Identification of the Atomic Scale Structures of the Gold-Thiol Interfaces of Molecular Nanowires by Inelastic Tunneling Spectroscopy

We examine theoretically the effects of the bonding geometries at the gold-thiol interfaces on the inelastic tunneling spectra of propanedithiolate (PDT) molecules bridging gold electrodes and show that inelastic tunneling spectroscopy combined with theory can be used to determine these bonding geometries experimentally. With the help of density functional theory, we calculate the relaxed geometries and vibrational modes of extended molecules each consisting of one or two PDT molecules connecting two gold nanoclusters. We formulate a perturbative theory of inelastic tunneling through molecules bridging metal contacts in terms of elastic transmission amplitudes, and use this theory to calculate the inelastic tunneling spectra of the gold-PDT-gold extended molecules. We consider PDT molecules with both trans and gauche conformations bound to the gold clusters at top, bridge and hollow bonding sites. Comparing our results with the experimental data of Hihath et al. [Nano Lett. 8, 1673 (2008)], we identify the most frequently realized conformation in the experiment as that of trans molecules top-site bonded to both electrodes. We find the switching from the 42 meV vibrational mode to the 46 meV mode observed in the experiment to be due to the transition of trans molecules from mixed top-bridge to pure top-site bonding geometries. Our results also indicate that gauche molecular conformations and hollow site bonding did not contribute significantly to the experimental inelastic tunneling spectra. For pairs of PDT molecules connecting the gold electrodes in parallel we find total elastic conductances close to twice those of single molecules bridging the contacts with similar bonding conformations and small splittings of the vibrational mode energies for the modes that are the most sensitive to the molecule-electrode bonding geometries.Comment: 14 pages, 8 figures, 1 table. arXiv admin note: significant text overlap with arXiv:1103.2378; http://jcp.aip.org/resource/1/jcpsa6/v136/i1/p014703_s

Unusual conductance of polyyne-based molecular wires

We report a full self-consistent ab initio calculation of the current-voltage curve and the conductance of thiolate capped polyynes in contact with gold electrodes. We find the conductance of polyynes an order of magnitude larger compared with other conjugated oligomers. The reason lies in the position of the Fermi level deep in the HOMO related resonance. With the conductance weakly dependent on the applied bias and almost independent of the length of the molecular chain, polyynes appear as nearly perfect molecular wires.Comment: 4 pages, 5 figures, 3 table

Consequences of a Change in the Galactic Environment of the Sun

The interaction of the heliosphere with interstellar clouds has attracted interest since the late 1920's, both with a view to explaining apparent quasi-periodic climate "catastrophes" as well as periodic mass extinctions. Until recently, however, models describing the solar wind - local interstellar medium (LISM) interaction self-consistently had not been developed. Here, we describe the results of a two-dimensional (2D) simulation of the interaction between the heliosphere and an interstellar cloud with the same properties as currently, except that the neutral H density is increased from the present value of n(H) ~ 0.2 cm^-3 to 10 cm^-3. The mutual interaction of interstellar neutral hydrogen and plasma is included. The heliospheric cavity is reduced considerably in size (approximately 10 - 14 AU to the termination shock in the upstream direction) and is highly dynamical. The interplanetary environment at the orbit of the Earth changes markedly, with the density of interstellar H increasing to ~2 cm^-3. The termination shock itself experiences periods where it disappears, reforms and disappears again. Considerable mixing of the shocked solar wind and LISM occurs due to Rayleigh-Taylor-like instabilities at the nose, driven by ion-neutral friction. Implications for two anomalously high concentrations of 10Be found in Antarctic ice cores 33 kya and 60 kya, and the absence of prior similar events, are discussed in terms of density enhancements in the surrounding interstellar cloud. The calculation presented here supports past speculation that the galactic environment of the Sun moderates the interplanetary environment at the orbit of the Earth, and possibly also the terrestrial climate.Comment: 23 pages, 2 color plates (jpg), 3 figures (eps

Universal decay of scalar turbulence

The asymptotic decay of passive scalar fields is solved analytically for the Kraichnan model, where the velocity has a short correlation time. At long times, two universality classes are found, both characterized by a distribution of the scalar -- generally non-Gaussian -- with global self-similar evolution in time. Analogous behavior is found numerically with a more realistic flow resulting from an inverse energy cascade.Comment: 4 pages, 3 Postscript figures, submitted to PR

