Atomistic model of DNA: phonons and base-pair opening

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dc.contributor.authorMerzel, Fen_AU
dc.contributor.authorFontaine-Vive, Fen_AU
dc.contributor.authorJohnson, MRen_AU
dc.contributor.authorKearley, GJen_AU
dc.date.accessioned2008-04-28T04:57:18Zen_AU
dc.date.accessioned2010-04-30T05:02:58Zen_AU
dc.date.available2008-04-28T04:57:18Zen_AU
dc.date.available2010-04-30T05:02:58Zen_AU
dc.date.issued2007-09en_AU
dc.date.statistics2007-09en_AU
dc.description.abstractA fully atomistic model of B-DNA using the CHARMM (chemistry at Harvard molecular mechanics) force field is presented. Molecular dynamics simulations were used to prepare an equilibrium structure. The Hessian of interatomic forces obtained from CHARMM for the equilibrium structure was used as input to a large scale phonon calculation. The calculated dispersion relations at low frequency are compared with recently published experimental data, which shows the model to have good accuracy for the low frequency, vibrational modes of DNA. These are discussed in the context of base-pair opening. In addition to the widely reported modes at, or below, ~12.5 meV, a continuous band of modes with strong base-pair opening character is found up to 40 meV, which coincides with the typical denaturation temperature of DNA. © 2007, American Physical Societyen_AU
dc.identifier.articlenumber31917en_AU
dc.identifier.citationMerzel, F., Fontaine-Vive, F., Johnson, M. R., & Kearley, G. J. (2007). Atomistic model of DNA: phonons and base-pair opening. Physical Review E, 76(3), 031917. doi:10.1103/PhysRevE.76.031917en_AU
dc.identifier.govdoc1189en_AU
dc.identifier.issn1539-3755en_AU
dc.identifier.issue3en_AU
dc.identifier.journaltitlePhysical Review Een_AU
dc.identifier.urihttp://dx.doi.org/10.1103/PhysRevE.76.031917en_AU
dc.identifier.urihttp://apo.ansto.gov.au/dspace/handle/10238/1134en_AU
dc.identifier.volume76en_AU
dc.language.isoenen_AU
dc.publisherAmerican Physical Societyen_AU
dc.subjectDispersion relationsen_AU
dc.subjectDNAen_AU
dc.subjectBiophysicsen_AU
dc.subjectIntermolecular forcesen_AU
dc.subjectEquilibriumen_AU
dc.subjectMolecular dynamics methoden_AU
dc.titleAtomistic model of DNA: phonons and base-pair openingen_AU
dc.typeJournal Articleen_AU
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