Rosa Di Felice

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Attempts to resolve the energy-level structure of single DNA molecules by scanning tunnelling spectroscopy span over the past two decades, owing to the unique ability of this technique to probe the local density of states of objects deposited on a surface. Nevertheless, success was hindered by extreme technical difficulties in stable deposition and(More)
We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional. Our(More)
We use a stepwise pulling protocol in molecular dynamics simulations to identify how a G-quadruplex selects and conducts Na(+), K(+), and NH4(+) ions. By estimating the minimum free-energy changes of the ions along the central channel via Jarzynski's equality, we find that the G-quadruplex selectively binds the ionic species in the following order: K(+) >(More)
G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. The superior(More)
We present a detailed study of the charge transport characteristics of double-stranded DNA oligomers including the oxidative damage 7,8-dihydro-8-oxoguanine (8-oxoG). The problem is treated by a hybrid methodology combining classical molecular dynamics simulations and semiempirical electronic structure calculations to formulate a coarse-grained charge(More)
We briefly present the results of recent experiments of transverse scanning tunneling spectroscopy of homogeneous poly(dG)-poly(dC) DNA molecules and discuss them in the light of theoretical investigation. A semiempirical theoretical model is adopted to describe the transverse tunneling current across a DNA molecule placed between a metallic gold substrate(More)
We report the inclusion of electron-electron correlation in the calculation of transport properties within an ab initio scheme. A key step is the reformulation of Landauer's approach in terms of an effective transmittance for the interacting electron system. We apply this framework to analyze the effect of short-range interactions on Pt atomic wires and(More)
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