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

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.

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

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

Structural relaxations in electronically excited poly(para-phenylene)

Structural relaxations in electronically excited poly(para-phenylene) are studied using many-body perturbation theory and density-functional-theory methods. A sophisticated description of the electron-hole interaction is required to describe the energies of the excitonic states, but we show that the structural relaxations associated with exciton formation can be obtained quite accurately within a constrained density-functional-theory approach. We find that the structural relaxations in the low-energy excitonic states extend over about 8 monomers, leading to an energy reduction of 0.22 eV and a Stokes shift of 0.40 eV.Comment: 4 pages, 3 figure

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

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states

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

Sonoluminescence: Nature's Smallest BlackBody

The Spectrum of the light emitted by a sonoluminescing bubble is extremely well fit by the spectrum of a blackbody. Furthermore the radius of emission can be smaller than the wavelength of the light. Consequences, for theories of sonoluminescence are discussed.Comment: 8 pages, 3 Figure