Topology of the Spin-polarized Charge Density in bcc and fcc Iron

We investigate the topology of the spin-polarized charge density in bcc and fcc iron. While the total spin-density is found to possess the topology of the non-magnetic prototypical structures, in some cases the spin-polarized densities are characterized by unique topologies; for example, the spin-polarized charge densities of bcc and high-spin fcc iron are atypical of any known for non-magnetic materials. In these cases, the two spin-densities are correlated: the spin-minority electrons have directional bond paths with deep minima in the minority density, while the spin-majority electrons fill these holes, reducing bond directionality. The presence of two distinct spin topologies suggests that a well-known magnetic phase transition in iron can be fruitfully reexamined in light of these topological changes. We show that the two phase changes seen in fcc iron (paramagnetic to low-spin and low-spin to high-spin) are different. The former follows the Landau symmetry-breaking paradigm and proceeds without a topological transformation, while the latter also involves a topological catastrophe.Comment: 5 pages, 3 figures. Phys. Rev. Lett. (in press

Detection and quantification of inverse spin Hall effect from spin pumping in permalloy/normal metal bilayers

Spin pumping is a mechanism that generates spin currents from ferromagnetic resonance (FMR) over macroscopic interfacial areas, thereby enabling sensitive detection of the inverse spin Hall effect that transforms spin into charge currents in non-magnetic conductors. Here we study the spin-pumping-induced voltages due to the inverse spin Hall effect in permalloy/normal metal bilayers integrated into coplanar waveguides for different normal metals and as a function of angle of the applied magnetic field direction, as well as microwave frequency and power. We find good agreement between experimental data and a theoretical model that includes contributions from anisotropic magnetoresistance (AMR) and inverse spin Hall effect (ISHE). The analysis provides consistent results over a wide range of experimental conditions as long as the precise magnetization trajectory is taken into account. The spin Hall angles for Pt, Pd, Au and Mo were determined with high precision to be $0.013\pm0.002$, $0.0064\pm0.001$, $0.0035\pm0.0003$ and $-0.0005\pm0.0001$, respectively.Comment: 11 page

Electronic Selection Rules Controlling Dislocation Glide in bcc Metals

The validity of the structure-property relationships governing the deformation behavior of bcc metals was brought into question with recent {\it ab initio} density functional studies of isolated screw dislocations in Mo and Ta. These existing relationships were semiclassical in nature, having grown from atomistic investigations of the deformation properties of the groups V and VI transition metals. We find that the correct form for these structure-property relationships is fully quantum mechanical, involving the coupling of electronic states with the strain field at the core of long $a/2$ screw dislocations.Comment: 4 pages, 2 figure

Window-based Streaming Graph Partitioning Algorithm

In the recent years, the scale of graph datasets has increased to such a degree that a single machine is not capable of efficiently processing large graphs. Thereby, efficient graph partitioning is necessary for those large graph applications. Traditional graph partitioning generally loads the whole graph data into the memory before performing partitioning; this is not only a time consuming task but it also creates memory bottlenecks. These issues of memory limitation and enormous time complexity can be resolved using stream-based graph partitioning. A streaming graph partitioning algorithm reads vertices once and assigns that vertex to a partition accordingly. This is also called an one-pass algorithm. This paper proposes an efficient window-based streaming graph partitioning algorithm called WStream. The WStream algorithm is an edge-cut partitioning algorithm, which distributes a vertex among the partitions. Our results suggest that the WStream algorithm is able to partition large graph data efficiently while keeping the load balanced across different partitions, and communication to a minimum. Evaluation results with real workloads also prove the effectiveness of our proposed algorithm, and it achieves a significant reduction in load imbalance and edge-cut with different ranges of dataset

Kinetic Energy Density Study of Some Representative Semilocal Kinetic Energy Functionals

There is a number of explicit kinetic energy density functionals for non-interacting electron systems that are obtained in terms of the electron density and its derivatives. These semilocal functionals have been widely used in the literature. In this work we present a comparative study of the kinetic energy density of these semilocal functionals, stressing the importance of the local behavior to assess the quality of the functionals. We propose a quality factor that measures the local differences between the usual orbital-based kinetic energy density distributions and the approximated ones, allowing to ensure if the good results obtained for the total kinetic energies with these semilocal functionals are due to their correct local performance or to error cancellations. We have also included contributions coming from the laplacian of the electron density to work with an infinite set of kinetic energy densities. For all the functionals but one we have found that their success in the evaluation of the total kinetic energy are due to global error cancellations, whereas the local behavior of their kinetic energy density becomes worse than that corresponding to the Thomas-Fermi functional.Comment: 12 pages, 3 figure

Quantifying spin Hall angles from spin pumping: Experiments and Theory

Spin Hall effects intermix spin and charge currents even in nonmagnetic materials and, therefore, ultimately may allow the use of spin transport without the need for ferromagnets. We show how spin Hall effects can be quantified by integrating permalloy/normal metal (N) bilayers into a coplanar waveguide. A dc spin current in N can be generated by spin pumping in a controllable way by ferromagnetic resonance. The transverse dc voltage detected along the permalloy/N has contributions from both the anisotropic magnetoresistance (AMR) and the spin Hall effect, which can be distinguished by their symmetries. We developed a theory that accounts for both. In this way, we determine the spin Hall angle quantitatively for Pt, Au and Mo. This approach can readily be adapted to any conducting material with even very small spin Hall angles.Comment: 4 pages, 4 figure

Fourier methods for the perturbed harmonic oscillator in linear and nonlinear Schr\"odinger equations

We consider the numerical integration of the Gross-Pitaevskii equation with a potential trap given by a time-dependent harmonic potential or a small perturbation thereof. Splitting methods are frequently used with Fourier techniques since the system can be split into the kinetic and remaining part, and each part can be solved efficiently using Fast Fourier Transforms. To split the system into the quantum harmonic oscillator problem and the remaining part allows to get higher accuracies in many cases, but it requires to change between Hermite basis functions and the coordinate space, and this is not efficient for time-dependent frequencies or strong nonlinearities. We show how to build new methods which combine the advantages of using Fourier methods while solving the timedependent harmonic oscillator exactly (or with a high accuracy by using a Magnus integrator and an appropriate decomposition).Comment: 12 pages of RevTex4-1, 8 figures; substantially revised and extended versio

RNA-Seq optimization with eQTL gold standards.

BackgroundRNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, mapping, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of differential expression, with results sensitive to systematic sample stratification or, in more extreme cases, to outliers. Further, a method to assess normalization and adjustment measures imposed on the data is lacking.ResultsTo address these issues, we utilize previously published eQTLs as a novel gold standard at the center of a framework that integrates DNA genotypes and RNA-Seq data to optimize analysis and aid in the understanding of genetic variation and gene expression. After detecting sample contamination and sequencing outliers in RNA-Seq data, a set of previously published brain eQTLs was used to determine if sample outlier removal was appropriate. Improved replication of known eQTLs supported removal of these samples in downstream analyses. eQTL replication was further employed to assess normalization methods, covariate inclusion, and gene annotation. This method was validated in an independent RNA-Seq blood data set from the GTEx project and a tissue-appropriate set of eQTLs. eQTL replication in both data sets highlights the necessity of accounting for unknown covariates in RNA-Seq data analysis.ConclusionAs each RNA-Seq experiment is unique with its own experiment-specific limitations, we offer an easily-implementable method that uses the replication of known eQTLs to guide each step in one's data analysis pipeline. In the two data sets presented herein, we highlight not only the necessity of careful outlier detection but also the need to account for unknown covariates in RNA-Seq experiments