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dc.contributor.author
Paz, Sergio Alexis
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dc.contributor.author
Abrams, Cameron F.
dc.date.available
2018-06-05T20:08:48Z
dc.date.issued
2015-09-04
dc.identifier.citation
Paz, Sergio Alexis; Abrams, Cameron F.; Free energy and hidden barriers of the β-sheet structure of Prion protein; American Chemical Society; Journal of Chemical Theory and Computation; 11; 10; 4-9-2015; 5024–5034
dc.identifier.issn
1549-9618
dc.identifier.uri
http://hdl.handle.net/11336/47384
dc.description.abstract
On-the-fly free-energy parametrization is a new collective variable biasing approach akin to metadynamics with one important distinction: rather than acquiring an accelerated distribution via a history-dependent bias potential, sampling on this distribution is achieved from the beginning of the simulation using temperature-accelerated molecular dynamics. In the present work, we compare the performance of both approaches to compute the free-energy profile along a scalar collective variable measuring the H-bond registry of the β-sheet structure of the mouse Prion protein. Both methods agree on the location of the free-energy minimum, but free-energy profiles from well-tempered metadynamics are subject to a much higher degree of statistical noise due to hidden barriers. The sensitivity of metadynamics to hidden barriers is shown to be a consequence of the history dependence of the bias potential, and we detail the nature of these barriers for the prion β-sheet. In contrast, on-the-fly parametrization is much less sensitive to these barriers and thus displays improved convergence behavior relative to that of metadynamics. While hidden barriers are a frequent and central issue in free-energy methods, on-the-fly free-energy parametrization appears to be a robust and preferable method to confront this issue.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
American Chemical Society
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
Temperature Accelerated Dynamics
dc.subject
Free Energy
dc.subject
Prion
dc.subject
Metadynamics
dc.subject.classification
Otras Ciencias Químicas
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dc.subject.classification
Ciencias Químicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
Free energy and hidden barriers of the β-sheet structure of Prion protein
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2018-05-07T18:03:09Z
dc.identifier.eissn
1549-9626
dc.journal.volume
11
dc.journal.number
10
dc.journal.pagination
5024–5034
dc.journal.pais
Estados Unidos
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dc.journal.ciudad
Washington
dc.description.fil
Fil: Paz, Sergio Alexis. Drexel University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
dc.description.fil
Fil: Abrams, Cameron F.. Drexel University; Estados Unidos
dc.journal.title
Journal of Chemical Theory and Computation
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1021/acs.jctc.5b00576
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.5b00576
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