Vis enkel innførsel

dc.contributor.authorDahlen, Oda
dc.contributor.authorvan Erp, Titus Sebastiaan
dc.date.accessioned2018-03-09T12:10:53Z
dc.date.available2018-03-09T12:10:53Z
dc.date.created2015-08-18T12:58:51Z
dc.date.issued2015
dc.identifier.citationJournal of Chemical Physics. 2015, 142, 235101.nb_NO
dc.identifier.issn0021-9606
dc.identifier.urihttp://hdl.handle.net/11250/2489801
dc.description.abstractUsing rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimental data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.nb_NO
dc.language.isoengnb_NO
dc.publisherAIP Publishingnb_NO
dc.titleMesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparisonnb_NO
dc.typeJournal articlenb_NO
dc.typePeer reviewednb_NO
dc.description.versionpublishedVersionnb_NO
dc.source.pagenumber9nb_NO
dc.source.volume142nb_NO
dc.source.journalJournal of Chemical Physicsnb_NO
dc.source.issue23nb_NO
dc.identifier.doi10.1063/1.4922519
dc.identifier.cristin1258587
dc.relation.projectNorges forskningsråd: 237423nb_NO
dc.relation.projectNorges forskningsråd: 209337nb_NO
dc.description.localcode© 2015 AIP Publishing LLC.Published by AIP Publishing. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in Journal of Chemical Physics and may be found at http://dx.doi.org/10.1063/1.4922519nb_NO
cristin.unitcode194,66,25,0
cristin.unitnameInstitutt for kjemi
cristin.ispublishedtrue
cristin.fulltextpreprint
cristin.qualitycode1


Tilhørende fil(er)

Thumbnail

Denne innførselen finnes i følgende samling(er)

Vis enkel innførsel