Browsing by Author "Fontaine-Vive, F"

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    Atomistic model of DNA: phonons and base-pair opening
    (American Physical Society, 2007-09) Merzel, F; Fontaine-Vive, F; Johnson, MR; Kearley, GJ
    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
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    Collagen and component polypeptides: low frequency and amide vibrations.
    (Elsevier, 2009-01-27) Fontaine-Vive, F; Merzel, F; Johnson, MR; Kearley, GJ
    Collagen is a fibrous protein, which exists widely in the human body. The biomechanical properties of collagen depend on its triple helix structure and the corresponding low frequency vibrations. We use first-principles, density functional theory methods and analytical force fields to investigate the molecular vibrations of a model collagen compound, the results being validated by comparison with published, inelastic neutron scattering data. The results from these atomistic simulations are used at higher frequency to Study the Amide I and V vibrations and therefore the vibrational signature of secondary and tertiary structure formation. In addition to collagen, its component homopolymers, poly-glycine and poly-proline are also studied. The Amide V vibration of glycine is strongly modified in going from the single helix of poly-glycine II to the triple helix of collagen. The collagen models are hydrated and this work allows LIS to discuss the relative merits of density functional theory and force field methods when tackling complex, partially crystalline systems. © 2008, Elsevier Ltd.