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

Seismic Wavefield Reconstruction based on Compressed Sensing using Data-Driven Reduced-Order Model

A seismic wavefield reconstruction framework based on compressed sensing using the data-driven reduced-order model (ROM) is proposed and its characteristics are investigated through numerical experiments. The data-driven ROM is generated from the dataset of the wavefield using the singular value decomposition. The spatially continuous seismic wavefield is reconstructed from the sparse and discrete observation and the data-driven ROM. The observation sites used for reconstruction are effectively selected by the sensor optimization method for linear inverse problems based on a greedy algorithm. The proposed framework was applied to simulation data of theoretical waveform with the subsurface structure of the horizontally-stratified three layers. The validity of the proposed method was confirmed by the reconstruction based on the noise-free observation. Since the ROM of the wavefield is used as prior information, the reconstruction error is reduced to an approximately lower error bound of the present framework, even though the number of sensors used for reconstruction is limited and randomly selected. In addition, the reconstruction error obtained by the proposed framework is much smaller than that obtained by the Gaussian process regression. For the numerical experiment with noise-contaminated observation, the reconstructed wavefield is degraded due to the observation noise, but the reconstruction error obtained by the present framework with all available observation sites is close to a lower error bound, even though the reconstructed wavefield using the Gaussian process regression is fully collapsed. Although the reconstruction error is larger than that obtained using all observation sites, the number of observation sites used for reconstruction can be reduced while minimizing the deterioration and scatter of the reconstructed data by combining it with the sensor optimization method

Observation Site Selection for Physical Model Parameter Estimation toward Process-Driven Seismic Wavefield Reconstruction

The seismic data not only acquired by seismometers but also acquired by vibrometers installed in buildings and infrastructure and accelerometers installed in smartphones will be certainly utilized for seismic research in the near future. Since it is impractical to utilize all the seismic big data in terms of the computational cost, methods which can select observation sites depending on the purpose are indispensable. We propose an observation site selection method for the accurate reconstruction of the seismic wavefield by process-driven approaches. The proposed method selects observation sites suitable for accurately estimating physical model parameters such as subsurface structures and source information to be input into a numerical simulation of the seismic wavefield. The seismic wavefield is reconstructed by the numerical simulation using the parameters estimated based on the observed signals at only observation sites selected by the proposed method. The observation site selection in the proposed method is based on the sensitivity of each observation site candidate to the physical model parameters; the matrix corresponding to the sensitivity is constructed by approximately calculating the derivatives based on the simulations, and then, observation sites are selected by evaluating the quantity of the sensitivity matrix based on the D-optimality criterion proposed in the optimal design of experiments. In the present study, physical knowledge on the sensitivity to the parameters such as seismic velocity, layer thickness, and hypocenter location was obtained by investigating the characteristics of the sensitivity matrix. Furthermore, the effectiveness of the proposed method was shown by verifying the accuracy of seismic wavefield reconstruction using the observation sites selected by the proposed method.Comment: Preprint submitted to Geophysical Journal International on 8-June-202

Structural Analysis of the Glycosylated Intact HIV-1 gp120-b12 Antibody Complex Using Hydroxyl Radical Protein Footprinting

Glycoprotein gp120 is a surface antigen and virulence factor of human immunodeficiency virus 1. Broadly neutralizing antibodies (bNAbs) that react to gp120 from a variety of HIV isolates offer hope for the development of broadly effective immunogens for vaccination purposes, if the interactions between gp120 and bNAbs can be understood. From a structural perspective, gp120 is a particularly difficult system because of its size, the presence of multiple flexible regions, and the large amount of glycosylation, all of which are important in gp120-bNAb interactions. Here, the interaction of full-length, glycosylated gp120 with bNAb b12 is probed using high-resolution hydroxyl radical protein footprinting (HR-HRPF) by fast photochemical oxidation of proteins. HR-HRPF allows for the measurement of changes in the average solvent accessible surface area of multiple amino acids without the need for measures that might alter the protein conformation, such as mutagenesis. HR-HRPF of the gp120-b12 complex coupled with computational modeling shows a novel extensive interaction of the V1/V2 domain, probably with the light chain of b12. Our data also reveal HR-HRPF protection in the C3 domain caused by interaction of the N330 glycan with the b12 light chain. In addition to providing information about the interactions of full-length, glycosylated gp120 with b12, this work serves as a template for the structural interrogation of full-length glycosylated gp120 with other bNAbs to better characterize the interactions that drive the broad specificity of the bNAb

Droplet digital PCR assay provides intrahepatic HBV cccDNA quantification tool for clinical application

