Critical comparison of electrode models in density functional theory based quantum transport calculations

We study the performance of two different electrode models in quantum transport calculations based on density functional theory: Parametrized Bethe lattices and quasi-one dimensional wires or nanowires. A detailed account of implementation details in both cases is given. From the systematic study of nanocontacts made of representative metallic elements, we can conclude that parametrized electrode models represent an excellent compromise between computational cost and electronic structure definition as long as the aim is to compare with experiments where the precise atomic structure of the electrodes is not relevant or defined with precision. The results obtained using parametrized Bethe lattices are essentially similar to the ones obtained with quasi one dimensional electrodes for large enough sections of these, adding a natural smearing to the transmission curves that mimics the true nature of polycrystalline electrodes. The latter are more demanding from the computational point of view, but present the advantage of expanding the range of applicability of transport calculations to situations where the electrodes have a well-defined atomic structure, as is case for carbon nanotubes, graphene nanoribbons or semiconducting nanowires. All the analysis is done with the help of codes developed by the authors which can be found in the quantum transport toolbox Alacant and are publicly available.Comment: 17 pages, 12 figure

Kondo effect and spin quenching in high-spin molecules on metal substrates

Using a state-of-the art combination of density functional theory and impurity solver techniques we present a complete and parameter-free picture of the Kondo effect in the high-spin ($S=3/2$) coordination complex known as Manganese Phthalocyanine adsorbed on the Pb(111) surface. We calculate the correlated electronic structure and corresponding tunnel spectrum and find an asymmetric Kondo resonance, as recently observed in experiments. Contrary to previous claims, the Kondo resonance stems from only one of three possible Kondo channels with origin in the Mn 3d-orbitals, its peculiar asymmetric shape arising from the modulation of the hybridization due to strong coupling to the organic ligand. The spectral signature of the second Kondo channel is strongly suppressed as the screening occurs via the formation of a many-body singlet with the organic part of the molecule. Finally, a spin-1/2 in the 3d-shell remains completely unscreened due to the lack of hybridization of the corresponding orbital with the substrate, hence leading to a spin-3/2 underscreened Kondo effect.Comment: 5 pages, 2 figure

Mechanical, Electrical, and Magnetic Properties of Ni Nanocontacts

The dynamic deformation upon stretching of Ni nanowires as those formed with mechanically controllable break junctions or with a scanning tunneling microscope is studied both experimentally and theoretically. Molecular dynamics simulations of the breaking process are performed. In addition, and in order to compare with experiments, we also compute the transport properties in the last stages before failure using the first-principles implementation of Landauer's formalism included in our transport package ALACANT.Comment: 5 pages, 6 figure

Competition between quantum spin tunneling and Kondo effect

Quantum spin tunneling (QST) and Kondo effect are two very different quantum phenomena that produce the same effect on quantized spins, namely, the quenching of their magnetization. However, the nature of this quenching is very different so that QST and Kondo effects compete with each other. Importantly, both QST and Kondo produce very characteristic features in the spectral function that can be measured by means of single spin scanning tunneling spectroscopy that makes it possible to probe the crossover from one regime to the other. We model this crossover, and the resulting changes in transport, using a non-perturbative treatment of a generalized Anderson model including magnetic anisotropy that leads to quantum spin tunneling. We predict that, at zero magnetic field, integer spins can feature a split-Kondo peak driven by quantum spin tunneling.Comment: 5 pages, 3 figures; accepted in EPJB; replaced with revised manuscrip

Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors.

Matrix metalloproteinases are zinc-containing enzymes capable of degrading all components of the extracellular matrix. Owing to their role in human disease, matrix metalloproteinase have been the subject of extensive study. A bioinorganic approach was recently used to identify novel inhibitors based on a maltol zinc-binding group, but accompanying molecular-docking studies failed to explain why one of these inhibitors, AM-6, had approximately 2500-fold selectivity for MMP-3 over MMP-2. A number of studies have suggested that the matrix-metalloproteinase active site is highly flexible, leading some to speculate that differences in active-site flexibility may explain inhibitor selectivity. To extend the bioinorganic approach in a way that accounts for MMP-2 and MMP-3 dynamics, we here investigate the predicted binding modes and energies of AM-6 docked into multiple structures extracted from matrix-metalloproteinase molecular dynamics simulations. Our findings suggest that accounting for protein dynamics is essential for the accurate prediction of binding affinity and selectivity. Additionally, AM-6 and other similar inhibitors likely select for and stabilize only a subpopulation of all matrix-metalloproteinase conformations sampled by the apo protein. Consequently, when attempting to predict ligand affinity and selectivity using an ensemble of protein structures, it may be wise to disregard protein conformations that cannot accommodate the ligand

Coherent transport in graphene nanoconstrictions

We study the effect of a structural nanoconstriction on the coherent transport properties of otherwise ideal zig-zag-edged infinitely long graphene ribbons. The electronic structure is calculated with the standard one-orbital tight-binding model and the linear conductance is obtained using the Landauer formula. We find that, since the zero-bias current is carried in the bulk of the ribbon, this is very robust with respect to a variety of constriction geometries and edge defects. In contrast, the curve of zero-bias conductance versus gate voltage departs from the $(2n+1) e^2/h$ staircase of the ideal case as soon as a single atom is removed from the sample. We also find that wedge-shaped constrictions can present non-conducting states fully localized in the constriction close to the Fermi energy. The interest of these localized states in regards the formation of quantum dots in graphene is discussed.Comment: 9 pages, 9 figure

The study of parameter optimization in vehicle-borne tracking systems Final technical report

Data smoothing technique for parameter optimization in free flight orbit vehicle-borne tracking system

Measurements of Coronal Faraday Rotation at 4.6 Solar Radii

Many competing models for the coronal heating and acceleration mechanisms of the high-speed solar wind depend on the solar magnetic field and plasma structure in the corona within heliocentric distances of $5R_\odot$. We report on sensitive VLA full-polarization observations made in August, 2011, at 5.0 and 6.1 GHz (each with a bandwidth of 128 MHz) of the radio galaxy 3C228 through the solar corona at heliocentric distances of $4.6-5.0R_\odot$. Observations at 5.0 GHz permit measurements deeper in the corona than previous VLA observations at 1.4 and 1.7 GHz. These Faraday rotation observations provide unique information on the magnetic field in this region of the corona. The measured Faraday rotation on this day was lower than our a priori expectations, but we have successfully modeled the measurement in terms of observed properties of the corona on the day of observation. Our data on 3C228 provide two lines of sight (separated by 46'', 33,000 km in the corona). We detected three periods during which there appeared to be a difference in the Faraday rotation measure between these two closely spaced lines of sight. These measurements (termed differential Faraday rotation) yield an estimate of $2.6$ to $4.1$ GA for coronal currents. Our data also allow us to impose upper limits on rotation measure fluctuations caused by coronal waves; the observed upper limits were $3.3$ and $6.4$ rad/m$^2$ along the two lines of sight. The implications of these results for Joule heating and wave heating are briefly discussed.Comment: This is a pre-print of an article submitted to the Astrophysical Journal. This version has been revised following the referee's suggestions and resubmitte