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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.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.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.publisherAmerican Physical Societyen_AU
dc.subjectDispersion relationsen_AU
dc.subjectIntermolecular forcesen_AU
dc.subjectMolecular dnamics methoden_AU
dc.titleAtomistic model of DNA: phonons and base-pair opening.en_AU
dc.typeJournal Articleen_AU
Appears in Collections:Journal Articles

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