Shen, R. | Search NASA

DOE OSTI2017

Analytical theory and possible detection of the ac quantum spin Hall effect

Here, we develop an analytical theory of the low-frequency ac quantum spin Hall (QSH) effect based upon the scattering matrix formalism. It is shown that the ac QSH effect can be interpreted as a bulk quantum pumping effect. When the electron spin is conserved, the integer-quantized ac spin Hall conductivity can be linked to the winding numbers of the reflection matrices in the electrodes, which also equal to the bulk spin Chern numbers of the QSH material. Furthermore, a possible experimental scheme by using ferromagnetic metals as electrodes is proposed to detect the topological ac spin current by electrical means.

36 MATERIALS SCIENCE↗

DOE OSTI2010

Supersplat--spliced RNA-seq alignment

Motivation: High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge. Here, we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data. Results: Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of ~11.4 million reads per hour. We further benchmark the performance of the algorithm by mapping Illumina RNA-seq reads to identify introns in the genome of the reference dicot plant Arabidopsis thaliana and we demonstrate the utility of supersplat for de novo empirical annotation of splice junctions using the reference monocot plant Brachypodium distachyon. Availability: Implemented in C++, supersplat source code and binaries are freely available on the web at http://mocklerlabtools.cgrb.oregonstate.edu/

59 BASIC BIOLOGICAL SCIENCES↗