Ab initio study of a mechanically gated molecule: From weak to strong correlation

The electronic spectrum of a chemically contacted molecule in the junction of a scanning tunneling microscope can be modified by tip retraction. We analyze this effect by a combination of density functional, many-body perturbation and numerical renormalization group theory, taking into account both the non-locality and the dynamics of electronic correlation. Our findings, in particular the evolution from a broad quasiparticle resonance below to a narrow Kondo resonance at the Fermi energy, correspond to the experimental observations.Comment: 4 pages, 3 figure

Imaging Pauli repulsion in scanning tunneling microscopy

A scanning tunneling microscope (STM) has been equipped with a nanoscale force sensor and signal transducer composed of a single D2 molecule that is confined in the STM junction. The uncalibrated sensor is used to obtain ultra-high geometric image resolution of a complex organic molecule adsorbed on a noble metal surface. By means of conductance-distance spectroscopy and corresponding density functional calculations the mechanism of the sensor/transducer is identified. It probes the short-range Pauli repulsion and converts this signal into variations of the junction conductance.Comment: 4 pages, 4 figures, accepted to Phys. Rev. Let

Electrical transport through a mechanically gated molecular wire

A surface-adsorbed molecule is contacted with the tip of a scanning tunneling microscope (STM) at a pre-defined atom. On tip retraction, the molecule is peeled off the surface. During this experiment, a two-dimensional differential conductance map is measured on the plane spanned by the bias voltage and the tip-surface distance. The conductance map demonstrates that tip retraction leads to mechanical gating of the molecular wire in the STM junction. The experiments are compared with a detailed ab initio simulation. We find that density functional theory (DFT) in the local density approximation (LDA) describes the tip-molecule contact formation and the geometry of the molecular junction throughout the peeling process with predictive power. However, a DFT-LDA-based transport simulation following the non-equilibrium Green's functions (NEGF) formalism fails to describe the behavior of the differential conductance as found in experiment. Further analysis reveals that this failure is due to the mean-field description of electron correlation in the local density approximation. The results presented here are expected to be of general validity and show that, for a wide range of common wire configurations, simulations which go beyond the mean-field level are required to accurately describe current conduction through molecules. Finally, the results of the present study illustrate that well-controlled experiments and concurrent ab initio transport simulations that systematically sample a large configuration space of molecule-electrode couplings allow the unambiguous identification of correlation signatures in experiment.Comment: 31 pages, 10 figure

Scanning Quantum Dot Microscopy

Interactions between atomic and molecular objects are to a large extent defined by the nanoscale electrostatic potentials which these objects produce. We introduce a scanning probe technique that enables three-dimensional imaging of local electrostatic potential fields with sub-nanometer resolution. Registering single electron charging events of a molecular quantum dot attached to the tip of a (qPlus tuning fork) atomic force microscope operated at 5 K, we quantitatively measure the quadrupole field of a single molecule and the dipole field of a single metal adatom, both adsorbed on a clean metal surface. Because of its high sensitivity, the technique can record electrostatic potentials at large distances from their sources, which above all will help to image complex samples with increased surface roughness.Comment: main text: 5 pages, 4 figures, supplementary information file: 4 pages, 2 figure

Quasiparticle energies for large molecules: a tight-binding GW approach

We present a tight-binding based GW approach for the calculation of quasiparticle energy levels in confined systems such as molecules. Key quantities in the GW formalism like the microscopic dielectric function or the screened Coulomb interaction are expressed in a minimal basis of spherically averaged atomic orbitals. All necessary integrals are either precalculated or approximated without resorting to empirical data. The method is validated against first principles results for benzene and anthracene, where good agreement is found for levels close to the frontier orbitals. Further, the size dependence of the quasiparticle gap is studied for conformers of the polyacenes ($C_{4n+2}H_{2n+4}$) up to n = 30.Comment: 10 pages, 5 eps figures submitted to Phys. Rev.

