Wigner crystal diode

We study the transport properties of a Wigner crystal in one- and two-dimensional asymmetric periodic potential. We show that the Aubry transition takes place above a certain critical amplitude of potential with the sliding and pinned phase below and above the transition. Due to the asymmetry the Aubry pinned phase is characterized by the diode charge transport of the Wigner crystal. We argue that the recent experimental observations of Aubry transition with cold ions and colloidal monolayers can be extended to asymmetric potentials making possible to observe Wigner crystal diode with these physical systems and electrons on liquid helium.Comment: 11 pages, 19 figures, accepted to Phys Rev

Zeroing neural networks for computing quaternion linear matrix equation with application to color restoration of images

The importance of quaternions in a variety of fields, such as physics, engineering and computer science, renders the effective solution of the time-varying quaternion matrix linear equation (TV-QLME) an equally important and interesting task. Zeroing neural networks (ZNN) have seen great success in solving TV problems in the real and complex domains, while quaternions and matrices of quaternions may be readily represented as either a complex or a real matrix, of magnified size. On that account, three new ZNN models are developed and the TV-QLME is solved directly in the quaternion domain as well as indirectly in the complex and real domains for matrices of arbitrary dimension. The models perform admirably in four simulation experiments and two practical applications concerning color restoration of images

Archaeal communities of frozen Quaternary sediments of marine origin on the coast of Western Spitsbergen,

The archaeal composition of permafrost samples taken during drilling of frozen marine sediments in the area of the Barentsburg coal mine on the east coast of Grønfjord Bay of Western Spitsbergen has been studied. The study was based on the analysis of the V4 region of the 16S rRNA gene, carried out using next generation sequencing. This is the second part of the work dedicated to the prokaryotic composition of the Western Spitsbergen, the fi rst part was devoted to the domain of Bacteria. The general phyla of the the Archaea domain were Euryarchaeota, Bathyarchaeota, Thaumarchaeota and Asgardarchaeota. As a result of phylogenetic analysis of the dominant operational taxonomic units, representatives of methanogenic methane- and ammonium-oxidizing archaea, as well as heterotrophic archaea were found. Methanobacteria class of methanogenic archaea was found in the controversial genesis, while methane-oxidizing archaea of the Methanomicrobia class of Methanosarcinales order were found in the marine permafrost of Cape Finneset: ANME-2a, -2b group was found in layers 8.6 and 11.7 m, and a group ANME-2d (Candidatus Methanoperedens) – in a layer of 6.5 m. Ammonium-oxidizing archaea of the phylum Thaumarchaeota was present in all types of permafrost, while Nitrososphaerales was detected in controversial genesis permafrost, and the order-Nitrosopumilales in the marine permafrost or controversial genesis ones. Representatives of phylum Bathyarchaeota were found in the stratigraphicly most ancient samples under this study. Superphylum Asgardarchaeota was met exclusively in the layers of permafrost with marine genesis and was represented by phyla Lokiarchaeota, Thorarchaeota and another group belonging to this superphylum that was not identified by us. The presence in the marine permafrost terrace of Cape Finneset at 11.7 m depth of methane, ethylene and ethane, as well as the composition of the archaeal community gives this layer to assume in it the presence of microbiological processes of the anaerobic oxidation of methane, probably received from Tertiary deposits before freezing. The results obtained are represented the permafrost of Spitsbergen as a rich archive of genetic information of little studied prokaryotic groups

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

ddemidov/amgcl-sdd-scaling: 0.1

Version of the benchmarks used in the submitted paper

Subdomain Deflation Combined with Local AMG: a Case Study Using AMGCL Library

The paper proposes a combination of the subdomain deflation method and local algebraic multigrid as a scalable distributed memory preconditioner that is able to solve large linear systems of equations. The implementation of the algorithm is made available for the community as part of an open source AMGCL library. The solution targets both homogeneous (CPU-only) and heterogeneous (CPU/GPU) systems, employing hybrid MPI/OpenMP approach in the former and a combination of MPI, OpenMP, and CUDA in the latter cases. The use of OpenMP minimizes the number of MPI processes, thus reducing the communication overhead of the deflation method and improving both weak and strong scalability of the preconditioner. The examples of scalar (single degree of freedom per grid node), Poisson-like, systems as well as non-scalar problems, stemming out of the discretization of the Navier-Stokes equations, are considered in order to estimate performance of the implemented algorithm. A comparison with a traditional global AMG preconditioner based on a well-established Trilinos ML package is provided