Highly parallel sparse Cholesky factorization

Several fine grained parallel algorithms were developed and compared to compute the Cholesky factorization of a sparse matrix. The experimental implementations are on the Connection Machine, a distributed memory SIMD machine whose programming model conceptually supplies one processor per data element. In contrast to special purpose algorithms in which the matrix structure conforms to the connection structure of the machine, the focus is on matrices with arbitrary sparsity structure. The most promising algorithm is one whose inner loop performs several dense factorizations simultaneously on a 2-D grid of processors. Virtually any massively parallel dense factorization algorithm can be used as the key subroutine. The sparse code attains execution rates comparable to those of the dense subroutine. Although at present architectural limitations prevent the dense factorization from realizing its potential efficiency, it is concluded that a regular data parallel architecture can be used efficiently to solve arbitrarily structured sparse problems. A performance model is also presented and it is used to analyze the algorithms

Optimal expression evaluation for data parallel architectures

A data parallel machine represents an array or other composite data structure by allocating one processor (at least conceptually) per data item. A pointwise operation can be performed between two such arrays in unit time, provided their corresponding elements are allocated in the same processors. If the arrays are not aligned in this fashion, the cost of moving one or both of them is part of the cost of the operation. The choice of where to perform the operation then affects this cost. If an expression with several operands is to be evaluated, there may be many choices of where to perform the intermediate operations. An efficient algorithm is given to find the minimum-cost way to evaluate an expression, for several different data parallel architectures. This algorithm applies to any architecture in which the metric describing the cost of moving an array is robust. This encompasses most of the common data parallel communication architectures, including meshes of arbitrary dimension and hypercubes. Remarks are made on several variations of the problem, some of which are solved and some of which remain open

SINFONI Integral Field Spectroscopy of z~2 UV-selected Galaxies: Rotation Curves and Dynamical Evolution

We present 0.5" resolution near-IR integral field spectroscopy of the Ha line emission of 14 z~2 UV-selected BM/BX galaxies obtained with SINFONI at ESO/VLT. The mean Ha half-light radius r_1/2 is about 4kpc and line emission is detected over > ~20kpc in several sources. In 9 sources, we detect spatially-resolved velocity gradients, from 40 to 410 km/s over ~10kpc. The observed kinematics of the larger systems are consistent with orbital motions. Four galaxies are well described by rotating disks with clumpy morphologies and we extract rotation curves out to radii > ~10kpc. One or two galaxies exhibit signatures more consistent with mergers. Analyzing all 14 galaxies in the framework of rotating disks, we infer mean inclination- and beam-corrected maximum circular velocities v_c of 180+-90 km/s and dynamical masses of (0.5-25)x10^10 Msun within r_1/2. On average, the dynamical masses are consistent with photometric stellar masses assuming a Chabrier/Kroupa IMF but too small for a 0.1-100 Msun Salpeter IMF. The specific angular momenta of our BM/BX galaxies are similar to those of local late-type galaxies. The specific angular momenta of their baryons are comparable to those of their dark matter halos. Extrapolating from the average v_c at 10kpc, the virial mass of the typical halo of a galaxy in our sample is 10^(11.7+-0.5) Msun. Kinematic modeling of the 3 best cases implies a ratio of v_c to local velocity dispersion of order 2-4 and accordingly a large geometric thickness. We argue that this suggests a mass accretion (alternatively, gas exhaustion) timescale of ~500Myr. We also argue that if our BM/BX galaxies were initially gas rich, their clumpy disks will subsequently lose their angular momentum and form compact bulges on a timescale of ~1 Gyr. [ABRIDGED]Comment: Accepted for publication in the Astrophysical Journal. 17 pages, 5 color figure

Efficient Distribution Analysis via Graph Contraction

Alignment and distribution of data by an optimizing compiler is a dream of both manufacturers and users of parallel computers. The distribution problem has been formulated as an NP-complete graph optimization problem. The graphs arising in applications are large, and the optimization problem does not lend itself to traditional heuristic optimization techniques. In this paper, we improve some earlier results on methods that use graph contraction to reduce the size of a distribution problem. We report on an experiment using seven example programs that show these contraction operations to be effective in practice; we obtain from 60 to 99 percent reductions in problem size, the larger number being more typical, without loss of solution quality

Assessing early memories of threat and subordination: Confirmatory factor analyisis of the early life experiences scale for adolescents.

The Early Life Experiences Scale (ELES) is a self-report questionnaire that assesses personal feelings of perceived threat and submissiveness in interactions within family. This paper presents the adaptation and validation of the ELES in Portuguese language for adolescents. The sample was composed of 771 adolescents from community schools with ages between 13 and 18 years old. Along with ELES, participants also answered the Early Memories of Warmth and Safeness Scale and the Positive and Negative Affect Schedule for Children and Adolescents. Confirmatory factor analysis (CFA) was performed to test the factor structure of the ELES and results confirm a three-factor structure, composed by Threat, Submissiveness and Unvalued dimensions. These emotional memories focused on perceived threat, submissiveness and unvalued seem to have a distinct nature. The scale also showed adequate internal consistency, good test-retest reliability and convergent validity with measures of positive emotional memories, positive and negative affect. There were sex differences for threat subscale and age differences for submissiveness subscale. Overall, these findings suggest that the ELES in its Portuguese version for adolescents may be a useful tool for research, educational and clinical contexts with school-aged adolescents

