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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Detection of the large-scale tidal field with galaxy multiplet alignment in the DESI Y1 spectroscopic survey

We explore correlations between the orientations of small galaxy groups, or ‘multiplets’, and the large-scale gravitational tidal field. Using data from the Dark Energy Spectroscopic Instrument (DESI) Y1 survey, we detect the intrinsic alignment (IA) of multiplets to the galaxy-traced matter field out to separations of $100\,h^{-1}$ Mpc. Unlike traditional IA measurements of individual galaxies, this estimator is not limited by imaging of galaxy shapes and allows for direct IA detection beyond redshift $z=1$. Multiplet alignment is a form of higher order clustering, for which the scale-dependence traces the underlying tidal field and amplitude is a result of small-scale ($\lt 1h^{-1}$ Mpc) dynamics. Within samples of bright galaxies, luminous red galaxies (LRG) and emission-line galaxies, we find similar scale-dependence regardless of intrinsic luminosity or colour. This is promising for measuring tidal alignment in galaxy samples that typically display no IA. DESI’s LRG mock galaxy catalogues created from the A BACUS S UMMIT N -body simulations produce a similar alignment signal, though with a 33 per cent lower amplitude at all scales. An analytic model using a non-linear power spectrum (NLA) only matches the signal down to 20 $h^{-1}$ Mpc. Our detection demonstrates that galaxy clustering in the non-linear regime of structure formation preserves an interpretable memory of the large-scale tidal field. Multiplet alignment complements traditional two-point measurements by retaining directional information imprinted by tidal forces, and contains additional line-of-sight information compared to weak lensing. This is a more effective estimator than the alignment of individual galaxies in dense, blue, or faint galaxy samples.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high-performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6× and 30.7× using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. Furthermore, to highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overall BELLA runtime by up to 10.6×. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near optimal on the NVIDIA Tesla V100s.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

SU-E-J-138: An IGRT QA Device for Measuring with Tenths-Millimeter Accuracy KV and MV Isocenter Congruence, Couch Travel and Laser Alignment of Accelerators Used for SRS and SBRT

Purpose: To develop a practical device having sufficient accuracy for daily QA tests of accelerators used for SRS and SBRT. Methods: The UAB (Universal Alignment Ball) consists of a 6.35 mm (1/4 inch) diameter tungsten sphere located concentrically within a 25.4 mm (1 inch) diameter acrylic plastic (PMMA) sphere. The spheres are embedded in polystyrene foam, which, in turn, is surrounded by a cylindrical PMMA shell. The UAB is placed on the couch and aligned with wall lasers according to marks that have known positions in relation to the center of the spheres. Using planar and cone beam images the couch is shifted till the surface of the PMMA sphere matches Eclipse-generated circular contours. Anterior and lateral MV images taken with small MLC openings allow measurement of distance between kV and MV isocenter, laser and MLC alignment. Measurements were taken over a one-month period. Results: Artifacts from the tungsten sphere were confined within the PMMA sphere and did not affect cone beam localization of the sphere boundary, allowing 0.1 mm precise alignment with a computer-generated circle centered at kV isocenter. In tests extending over a one-month period, the distance between kV and MV isocenters along the vertical, longitudinal and lateral directions was 0.125 +/−0.06, 0.19 +/−0.08, and 0.02 +/−0.08 mm, respectively. Laser misalignment along these directions was 0.34 +/- 0.15, 0.74 +/−0.29, and 0.49 +/−0.22 mm. Automated couch shifts moved the spheres to within 0.1 mm of the selected position. The center of a 1cmx1cm MLC-defined field remained within +/−0.2 mm of the tungsten sphere center as the gantry was rotated. Conclusion: The UAB is practical for daily end-to-end QA tests of accelerator alignment. It provides tenths-mm accuracy for measuring agreement of kV and MV isocenters, couch motions, gantry flex and laser alignment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based on a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Macroscopic Ensembles of Aligned Carbon Nanotubes in Bubble Imprints Studied by Polarized Raman Microscopy