Nonlocal vortex motion in mesoscopic amorphous Nb0.7Ge0.3 structures

We study nonlocal vortex transport in mesoscopic amorphous Nb0.7Ge0.3 samples. A dc current I is passed through a wire connected via a perpendicular channel, of a length L= 2-5 um, with a pair of voltage probes where a nonlocal response Vnl ~ I is measured. The maximum of Rnl=Vnl/I for a given temperature occurs at an L-independent magnetic field and is proportional to 1/L. The results are interpreted in terms of the dissipative vortex motion along the channel driven by a remote current, and can be understood in terms of a simple model.Comment: 4 pages, 3 figure

Doppler Shift in Andreev Reflection from a Moving Superconducting Condensate in Nb/InAs Josephson Junctions

We study narrow ballistic Josephson weak links in a InAs quantum wells contacted by Nb electrodes and find a dramatic magnetic-field suppression of the Andreev reflection amplitude, which occurs even for in-plane field orientation with essentially no magnetic flux through the junction. Our observations demonstrate the presence of a Doppler shift in the energy of the Andreev levels, which results from diamagnetic screening currents in the hybrid Nb/InAs-banks. The data for conductance, excess and critical currents can be consistently explained in terms of the sample geometry and the McMillan energy, characterizing the transparency of the Nb/InAs-interface.Comment: 4 pages, 5 figures, title modifie

Ab-initio calculation of optical absorption in semiconductors: A density-matrix description

We show how to describe Coulomb renormalization effects and dielectric screening in semiconductors and semiconductor nanostructures within a first-principles density-matrix description. Those dynamic variables and approximation schemes which are required for a proper description of dielectric screening are identified. It is shown that within the random-phase approximation the direct Coulomb interactions become screened, with static screening being a good approximation, whereas the electron-hole exchange interactions remain unscreened. Differences and similarities of our results with those obtained from a corresponding GW approximation and Bethe-Salpeter equation Green's function analysis are discussed.Comment: 10 pages, to be published in Physical Review

Dynamical bi-stability of single-molecule junctions: A combined experimental/theoretical study of PTCDA on Ag(111)

The dynamics of a molecular junction consisting of a PTCDA molecule between the tip of a scanning tunneling microscope and a Ag(111) surface have been investigated experimentally and theoretically. Repeated switching of a PTCDA molecule between two conductance states is studied by low-temperature scanning tunneling microscopy for the first time, and is found to be dependent on the tip-substrate distance and the applied bias. Using a minimal model Hamiltonian approach combined with density-functional calculations, the switching is shown to be related to the scattering of electrons tunneling through the junction, which progressively excite the relevant chemical bond. Depending on the direction in which the molecule switches, different molecular orbitals are shown to dominate the transport and thus the vibrational heating process. This in turn can dramatically affect the switching rate, leading to non-monotonic behavior with respect to bias under certain conditions. In this work, rather than simply assuming a constant density of states as in previous works, it was modeled by Lorentzians. This allows for the successful description of this non-monotonic behavior of the switching rate, thus demonstrating the importance of modeling the density of states realistically.Comment: 20 pages, 6 figures, 1 tabl

Predicting Fluid Intelligence of Children using T1-weighted MR Images and a StackNet

In this work, we utilize T1-weighted MR images and StackNet to predict fluid intelligence in adolescents. Our framework includes feature extraction, feature normalization, feature denoising, feature selection, training a StackNet, and predicting fluid intelligence. The extracted feature is the distribution of different brain tissues in different brain parcellation regions. The proposed StackNet consists of three layers and 11 models. Each layer uses the predictions from all previous layers including the input layer. The proposed StackNet is tested on a public benchmark Adolescent Brain Cognitive Development Neurocognitive Prediction Challenge 2019 and achieves a mean squared error of 82.42 on the combined training and validation set with 10-fold cross-validation. In addition, the proposed StackNet also achieves a mean squared error of 94.25 on the testing data. The source code is available on GitHub.Comment: 8 pages, 2 figures, 3 tables, Accepted by MICCAI ABCD-NP Challenge 2019; Added ND