical Physics. - 146 (2017), 15, Artikel Nr. 154104
dc.title.subtitle
Slow collective variables and molecular kinetics from short off-equilibrium
simulations
dcterms.bibliographicCitation.doi
10.1063/1.4979344
dcterms.bibliographicCitation.url
http://dx.doi.org/10.1063/1.4979344
refubium.affiliation
Physik
de
refubium.mycore.fudocsId
FUDOCS_document_000000027108
refubium.resourceType.isindependentpub
no
refubium.mycore.derivateId
FUDOCS_derivate_000000008267
dcterms.accessRights.openaire
open access