We study the alignment of single-wall carbon nanotubes (SWCNTs) in bubble imprints through polarized Raman microscopy. A hemispherical bubble containing SWCNTs is pressed against a glass substrate, resulting in an imprint of the bubble membrane with a coffee ring on the substrate. We find that macroscopic ensembles of aligned SWCNTs are obtained in the imprints, in which there are three patterns of orientations: (i) azimuthal alignment on the coffee ring, (ii) radial alignment at the edge of the membrane, and (iii) random orientation at the center of the membrane. We also find that the alignment of SWCNTs in the imprints can be manipulated by spinning bubbles. The orientation of SWCNTs on the coffee ring is directed radially, which is orthogonal to the case of unspun bubbles. This approach enables one to align SWCNTs in large quantities and in a short time, potentially opening up a wide range of CNT-based electronic and optical applications.

Ushiba, Shota↗
DOE OSTI2014

Combining Multiple Pairwise Structure-based Alignments

CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a new tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.

Source record↗
DOE OSTI2015

Pairwise Sequence Alignment Library

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Jeff Daily, PNNL↗
DOE OSTI2019

Micro-aligned 1 Tesla Solenoid for High-energy Bunched-beam Electron Cooling

Electron cooling of ion beams requires precise alignment of the electron beam with the equilibrium trajectory of the ion bunch. In magnetized cooling the cooling rate is enhanced by transverse confinement of each electron on a magnetic line of force. The magnetic lines of force must therefore be aligned with the ion bunch trajectory everywhere along the extent of the solenoid. For the parameters required for JLEIC, a solenoid with bore field ~1 T, length ~30 m, and rms alignment of ~micro-radian is required. Such alignment has never been accomplished. The design of a micro-aligned solenoid is presented. A gap-separated stack of thin steel washers is located along the bore of the solenoid. The flux plate stack shields transverse magnetic fields from the interior, so that axial alignment is enhanced by a factor of ~10.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Mass Dependence of Galaxy–Halo Alignment in LOWZ and CMASS

We measure the galaxy-ellipticity (GI) correlations for the Sloan Digital Sky Survey Data Release 12 LOWZ and CMASS samples with the shape measurements from the DESI Legacy Imaging Surveys. We model the GI correlations in an N-body simulation with our recent accurate stellar–halo mass relation from the Photometric object Around Cosmic webs (PAC) method. The large data set and our accurate modeling turns out an accurate measurement of the alignment angle between central galaxies and their host halos. We find that the alignment of central elliptical galaxies with their host halos increases monotonically with galaxy stellar mass or host halo mass, which can be well described by a power law for the massive galaxies. We also find that central elliptical galaxies are more aligned with their host halos in LOWZ than in CMASS, which might indicate an evolution of galaxy–halo alignment, though future studies are needed to verify this is not induced by the sample selections. In contrast, central disk galaxies are aligned with their host halos about 10 times more weakly in the GI correlation. These results have important implications for intrinsic alignment (IA) correction in weak lensing studies, IA cosmology, and theory of massive galaxy formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Current Sheet Alignment in Oblique Black Hole Magnetospheres: A Black Hole Pulsar?

Abstract We study the magnetospheric evolution of a nonaccreting spinning black hole (BH) with an initially inclined split monopole magnetic field by means of 3D general relativistic magnetohydrodynamic simulations. This serves as a model for a neutron star (NS) collapse or a BH–NS merger remnant after the inherited magnetosphere has settled into a split monopole field creating a striped wind. We show that the initially inclined split monopolar current sheet aligns over time with the BH equatorial plane. The inclination angle evolves exponentially toward alignment, with an alignment timescale that is inversely proportional to the square of the BH angular velocity, where higher spin results in faster alignment. Furthermore, magnetic reconnection in the current sheet leads to exponential decay of event-horizon-penetrating magnetic flux with nearly the same timescale for all considered BH spins. In addition, we present relations for the BH mass and spin in terms of the period and alignment timescale of the striped wind. The explored scenario of a rotating, aligning, and reconnecting current sheet can potentially lead to multimessenger electromagnetic counterparts to a gravitational-wave event due to the acceleration of particles powering high-energy radiation, plasmoid mergers resulting in coherent radio signals, and pulsating emission due to the initial misalignment of the BH magnetosphere.

