Automated code generation for discontinuous Galerkin methods

A compiler approach for generating low-level computer code from high-level input for discontinuous Galerkin finite element forms is presented. The input language mirrors conventional mathematical notation, and the compiler generates efficient code in a standard programming language. This facilitates the rapid generation of efficient code for general equations in varying spatial dimensions. Key concepts underlying the compiler approach and the automated generation of computer code are elaborated. The approach is demonstrated for a range of common problems, including the Poisson, biharmonic, advection--diffusion and Stokes equations

Electrochemical control of quantum interference in anthraquinone-based molecular switches

Using first-principles calculations we analyze the electronic transport properties of a recently proposed anthraquinone based electrochemical switch. Robust conductance on/off ratios of several orders of magnitude are observed due to destructive quantum interference present in the anthraquinone, but absent in the hydroquinone molecular bridge. A simple explanation of the interference effect is achieved by transforming the frontier molecular orbitals into localized molecular orbitals thereby obtaining a minimal tight-binding model describing the transport in the relevant energy range in terms of hopping via the localized orbitals. The topology of the tight-binding model, which is dictated by the symmetries of the molecular orbitals, determines the amount of quantum interference.Comment: 6 pages, 6 figure

Edge-dependent reflection and inherited fine structure of higher-order plasmons in graphene nanoribbons

We investigate higher-order plasmons in graphene nanoribbons, and present how electronic edge states and wavefunction fine structure influence the graphene plasmons. Based on nearest-neighbor tight-binding calculations, we find that a standing-wave model based on nonlocal bulk plasmon dispersion is surprisingly accurate for armchair ribbons of widths even down to a few nanometers, and we determine the corresponding phase shift upon edge reflection and an effective ribbon width. Wider zigzag ribbons exhibit a similar phase shift, whereas the standing-wave model describes few-nanometer zigzag ribbons less satisfactorily, to a large extent because of their edge states. We directly confirm that also the larger broadening of plasmons for zigzag ribbons is due to their edge states. Furthermore, we report a prominent fine structure in the induced charges of the ribbon plasmons, which for armchair ribbons follows the electronic wavefunction oscillations induced by inter-valley coupling. Interestingly, the wavefunction fine structure is also found in our analogous density-functional theory calculations, and both these and tight-binding numerical calculations are explained quite well with analytical Dirac theory for graphene ribbons

Predicting B Cell Receptor Substitution Profiles Using Public Repertoire Data

B cells develop high affinity receptors during the course of affinity maturation, a cyclic process of mutation and selection. At the end of affinity maturation, a number of cells sharing the same ancestor (i.e. in the same "clonal family") are released from the germinal center, their amino acid frequency profile reflects the allowed and disallowed substitutions at each position. These clonal-family-specific frequency profiles, called "substitution profiles", are useful for studying the course of affinity maturation as well as for antibody engineering purposes. However, most often only a single sequence is recovered from each clonal family in a sequencing experiment, making it impossible to construct a clonal-family-specific substitution profile. Given the public release of many high-quality large B cell receptor datasets, one may ask whether it is possible to use such data in a prediction model for clonal-family-specific substitution profiles. In this paper, we present the method "Substitution Profiles Using Related Families" (SPURF), a penalized tensor regression framework that integrates information from a rich assemblage of datasets to predict the clonal-family-specific substitution profile for any single input sequence. Using this framework, we show that substitution profiles from similar clonal families can be leveraged together with simulated substitution profiles and germline gene sequence information to improve prediction. We fit this model on a large public dataset and validate the robustness of our approach on an external dataset. Furthermore, we provide a command-line tool in an open-source software package (https://github.com/krdav/SPURF) implementing these ideas and providing easy prediction using our pre-fit models.Comment: 23 page

Emergent scale invariance of non-classical plasmons in graphene nanoribbons

Using a nearest-neighbor tight-binding model we investigate quantum effects of plasmons on few-nanometer wide graphene nanoribbons, both for zigzag and armchair edge terminations. With insight from the Dirac description we find an emerging scale-invariant behavior that deviates from the classical model both for zigzag and armchair structures. The onset of the deviation can be related to the position of the lowest parabolic band in the band structure. Dirac theory is only valid in the parameter subspace where the scale invariance holds that relates narrow ribbons with high doping to wide ribbons with low doping. We also find that the edge states present in zigzag ribbons give rise to a blueshift of the plasmon, in contrast to earlier findings for graphene nanodisks and nanotriangles

Calibration of the Mass-Temperature Relation for Clusters of Galaxies Using Weak Gravitational Lensing