Enhanced Gilbert Damping in Thin Ferromagnetic Films

Using a scattering matrix approach, the precession of the magnetization of a ferromagnet is shown to transfer spins into adjacent normal metal layers. This ``pumping'' of spins slows down the precession corresponding to an enhanced Gilbert damping factor in the Landau-Lifshitz equation. The damping is expressed in terms of the scattering matrix of the ferromagnet-normal metal interface, which is accessible to model and first-principles calculations. Our estimates for permalloy thin films explain the trends observed in recent experiments.Comment: 1 figur

Evidence for powerful AGN winds at high redshift: Dynamics of galactic outflows in radio galaxies during the "Quasar Era"

AGN feedback now appears as an attractive mechanism to resolve some of the outstanding problems with the "standard" cosmological models, in particular those related to massive galaxies. To directly constrain how this may influence the formation of massive galaxies near the peak in the redshift distribution of powerful quasars, z~2, we present an analysis of the emission-line kinematics of 3 powerful radio galaxies at z~2-3 (HzRGs) based on rest-frame optical integral-field spectroscopy obtained with SINFONI on the VLT. HzRGs are among the most massive galaxies, so AGN feedback may have a particularly clear signature. We find evidence for bipolar outflows in all HzRGs, with kinetic energies that are equivalent to 0.2% of the rest-mass of the supermassive black hole. Velocity offsets in the outflows are ~800-1000 km s^-1 between the blueshifted and redshifted line emission, FWHMs ~1000 km s^-1 suggest strong turbulence. Ionized gas masses estimated from the Ha luminosity are of order 10^10 M_s, similar to the molecular gas content of HzRGs, underlining that these outflows may indicate a significant phase in the evolution of the host galaxy. The total energy release of ~10^60 erg during a dynamical time of ~10^7 yrs corresponds to about the binding energy of a massive galaxy. Geometry, timescales and energy injection rates of order 10% of the kinetic energy flux of the jet suggest that the outflows are most likely driven by the radio source. The global energy density release of ~10^57 erg s^-1 Mpc^-3 may also influence the subsequent evolution of the HzRG by enhancing the entropy and pressure in the surrounding halo and facilitating ram-pressure stripping of gas in satellite galaxies that may contribute to the subsequent mass assembly of the HzRG through low-dissipation "dry" mergers.Comment: A&A in press, minor edits & typo in table captions 2-

XRCC1 interacts with the p58 subunit of DNA Pol α-primase and may coordinate DNA repair and replication during S phase

Repair of single-stranded DNA breaks before DNA replication is critical in maintaining genomic stability; however, how cells deal with these lesions during S phase is not clear. Using combined approaches of proteomics and in vitro and in vivo protein–protein interaction, we identified the p58 subunit of DNA Pol α-primase as a new binding partner of XRCC1, a key protein of the single strand break repair (SSBR) complex. In vitro experiments reveal that the binding of poly(ADP-ribose) to p58 inhibits primase activity by competition with its DNA binding property. Overexpression of the XRCC1-BRCT1 domain in HeLa cells induces poly(ADP-ribose) synthesis, PARP-1 and XRCC1-BRCT1 poly(ADP-ribosyl)ation and a strong S phase delay in the presence of DNA damage. Addition of recombinant XRCC1-BRCT1 to Xenopus egg extracts slows down DNA synthesis and inhibits the binding of PCNA, but not MCM2 to alkylated chromatin, thus indicating interference with the assembly of functional replication forks. Altogether these results suggest a critical role for XRCC1 in connecting the SSBR machinery with the replication fork to halt DNA synthesis in response to DNA damage

Toward autonomous measurements of photosynthetic electron transport rates: An evaluation of active fluorescence-based measurements of photochemistry

This study presents a methods evaluation and intercalibration of active fluorescence-based measurements of the quantum yield (ϕʹ 0 PSII) and absorption coefficient (aPSII) of photosystem II (PSII) photochemistry. Measurements of ϕʹ PSII , aPSII, and irradiance (E) can be scaled to derive photosynthetic electron transport rates (P e ), the process that fuels phytoplankton carbon fixation and growth. Bio-optical estimates of ϕ PSII and aPSII were evaluated using 10 phytoplankton cultures across different pigment groups with varying bio-optical absorption characteristics on six different fast-repetition rate fluorometers that span two different manufacturers and four different models. Culture measurements of ϕʹ PSII and the effective absorption cross section of PSII photochemistry (σPSII, a constituent of aPSII) showed a high degree of correspondence across instruments, although some instrument-specific biases are identified. A range of approaches have been used in the literature to estimate aPSII(λ) and are evaluated here.With the exception of ex situ aPSII(λ) estimates from paired σPSII and PSII reaction center concentration ([RCII]) measurements, the accuracy and precision of in situ aPSII(λ) methodologies are largely determined by the variance of method-specific coefficients. The accuracy and precision of these coefficients are evaluated, compared to literature data, and discussed within a framework of autonomous P e measurements. This study supports the application of an instrument-specific calibration coefficient (KR) that scales minimum fluorescence in the dark (F 0 ) to aPSII as both the most accurate in situ measurement of aPSII, and the methodology best suited for highly resolved autonomous P e measurements