Astronomy & Astrophysics↗
NASA NTRS1978

IUS prerelease alignment

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

Evans, F. A.↗
NASA NTRS1980

Onorbit IMU alignment error budget

The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

Corson, R. W.↗
NASA NTRS1986

Development and evaluation of an airplane electronic display format aligned with the inertial velocity vector

The development of an electronic primary flight display format aligned with the aircraft velocity vector, a simulation evaluation comparing this format with an electronic attitude-aligned primary flight display format, and a flight evaluation of the velocity-vector-aligned display format are described. Earlier tests in turbulent conditions with the electronic attitude-aligned display format had exhibited unsteadiness. A primary objective of aligning the display format with the velocity vector was to take advantage of a velocity-vector control-wheel steering system to provide steadiness of display during turbulent conditions. Better situational awareness under crosswind conditions was also achieved. The evaluation task was a curved, descending approach with turbulent and crosswind conditions. Primary flight display formats contained computer-drawn perspective runway images and flight-path angle information. The flight tests were conducted aboard the NASA Transport Systems Research Vehicle (TSRV). Comparative results of the simulation and flight tests were principally obtained from subjective commentary. Overall, the pilots preferred the display format aligned with the velocity vector.

Steinmetz, G. G.↗
NASA NTRS1988

Effect of field-aligned potential drop in a global magnetosphere-ionosphere coupling model

Effects of field-aligned potential drops on the magnetosphere-ionosphere coupling in a steady state are studied on a global ionospheric scale. It is shown that a constant-current generator can support a larger field-aligned potential drop than a constant voltage generator under similar conditions. The magnetospheric convection pattern is distorted more in the constant current generator case than in the constant voltage generator case. The main difference between a constant current generator and a constant voltage generator is found to lie in their ability to adjust the vorticity of the magnetospheric convection. The results show that a constant current generator allows the vorticity of the magnetospheric convection to adjust so that the field-aligned current can be kept constant under the loading influence of the field-aligned potential. On the other hand, a constant voltage generator by definition cannot adjust the vorticity of the magnetospheric convection to maintain the field-aligned current under the loading influence of the field-aligned potential.

Kan, J. R.↗
NASA NTRS1993

Characterization of the IMF By-dependent field-aligned currents in the cleft region based on DE 2 observations

The magnetic field and plasma data from 47 passes of DE-2 are used to study the IMF By-dependent distribution of field-aligned currents in the cleft region. It is proposed that the low-latitude cleft current (LCC) region is not an extension of the region 1 or region 2 current system and that a pair of LCCs and high-latitude cleft currents (HCCs) constitutes the cleft field-aligned current regime. The proposed pair of cleft field-aligned currents is explained with a qualitative model in which this pair of currents is generated on open field lines that have just been reconnected on the dayside magnetopause. The electric fields are transmitted along the field lines to the ionosphere, creating a poleward electric field and a pair of field-aligned currents when By is positive; the pair of field-aligned currents consists of a downward current at lower latitudes and an upward current at higher latitudes. In the By negative case, the model explains the reversal of the field-aligned current direction in the LCC and HCC regions.

Taguchi, S.↗
NASA NTRS1993

Neural-network-directed alignment of optical systems using the laser-beam spatial filter as an example

This report describes an effort at NASA Lewis Research Center to use artificial neural networks to automate the alignment and control of optical measurement systems. Specifically, it addresses the use of commercially available neural network software and hardware to direct alignments of the common laser-beam-smoothing spatial filter. The report presents a general approach for designing alignment records and combining these into training sets to teach optical alignment functions to neural networks and discusses the use of these training sets to train several types of neural networks. Neural network configurations used include the adaptive resonance network, the back-propagation-trained network, and the counter-propagation network. This work shows that neural networks can be used to produce robust sequencers. These sequencers can learn by example to execute the step-by-step procedures of optical alignment and also can learn adaptively to correct for environmentally induced misalignment. The long-range objective is to use neural networks to automate the alignment and operation of optical measurement systems in remote, harsh, or dangerous aerospace environments. This work also shows that when neural networks are trained by a human operator, training sets should be recorded, training should be executed, and testing should be done in a manner that does not depend on intellectual judgments of the human operator.