The persistence of covalently closed circular DNA (cccDNA) poses a major obstacle to curing chronic hepatitis B (CHB). Here, we used droplet digital PCR (ddPCR) for cccDNA quantitation. The cccDNA-specific ddPCR showed high accuracy with the dynamic range of cccDNA detection from 101 to 105 copies/assay. The ddPCR had higher sensitivity, specificity and precisely than qPCR. The results of ddPCR correlated closely with serum HB core-related antigen and HB surface antigen (HBsAg) in 24 HBV-infected human-liver-chimeric mice (PXB-mice). We demonstrated that in 2 PXB-mice after entecavir treatment, the total cccDNA content did not change during liver repopulation, although the cccDNA content per hepatocyte was reduced after the treatment. In the 6 patients with HBV-related hepatocellular carcinoma, ddPCR detected cccDNA in both tumor and non-tumor tissues. In 13 HBeAg-negative CHB patients with pegylated interferon alpha-2a, cccDNA contents from paired biopsies were more significantly reduced in virological response (VR) than in non-VR at week 48 (p = 0.0051). Interestingly, cccDNA levels were the lowest in VR with HBsAg clearance but remained detectable after the treatment. Collectively, ddPCR revealed that cccDNA content is stable during hepatocyte proliferation and persists at quantifiable levels, even after serum HBsAg clearance

Real-time In Situ Electron Spin Resonance Measurements on Fungal Spores of Penicillium digitatum during Exposure of Oxygen Plasmas

We report the kinetic analysis of free radicals on fungal spores of Penicillium digitatum interacted with atomic oxygen generated plasma electric discharge using real time in situ electron spin resonance (ESR) measurements. We have obtained information that the ESR signal from the spores was observed and preliminarily assignable to semiquinone radical with a g-value of around 2.004 and a line width of approximately 5G. The decay of the signal is possibly linked to the inactivation of the fungal spore. The real-time in situ ESR has proven to be a useful method to elucidate plasma-induced surface reactions on biological specimens.Comment: 11 pages, 5 figure

FcɛRI-mediated mast cell degranulation requires calcium-independent microtubule-dependent translocation of granules to the plasma membrane

The aggregation of high affinity IgE receptors (Fcɛ receptor I [FcɛRI]) on mast cells is potent stimulus for the release of inflammatory and allergic mediators from cytoplasmic granules. However, the molecular mechanism of degranulation has not yet been established. It is still unclear how FcɛRI-mediated signal transduction ultimately regulates the reorganization of the cytoskeleton and how these events lead to degranulation. Here, we show that FcɛRI stimulation triggers the formation of microtubules in a manner independent of calcium. Drugs affecting microtubule dynamics effectively suppressed the FcɛRI-mediated translocation of granules to the plasma membrane and degranulation. Furthermore, the translocation of granules to the plasma membrane occurred in a calcium-independent manner, but the release of mediators and granule–plasma membrane fusion were completely dependent on calcium. Thus, the degranulation process can be dissected into two events: the calcium-independent microtubule-dependent translocation of granules to the plasma membrane and calcium-dependent membrane fusion and exocytosis. Finally, we show that the Fyn/Gab2/RhoA (but not Lyn/SLP-76) signaling pathway plays a critical role in the calcium-independent microtubule-dependent pathway

Honeycomb-Layered Oxides With Silver Atom Bilayers and Emergence of Non-Abelian SU(2) Interactions

Honeycomb-layered oxides with monovalent or divalent, monolayered cationic lattices generally exhibit myriad crystalline features encompassing rich electrochemistry, geometries, and disorders, which particularly places them as attractive material candidates for next-generation energy storage applications. Herein, global honeycomb-layered oxide compositions, Ag2M2TeO6 ((Formula presented.).) exhibiting (Formula presented.) atom bilayers with sub-valent states within Ag-rich crystalline domains of Ag6M2TeO6 and (Formula presented.) -deficient domains of (Formula presented.) ((Formula presented.)). The (Formula presented.) -rich material characterized by aberration-corrected transmission electron microscopy reveals local atomic structural disorders characterized by aperiodic stacking and incoherency in the bilayer arrangement of (Formula presented.) atoms. Meanwhile, the global material not only displays high ionic conductivity but also manifests oxygen-hole electrochemistry during silver-ion extraction. Within the (Formula presented.) -rich domains, the bilayered structure, argentophilic interactions therein and the expected (Formula presented.) sub-valent states ((Formula presented.), etc.) are theoretically understood via spontaneous symmetry breaking of SU(2) 7 U(1) gauge symmetry interactions amongst 3 degenerate mass-less chiral fermion states, justified by electron occupancy of silver (Formula presented.) and 5s orbitals on a bifurcated honeycomb lattice. This implies that bilayered frameworks have research applications that go beyond the confines of energy storage