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• W1504966425 abstract "Using 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." @default.
• W1504966425 created "2016-06-24" @default.
• W1504966425 creator A5013343035 @default.
• W1504966425 creator A5063946606 @default.
• W1504966425 date "2015-06-19" @default.
• W1504966425 modified "2023-10-14" @default.
• W1504966425 title "Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison" @default.
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• W1504966425 doi "https://doi.org/10.1063/1.4922519" @default.
• W1504966425 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26093580" @default.
• W1504966425 hasPublicationYear "2015" @default.
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