SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors

The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm computationally demanding for big databases. In this paper, we present SWAPHI, the first parallelized algorithm employing Xeon Phi coprocessors to accelerate SW protein database search. SWAPHI is designed based on the scale-and-vectorize approach, i.e. it boosts alignment speed by effectively utilizing both the coarse-grained parallelism from the many co-processing cores (scale) and the fine-grained parallelism from the 512-bit wide single instruction, multiple data (SIMD) vectors within each core (vectorize). By searching against the large UniProtKB/TrEMBL protein database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on one coprocessor and up to 228.4 GCUPS on four coprocessors. Furthermore, it demonstrates good parallel scalability on varying number of coprocessors, and is also superior to both SWIPE on 16 high-end CPU cores and BLAST+ on 8 cores when using four coprocessors, with the maximum speedup of 1.52 and 1.86, respectively. SWAPHI is written in C++ language (with a set of SIMD intrinsics), and is freely available at http://swaphi.sourceforge.net.Comment: A short version of this paper has been accepted by the IEEE ASAP 2014 conferenc

Magnetic flux emergence in granular convection: Radiative MHD simulations and observational signatures

We study the emergence of magnetic flux from the near-surface layers of the solar convection zone into the photosphere. To model magnetic flux emergence, we carried out a set of numerical radiative magnetohydrodynamics simulations. Our simulations take into account the effects of compressibility, energy exchange via radiative transfer, and partial ionization in the equation of state. All these physical ingredients are essential for a proper treatment of the problem. Furthermore, the inclusion of radiative transfer allows us to directly compare the simulation results with actual observations of emerging flux. We find that the interaction between the magnetic flux tube and the external flow field has an important influence on the emergent morphology of the magnetic field. Depending on the initial properties of the flux tube (e.g. field strength, twist, entropy etc.), the emergence process can also modify the local granulation pattern. The emergence of magnetic flux tubes with a flux of $10^{19}$ Mx disturbs the granulation and leads to the transient appearance of a dark lane, which is coincident with upflowing material. These results are consistent with observed properties of emerging magnetic flux.Comment: To appear in A&

Dna2p Helicase/Nuclease Is a Tracking Protein, Like FEN1, for Flap Cleavage during Okazaki Fragment Maturation

During cellular DNA replication the lagging strand is generated as discontinuous segments called Okazaki fragments. Each contains an initiator RNA primer that is removed prior to joining of the strands. Primer removal in eukaryotes requires displacement of the primer into a flap that is cleaved off by flap endonuclease 1 (FEN1). FEN1 employs a unique tracking mechanism that requires the recognition of the free 5' terminus and then movement to the base of the flap for cleavage. Abnormally long flaps are coated by replication protein A (RPA), inhibiting FEN1 cleavage. A second nuclease, Dna2p, is needed to cleave an RPA-coated flap producing a short RPA-free flap, favored by FEN1. Here we show that Dna2p is also a tracking protein. Annealed primers or conjugated biotin-streptavidin complex block Dna2p entry and movement. Single-stranded binding protein-coated flaps inhibit Dna2p cleavage. Like FEN1, Dna2p can track over substrates with a non-Watson Crick base, such as a biotin, or a missing base within a chain. Unlike FEN1, Dna2p shows evidence of a "threading-like" mechanism that does not support tracking over a branched substrate. We propose that the two nucleases both track, Dna2p first and then FEN1, to remove initiator RNA via long flap intermediates

GeantV: Results from the prototype of concurrent vector particle transport simulation in HEP

Full detector simulation was among the largest CPU consumer in all CERN experiment software stacks for the first two runs of the Large Hadron Collider (LHC). In the early 2010's, the projections were that simulation demands would scale linearly with luminosity increase, compensated only partially by an increase of computing resources. The extension of fast simulation approaches to more use cases, covering a larger fraction of the simulation budget, is only part of the solution due to intrinsic precision limitations. The remainder corresponds to speeding-up the simulation software by several factors, which is out of reach using simple optimizations on the current code base. In this context, the GeantV R&D project was launched, aiming to redesign the legacy particle transport codes in order to make them benefit from fine-grained parallelism features such as vectorization, but also from increased code and data locality. This paper presents extensively the results and achievements of this R&D, as well as the conclusions and lessons learnt from the beta prototype.Comment: 34 pages, 26 figures, 24 table

1.3 mm Polarized emission in the circumstellar disk of a massive protostar

We present the first resolved observations of the 1.3 mm polarized emission from the disk-like structure surrounding the high-mass protostar Cepheus A HW2. These CARMA data partially resolve the dust polarization, suggesting a uniform morphology of polarization vectors with an average position angle of 57° ± 6° and an average polarization fraction of 2.0% ± 0.4%. The distribution of the polarization vectors can be attributed to (1) the direct emission of magnetically aligned grains of dust by a uniform magnetic field, or (2) the pattern produced by the scattering of an inclined disk. We show that both models can explain the observations, and perhaps a combination of the two mechanisms produces the polarized emission. A third model including a toroidal magnetic field does not match the observations. Assuming scattering is the polarization mechanism, these observations suggest that during the first few 104 years of high-mass star formation, grain sizes can grow from1 mm to several 10s μm.Fil: Fernandez Lopez, Manuel. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Instituto Argentino de Radioastronomía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Argentino de Radioastronomia; ArgentinaFil: Stephens, I. W.. Harvard-Smithsonian Center for Astrophysics; Estados Unidos. Boston University; Estados Unidos. University of Illinois; Estados UnidosFil: Girart, J. M.. Harvard-Smithsonian Center for Astrophysics; Estados Unidos. Institut de Ciències de l’Espai; EspañaFil: Looney, L.. University of Illinois; Estados UnidosFil: Curiel, S.. Universidad Nacional Autónoma de México; MéxicoFil: Segura Cox, D.. University of Illinois; Estados UnidosFil: Eswaraiah, C.. National Tsing Hua University; República de ChinaFil: Lai, S. P.. National Tsing Hua University; República de Chin

Pendant NDI bisintercalator derivatives

Sequence specific binding of DNA by small molecules potentially offers the ability to control gene expression. In the past, our laboratory has developed sequence specific threading polyintercalators based on naphthalene diimide (NDI) groups linked head-to-tail by peptides. This design yielded a tetraintercalator with the ability to bind its specific 14 base pair site with a 57 day dissociation half-life, a record for a synthetic DNA-binding molecule (Rhoden Smith and Iverson, 2013). A longer hexaintercalator binds specifically to a 22 base pair site, the longest for a synthetic non-nucleic acid based-DNA binding molecule (Rhoden Smith and Iverson, 2013). The following work attempts to expand our family of DNA binding molecules by focusing on an alternative bisintercalator design where peptide backbones vary while incorporating NDI units at the ε-amino group of lysine residues, as initially proposed by Dr. Chelsea Martinez (Martinez, 2011). Several pendant or comb-like polyintercalator derivatives analyzed by DNase I footprinting show a preference for GC-rich sequences.Chemistr