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Title: Atomistic model of DNA: phonons and base-pair opening
Authors: Merzel, F
Fontaine-Vive, F
Johnson, MR
Kearley, GJ
Keywords: Dispersion relations
Intermolecular forces
Molecular dynamics method
Issue Date: Sep-2007
Publisher: American Physical Society
Citation: Merzel, 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.76.031917
Abstract: A 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 Society
Gov't Doc #: 1189
ISSN: 1539-3755
Appears in Collections:Journal Articles

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