Comment on "Magnetism in atomic-size palladium contacts and nanowires".
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Comment↗
Biomedical subjects
José M Soler
Publications and source records attributed to José M Soler.
Strain-dependence of the electronic properties in periodic quadruple helical G4-wires.
The electronic structure of periodic quadruple helix guanine wires, which mimic G4-DNA molecules, was studied as a function of the stacking distance between consecutive planes, by means of first principles density functional theory calculations. We show that, whereas for the native DNA interplane separation of 3.4 A the HOMO- and LUMO-derived bands are poorly dispersive, the bandwidths can be significantly increased when compressive strain is applied along the helical axis. Our findings indicate that efficient band conduction for both holes and electrons can be supported by such wires for stacking distances below 2.6 A, which imply a huge axial deformation with respect to double and quadruple helices in solutions and in crystals.
Computer Simulation↗
Tip and surface determination from experiments and simulations of scanning tunneling microscopy and spectroscopy.
We present a very efficient and accurate method to simulate scanning tunneling microscopy images and spectra from first-principles density functional calculations. The wave functions of the tip and sample are calculated separately on the same footing and propagated far from the surface using the vacuum Green function. This allows us to express the Bardeen matrix elements in terms of convolutions and to obtain the tunneling current at all tip positions and bias voltages in a single calculation. The efficiency of the method opens the door to real time determination of both tip and surface composition and structure, by comparing experiments to simulated images for a variety of precomputed tips. Comparison with the experimental topography and spectra of the Si111-(7 x 7) surface shows a much better agreement with Si than with W tips, implying that the metallic tip is terminated by silicon.
Journal Article↗
Efficient mixed-force first-principles molecular dynamics.
We present an efficient method to mix well converged ab initio forces with simpler and faster ones in molecular dynamics. While the cheap forces are evaluated every time step, the converged ones correct the trajectory only every n time steps. For convenience, both types of forces are calculated with the same basic scheme, using density functional theory, norm-conserving pseudopotentials, and a basis set of numerical atomic orbitals. The cheap forces are evaluated with a short-range minimal basis set and the non-self-consistent Harris functional. Since these evaluations are hundreds of times faster than those of the converged forces, they add a negligible cost, and the boost in computational efficiency is approximately a factor n. Our results indicate that one can use values of n of up to 10, without affecting significantly the calculated structural and dynamical magnitudes.
Journal Article↗
Small polarons in dry DNA.
We report ab initio calculations for positively charged fragments of dry poly(dC)-poly(dG) DNA, with up to 4 C-G pairs. We find a strong hole-lattice coupling and clear evidence for the formation of small polarons. The largest geometry distortions occur in only one or two base pairs. They involve the stretching of weak bonds within each base pair, increasing the distance of positive hydrogens, and decreasing that of negative oxygens, to the region in which the hole localizes. We obtain an energy of approximately 0.30 eV for the polaron formation, nearly independent of the chain size. From it, we can estimate an activation energy for polaron hopping of approximately 0.15 eV, consistent with the available experimental value.
Base Pairing↗