N-body simulation for self-gravitating collisional systems with a new SIMD instruction set extension to the x86 architecture, Advanced Vector eXtensions

We present a high-performance N-body code for self-gravitating collisional systems accelerated with the aid of a new SIMD instruction set extension of the x86 architecture: Advanced Vector eXtensions (AVX), an enhanced version of the Streaming SIMD Extensions (SSE). With one processor core of Intel Core i7-2600 processor (8 MB cache and 3.40 GHz) based on Sandy Bridge micro-architecture, we implemented a fourth-order Hermite scheme with individual timestep scheme (Makino and Aarseth, 1992), and achieved the performance of 20 giga floating point number operations per second (GFLOPS) for double-precision accuracy, which is two times and five times higher than that of the previously developed code implemented with the SSE instructions (Nitadori et al., 2006b), and that of a code implemented without any explicit use of SIMD instructions with the same processor core, respectively. We have parallelized the code by using so-called NINJA scheme (Nitadori et al., 2006a), and achieved 90 GFLOPS for a system containing more than N = 8192 particles with 8 MPI processes on four cores. We expect to achieve about 10 tera FLOPS (TFLOPS) for a self-gravitating collisional system with N 105 on massively parallel systems with at most 800 cores with Sandy Bridge micro-architecture. This performance will be comparable to that of Graphic Processing Unit (GPU) cluster systems, such as the one with about 200 Tesla C1070 GPUs (Spurzem et al., 2010). This paper offers an alternative to collisional N-body simulations with GRAPEs and GPUs.Comment: 14 pages, 9 figures, 3 tables, accepted for publication in New Astronomy. The code is publicly available at http://code.google.com/p/phantom-grape

Phenomenology of NMSSM in TeV scale mirage mediation

We study the next-to-minimal supersymmetric standard model (NMSSM) with the TeV scale mirage mediation, which is known as a solution for the little hierarchy problem in supersymmetry. Our previous study showed that 125 GeV Higgs boson is realized with O(10) % fine-tuning for 1.5 TeV gluino (1 TeV stop) mass. The $\mu$ term could be as large as 500 GeV without sacrificing the fine-tuning thanks to a cancellation mechanism. The singlet-doublet mixing is suppressed by $\tan\beta$. In this paper, we further extend this analysis. We argue that approximate scale symmetries play a role behind the suppression of the singlet-doublet mixing. They reduce the mixing matrix to a simple form that is useful to understand the results of the numerical analysis. We perform a comprehensive analysis of the fine-tuning including the singlet sector by introducing a simple formula for the fine-tuning measure. This shows that the singlet mass of the least fine-tuning is favored by the LEP anomaly for moderate $\tan\beta$. We also discuss prospects for the precision measurements of the Higgs couplings at LHC and ILC and direct/indirect dark matter searches in the model.Comment: 47 pages, 46 figures, version accepted by JHE

Tailor-made Biological Conservation of Endangered Plant Species with Genomic Information

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Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions

Estimated regions of linkage disequilibrium and associations between SNPs and expression level in regions flanking CPRs for which sequence variation could explain gene expression variation and was subject to purifying selection or selective sweep. Flanking regions (±5000 bp) of CPRs for CG15743 (A), CG9044 (B), brat (C), Cyp4d1 (D), CG14253 (E), Nmda1 (F), CG6950 (G), CG10463 (H), and CG33506 (I) are shown. Gray shades indicate haplotype blocks within which linkage disequilibrium could be found. Orange bars indicate coding region. Green bar indicates CPR. Each dot indicates a false discovery rate value (FDR) using the Wald test for the association between expression levels and SNPs. Horizontal line indicates FDR threshold (α = 0.01). (PDF 626 kb

Duplicability of self-interacting human genes

BACKGROUND There is increasing interest in the evolution of protein-protein interactions because this should ultimately be informative of the patterns of evolution of new protein functions within the cell. One model proposes that the evolution of new protein-protein interactions and protein complexes proceeds through the duplication of self-interacting genes. This model is supported by data from yeast. We examined the relationship between gene duplication and self-interaction in the human genome. RESULTS We investigated the patterns of self-interaction and duplication among 34808 interactions encoded by 8881 human genes, and show that self-interacting proteins are encoded by genes with higher duplicability than genes whose proteins lack this type of interaction. We show that this result is robust against the system used to define duplicate genes. Finally we compared the presence of self-interactions amongst proteins whose genes have duplicated either through whole-genome duplication (WGD) or small-scale duplication (SSD), and show that the former tend to have more interactions in general. After controlling for age differences between the two sets of duplicates this result can be explained by the time since the gene duplication. CONCLUSIONS Genes encoding self-interacting proteins tend to have higher duplicability than proteins lacking self-interactions. Moreover these duplicate genes have more often arisen through whole-genome rather than small-scale duplication. Finally, self-interacting WGD genes tend to have more interaction partners in general in the PIN, which can be explained by their overall greater age. This work adds to our growing knowledge of the importance of contextual factors in gene duplicability.At the time of publication the author Pérez-Bercoff was affiliated with Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin

Identifying the Impact of the Built Environment on Wildfire Property Damage in California

Wildfires are a natural hazard that present an increasing risk to communities in fire-prone areas. This study examines the impacts of the municipal-level built environment upon fire damages in California, a particularly fire-vulnerable state. This study uses a multivariate linear regression model to isolate the effects of the human built environment upon reported monetary wildfire damages. Reported monetary losses from wildfires for the years 2007 to 2010 are examined against relevant built environment variables, while statistically controlling for biophysical and socio-economic variables. The fully-specified regression model indicates that wildfire property damage is driven primarily by the built environment. Socioeconomic and biophysical variables contribute comparatively little explanatory power to the model. Findings from this study will be of particular interest to fire management officials, land developers, and urban planners interested in creating a more fire-resilient future for cities within California

Grain boundary diffusion of W in lower mantle phase with implications for isotopic heterogeneity in oceanic island basalts by core-mantle interactions

Tungsten isotopes provide important constraints on the ocean-island basalt (OIB) source regions. Recent analyses of μ182W in modern basalts with high 3He/4He originating from the core-mantle boundary region reveal two distinct features: positive μ182W in Phanerozoic flood basalts indicating the presence of primordial reservoir, and negative μ182W in modern OIBs. One possibility to produce large variations in μ182W is interaction between the mantle and outer core. Here, we report grain boundary diffusion of W in lower mantle phases. High pressure experimental results show that grain boundary diffusion of W is fast and strongly temperature dependent. Over Earth's history, diffusive transport of W from the core to the lowermost mantle may have led to significant modification of the W isotopic composition of the lower mantle at length scales exceeding one kilometer. Such grain boundary diffusion can lead to large variations in μ182W in modern basalts as a function of the distance of their source regions from the core mantle boundary. Modern oceanic island basalts from Hawaii, Samoa and Iceland exhibit negative μ182W and likely originated from the modified isotope region just above the core-mantle boundary, whereas those with positive μ182W could be derived from the thick Large Low Shear Velocity Provinces (LLSVPs) far from the core-mantle boundary (CMB). When highly-oxidized slabs accumulate at the CMB oxidizing the outer core at the interface, a large W flux with negative μ182W can be added to the silicate mantle. As a result, the source region of the OIB would be effectively modified to a negative μ182W