Decker, Arthur J.↗
NASA NTRS1994

Convection and electrodynamic signatures in the vicinity of a Sun-aligned arc: Results from the Polar Acceleration Regions and Convection Study (Polar ARCS)

An experimental campaign designed to study high-latitude auroral arcs was conducted in Sondre Stromfjord, Greenland, on February 26, 1987. The Polar Acceleration Regions and Convection Study (Polar ARCS) consisted of a coordinated set of ground-based, airborne, and sounding rocket measurements of a weak, sun-aligned arc system within the duskside polar cap. A rocket-borne barium release experiment, two DMSP satellite overflights, all-sky photography, and incoherent scatter radar measurements provided information on the large-scale plasma convection over the polar cap region while a second rocket instrumented with a DC magnetometer, Langmuir and electric field probes, and an electron spectrometer provided measurements of small-scale electrodynamics. The large-scale data indicate that small, sun-aligned precipitation events formed within a region of antisunward convection between the duskside auroral oval and a large sun-aligned arc further poleward. This convection signature, used to assess the relationship of the sun-aligned arc to the large-scale magnetospheric configuration, is found to be consistent with either a model in which the arc formed on open field lines on the dusk side of a bifurcated polar cap or on closed field lines threading an expanded low-latitude boundary layer, but not a model in which the polar cap arc field lines map to an expanded plasma sheet. The antisunward convection signature may also be explained by a model in which the polar cap arc formed on long field lines recently reconnected through a highly skewed plasma sheet. The small-scale measurements indicate the rocket passed through three narrow (less than 20 km) regions of low-energy (less than 100 eV) electron precipitation in which the electric and magnetic field perturbations were well correlated. These precipitation events are shown to be associated with regions of downward Poynting flux and small-scale upward and downward field-aligned currents of 1-2 micro-A/sq m. The paired field-aligned currents are associated with velocity shears (higher and lower speed streams) embedded in the region of antisunward flow.

Weiss, L. A.↗
NASA NTRS1994

Characteristics of the field-aligned current system in the nighttime sector during auroral substorms

Fujii et al. (1994) obtained characteristics of the electrodynamic parameters, that is, field-aligned currents, electric fields, and electron precipitation, which are associted with auroral substorm events in the nighttime sector, through a unique analysis that places the ionospheric measurements of these parameters into the context of a generic substorm determined from global auroral images. In this paper we investigate in considerably more detail the characteristics of the field-aligned currents using data from the same set of passes as the previuos study. We show for the first time that the net upward field-aligned currents throughout the surge and surge horn are sufficient to account for most if not all of the converging currents of the auroral electrojets. Current densities are largest in the surge and surge horn. Current region continuity does not appear to exist across the substorm bulge region. Much of the auroral substorm field-aligned current is composed of filamentary currents and finite current segments at large angles to each other. The westward electrojet may contain large gradients in intensity both in local time and latitude due to sets of localized field-aligned currents. The net downward current for several hours to the west of the surge is insufficient to account for the eastward electrojet, consistent with the concept that this electrojet originates primarily on the dayside. Our pattern of field-aligned currents associated with the surge has common features and also differs significantly from the patterns previously derived from data from radars and ground-based magnetometer arrays. Our pattern is considerably more complex, probably due to the much higher resolution in latitude of the satellite data. It is also larger in area, since our average substorm is much larger than those pertaining to the previous patterns, giving a substorm wedge considerably wider than that obtained from the radar and array data.

Hoffman, R. A.↗