The main uncertainty in current determinations of the power spectrum normalization, sigma_8, from abundances of X-ray luminous galaxy clusters arises from the calibration of the mass-temperature relation. We use our weak lensing mass determinations of 30 clusters from the hitherto largest sample of clusters with lensing masses, combined with X-ray temperature data from the literature, to calibrate the normalization of this relation at a temperature of 8 keV, M_{500c,8 keV}=(8.7 +/- 1.6) h^{-1} 10^{14} M_sun. This normalization is consistent with previous lensing-based results based on smaller cluster samples, and with some predictions from numerical simulations, but higher than most normalizations based on X-ray derived cluster masses. Assuming the theoretically expected slope alpha=3/2 of the mass-temperature relation, we derive sigma_8 = 0.88 +/-0.09 for a spatially-flat LambdaCDM universe with Omega_m = 0.3. The main systematic errors on the lensing masses result from extrapolating the cluster masses beyond the field-of-view used for the gravitational lensing measurements, and from the separation of cluster/background galaxies, contributing each with a scatter of 20%. Taking this into account, there is still significant intrinsic scatter in the mass-temperature relation indicating that this relation may not be very tight, at least at the high mass end. Furthermore, we find that dynamically relaxed clusters are 75 +/-40% hotter than non-relaxed clusters.Comment: 8 pages, 4 figures, revised version submitted to Ap

Motor-driven Dynamics of Cytoskeletal FIlaments in Motility Assays

We model analytically the dynamics of a cytoskeletal filament in a motility assay. The filament is described as rigid rod free to slide in two dimensions. The motor proteins consist of polymeric tails tethered to the plane and modeled as linear springs and motor heads that bind to the filament. As in related models of rigid and soft two-state motors, the binding/unbinding dynamics of the motor heads and the dependence of the transition rates on the load exerted by the motor tails play a crucial role in controlling the filament's dynamics. Our work shows that the filament effectively behaves as a self-propelled rod at long times, but with non-Markovian noise sources arising from the coupling to the motor binding/unbinding dynamics. The effective propulsion force of the filament and the active renormalization of the various friction and diffusion constants are calculated in terms of microscopic motor and filament parameters. These quantities could be probed by optical force microscopy.Comment: 13 pages, 8 figures, 1 Tabl

Plasmonic eigenmodes in individual and bow-tie graphene nanotriangles

Serving as a new two-dimensional plasmonic material, graphene has stimulated an intensive study of its optical properties which benefit from the unique electronic band structure of the underlying honeycomb lattice of carbon atoms. In classical electrodynamics, nanostructured graphene is commonly modeled by the computationally demanding problem of a three-dimensional conducting film of atomic-scale thickness. Here, we propose an efficient alternative two-dimensional electrostatic approach where all the calculation procedures are restricted to the plane of the graphene sheet. To explore possible quantum effects, we perform tight-binding calculations, adopting a random-phase approximation. We investigate the multiple plasmon modes in triangles of graphene, treating the optical response classically as well as quantum mechanically in the case of both armchair and zigzag edge termination of the underlying atomic lattice. Compared to the classical plasmonic spectrum which is "blind" to the edge termination, we find that the quantum plasmon frequencies exhibit blueshifts in the case of armchair edge termination, while redshifts are found for zigzag edges. Furthermore, we find spectral features in the zigzag case which are associated with electronic edge states not present for armchair termination. Merging pairs of such triangles into dimers, the plasmon hybridization leads to energy splitting in accordance with plasmon-hybridization theory, with a lower energy for the antisymmetric modes and a smaller splitting for modes with less confinement to the gap region. The hybridization appears strongest in classical calculations while the splitting is lower for armchair edges and even more reduced for zigzag edges. Our various results illustrate a surprising phenomenon: Even 20 nm large graphene structures clearly exhibit quantum plasmonic features due to atomic-scale details in the edge termination.Comment: 27 pages including 7 figures. Supplementary information available upon request to author

Visualizing hybridized quantum plasmons in coupled nanowires:From classical to tunneling regime

We present full quantum mechanical calculations of the hybridized plasmon modes of two nanowires at small separation, providing real space visualization of the modes in the transition from the classical to the quantum tunneling regime. The plasmon modes are obtained as certain eigenfunctions of the dynamical dielectric function which is computed using time dependent density functional theory (TDDFT). For freestanding wires, the energy of both surface and bulk plasmon modes deviate from the classical result for low wire radii and high momentum transfer due to effects of electron spill-out, non-local response, and coupling to single-particle transitions. For the wire dimer the shape of the hybridized plasmon modes are continuously altered with decreasing separation, and below 6 {\AA} the energy dispersion of the modes deviate from classical results due to the onset of weak tunneling. Below 2-3 {\AA} separation this mode is replaced by a charge-transfer plasmon which blue shifts with decreasing separation in agreement with experiment, and marks the onset of the strong tunneling regime.Comment: To appear in PR