485 research outputs found
A Bulk-Parallel Priority Queue in External Memory with STXXL
We propose the design and an implementation of a bulk-parallel external
memory priority queue to take advantage of both shared-memory parallelism and
high external memory transfer speeds to parallel disks. To achieve higher
performance by decoupling item insertions and extractions, we offer two
parallelization interfaces: one using "bulk" sequences, the other by defining
"limit" items. In the design, we discuss how to parallelize insertions using
multiple heaps, and how to calculate a dynamic prediction sequence to prefetch
blocks and apply parallel multiway merge for extraction. Our experimental
results show that in the selected benchmarks the priority queue reaches 75% of
the full parallel I/O bandwidth of rotational disks and and 65% of SSDs, or the
speed of sorting in external memory when bounded by computation.Comment: extended version of SEA'15 conference pape
Wave Energy: a Pacific Perspective
This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by The Royal Society and can be found at: http://rsta.royalsocietypublishing.org/.This paper illustrates the status of wave energy development in Pacific Rim countries by characterizing the available resource and introducing the region‟s current and potential future leaders in wave energy converter development. It also describes the existing licensing and permitting process as well as potential environmental concerns. Capabilities of Pacific Ocean testing facilities are described in addition to the region‟s vision of the future of wave energy
Low Space External Memory Construction of the Succinct Permuted Longest Common Prefix Array
The longest common prefix (LCP) array is a versatile auxiliary data structure
in indexed string matching. It can be used to speed up searching using the
suffix array (SA) and provides an implicit representation of the topology of an
underlying suffix tree. The LCP array of a string of length can be
represented as an array of length words, or, in the presence of the SA, as
a bit vector of bits plus asymptotically negligible support data
structures. External memory construction algorithms for the LCP array have been
proposed, but those proposed so far have a space requirement of words
(i.e. bits) in external memory. This space requirement is in some
practical cases prohibitively expensive. We present an external memory
algorithm for constructing the bit version of the LCP array which uses
bits of additional space in external memory when given a
(compressed) BWT with alphabet size and a sampled inverse suffix array
at sampling rate . This is often a significant space gain in
practice where is usually much smaller than or even constant. We
also consider the case of computing succinct LCP arrays for circular strings
Capture of particles of dust by convective flow
Interaction of particles of dust with vortex convective flows is under
theoretical consideration. It is assumed that the volume fraction of solid
phase is small, variations of density due to nonuniform distribution of
particles and those caused by temperature nonisothermality of medium are
comparable. Equations for the description of thermal buoyancy convection of a
dusty medium are developed in the framework of the generalized Boussinesq
approximation taking into account finite velocity of particle sedimentation.
The capture of a cloud of dust particles by a vortex convective flow is
considered, general criterion for the formation of such a cloud is obtained.
The peculiarities of a steady state in the form of a dust cloud and backward
influence of the solid phase on the carrier flow are studied in detail for a
vertical layer heated from the sidewalls. It is shown that in the case, when
this backward influence is essential, a hysteresis behavior is possible. The
stability analysis of the steady state is performed. It turns out that there is
a narrow range of governing parameters, in which such a steady state is stable.Comment: 14 pages, 10 figures, published in Physics of Fluid
ReCoil - an algorithm for compression of extremely large datasets of dna data
The growing volume of generated DNA sequencing data makes the problem of its long term storage increasingly important. In this work we present ReCoil - an I/O efficient external memory algorithm designed for compression of very large collections of short reads DNA data. Typically each position of DNA sequence is covered by multiple reads of a short read dataset and our algorithm makes use of resulting redundancy to achieve high compression rate
In silico assessment of potential druggable pockets on the surface of α1-Antitrypsin conformers
The search for druggable pockets on the surface of a protein is often performed on a single conformer, treated as a rigid body. Transient druggable pockets may be missed in this approach. Here, we describe a methodology for systematic in silico analysis of surface clefts across multiple conformers of the metastable protein α1-antitrypsin (A1AT). Pathological mutations disturb the conformational landscape of A1AT, triggering polymerisation that leads to emphysema and hepatic cirrhosis. Computational screens for small molecule inhibitors of polymerisation have generally focused on one major druggable site visible in all crystal structures of native A1AT. In an alternative approach, we scan all surface clefts observed in crystal structures of A1AT and in 100 computationally produced conformers, mimicking the native solution ensemble. We assess the persistence, variability and druggability of these pockets. Finally, we employ molecular docking using publicly available libraries of small molecules to explore scaffold preferences for each site. Our approach identifies a number of novel target sites for drug design. In particular one transient site shows favourable characteristics for druggability due to high enclosure and hydrophobicity. Hits against this and other druggable sites achieve docking scores corresponding to a Kd in the µM–nM range, comparing favourably with a recently identified promising lead. Preliminary ThermoFluor studies support the docking predictions. In conclusion, our strategy shows considerable promise compared with the conventional single pocket/single conformer approach to in silico screening. Our best-scoring ligands warrant further experimental investigation
Combined QCD and electroweak analysis of HERA data
A simultaneous fit of parton distribution functions (PDFs) and electroweak
parameters to HERA data on deep inelastic scattering is presented. The input
data are the neutral current and charged current inclusive cross sections which
were previously used in the QCD analysis leading to the HERAPDF2.0 PDFs. In
addition, the polarisation of the electron beam was taken into account for the
ZEUS data recorded between 2004 and 2007. Results on the vector and
axial-vector couplings of the Z boson to u- and d-type quarks, on the value of
the electroweak mixing angle and the mass of the W boson are presented. The
values obtained for the electroweak parameters are in agreement with Standard
Model predictions.Comment: 32 pages, 10 figures, accepted by Phys. Rev. D. Small corrections
from proofing process and small change to Fig. 12 and Table
Limits on the effective quark radius from inclusive scattering at HERA
The high-precision HERA data allows searches up to TeV scales for Beyond the
Standard Model contributions to electron-quark scattering. Combined
measurements of the inclusive deep inelastic cross sections in neutral and
charged current scattering corresponding to a luminosity of around 1
fb have been used in this analysis. A new approach to the beyond the
Standard Model analysis of the inclusive data is presented; simultaneous
fits of parton distribution functions together with contributions of "new
physics" processes were performed. Results are presented considering a finite
radius of quarks within the quark form-factor model. The resulting 95% C.L.
upper limit on the effective quark radius is cm.Comment: 10 pages, 4 figures, accepted by Phys. Lett.
Search for a narrow baryonic state decaying to and in deep inelastic scattering at HERA
A search for a narrow baryonic state in the and
system has been performed in collisions at HERA with the ZEUS detector
using an integrated luminosity of 358 pb taken in 2003-2007. The search
was performed with deep inelastic scattering events at an centre-of-mass
energy of 318 GeV for exchanged photon virtuality, , between 20 and 100
. Contrary to evidence presented for such a state around 1.52
GeV in a previous ZEUS analysis using a sample of 121 pb taken in
1996-2000, no resonance peak was found in the invariant-mass
distribution in the range 1.45-1.7 GeV. Upper limits on the production cross
section are set.Comment: 16 pages, 4 figures, accepted by Phys. Lett. B. Minor changes from
journal reviewing process, including a small correction to figure
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