Lagrangian Velocity Statistics in Turbulent Flows: Effects of Dissipation

We use the multifractal formalism to describe the effects of dissipation on Lagrangian velocity statistics in turbulent flows. We analyze high Reynolds number experiments and direct numerical simulation (DNS) data. We show that this approach reproduces the shape evolution of velocity increment probability density functions (PDF) from Gaussian to stretched exponentials as the time lag decreases from integral to dissipative time scales. A quantitative understanding of the departure from scaling exhibited by the magnitude cumulants, early in the inertial range, is obtained with a free parameter function D(h) which plays the role of the singularity spectrum in the asymptotic limit of infinite Reynolds number. We observe that numerical and experimental data are accurately described by a unique quadratic D(h) spectrum which is found to extend from $h_{min} \approx 0.18$ to $h_{max} \approx 1$, as the signature of the highly intermittent nature of Lagrangian velocity fluctuations.Comment: 5 pages, 3 figures, to appear in PR

Set-Theoretic Types for Polymorphic Variants

Polymorphic variants are a useful feature of the OCaml language whose current definition and implementation rely on kinding constraints to simulate a subtyping relation via unification. This yields an awkward formalization and results in a type system whose behaviour is in some cases unintuitive and/or unduly restrictive. In this work, we present an alternative formalization of poly-morphic variants, based on set-theoretic types and subtyping, that yields a cleaner and more streamlined system. Our formalization is more expressive than the current one (it types more programs while preserving type safety), it can internalize some meta-theoretic properties, and it removes some pathological cases of the current implementation resulting in a more intuitive and, thus, predictable type system. More generally, this work shows how to add full-fledged union types to functional languages of the ML family that usually rely on the Hindley-Milner type system. As an aside, our system also improves the theory of semantic subtyping, notably by proving completeness for the type reconstruction algorithm.Comment: ACM SIGPLAN International Conference on Functional Programming, Sep 2016, Nara, Japan. ICFP 16, 21st ACM SIGPLAN International Conference on Functional Programming, 201

Dynamic mean-field and cavity methods for diluted Ising systems

We compare dynamic mean-field and dynamic cavity as methods to describe the stationary states of dilute kinetic Ising models. We compute dynamic mean-field theory by expanding in interaction strength to third order, and compare to the exact dynamic mean-field theory for fully asymmetric networks. We show that in diluted networks the dynamic cavity method generally predicts magnetizations of individual spins better than both first order ("naive") and second order ("TAP") dynamic mean field theory

Log-Poisson Cascade Description of Turbulent Velocity Gradient Statistics

The Log-Poisson phenomenological description of the turbulent energy cascade is evoked to discuss high-order statistics of velocity derivatives and the mapping between their probability distribution functions at different Reynolds numbers. The striking confirmation of theoretical predictions suggests that numerical solutions of the flow, obtained at low/moderate Reynolds numbers can play an important quantitative role in the analysis of experimental high Reynolds number phenomena, where small scales fluctuations are in general inaccessible from direct numerical simulations

Localness of energy cascade in hydrodynamic turbulence, II. Sharp spectral filter

We investigate the scale-locality of subgrid-scale (SGS) energy flux and inter-band energy transfers defined by the sharp spectral filter. We show by rigorous bounds, physical arguments and numerical simulations that the spectral SGS flux is dominated by local triadic interactions in an extended turbulent inertial-range. Inter-band energy transfers are also shown to be dominated by local triads if the spectral bands have constant width on a logarithmic scale. We disprove in particular an alternative picture of ``local transfer by nonlocal triads,'' with the advecting wavenumber mode at the energy peak. Although such triads have the largest transfer rates of all {\it individual} wavenumber triads, we show rigorously that, due to their restricted number, they make an asymptotically negligible contribution to energy flux and log-banded energy transfers at high wavenumbers in the inertial-range. We show that it is only the aggregate effect of a geometrically increasing number of local wavenumber triads which can sustain an energy cascade to small scales. Furthermore, non-local triads are argued to contribute even less to the space-average energy flux than is implied by our rigorous bounds, because of additional cancellations from scale-decorrelation effects. We can thus recover the -4/3 scaling of nonlocal contributions to spectral energy flux predicted by Kraichnan's ALHDIA and TFM closures. We support our results with numerical data from a $512^3$ pseudospectral simulation of isotropic turbulence with phase-shift dealiasing. We conclude that the sharp spectral filter has a firm theoretical basis for use in large-eddy simulation (LES) modeling of turbulent flows.Comment: 42 pages, 9 figure