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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
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↗
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 OSTI2014

BBMap: A Fast, Accurate, Splice-Aware Aligner

Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding, string-graph assembly, homology detection, assembly evaluation, error-correction, expression quantification, and even as a tool to evaluate other tools. An optimal aligner would greatly improve virtually any sequencing process, but optimal alignment is prohibitively expensive for gigabases of data. Here, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6].

09 BIOMASS FUELS↗
DOE OSTI2023

Ducted fuel injection system alignment device

An alignment device for a ducted fuel injection system comprising a mounting block removably attachable to a duct of the ducted fuel injection system. The mounting block can include a passageway extending therethrough. The passageway can align with the duct when the mounting block is attached to the duct. The alignment device further comprises an imaging device configured to capture an image viewing through the duct toward an outlet of a fuel injector. A portion of the imaging device can extend in the passageway. The alignment device additionally comprises a centering structure configured to align a portion of the imaging device with a central axis of the duct. The image captured by the imaging device can be configured for use aligning a position of an outlet of a fuel injector with respect to a position of the duct.

Nilsen, Christopher William↗
DOE OSTI2023

Stereolithography additive manufacturing of magnetically aligned liquid crystal elastomers

A method of forming a three-dimensional structure includes forming a layer of resin comprising liquid crystal oligomers and a photoinitiator, applying a magnetic field to the formed layer in a predefined alignment direction for substantially aligning the liquid crystal oligomers in a first orientation; and exposing the formed layer to radiation for curing a first portion of the layer during application of the magnetic field thereby resulting in the first portion having liquid crystal elastomers substantially aligned in the first orientation. The method includes applying a second magnetic field to the formed layer in a predefined second alignment direction for substantially aligning uncured liquid crystal oligomers in a second orientation, and exposing the layer to radiation for curing a second portion of the layer during application of the second magnetic field thereby resulting in the second portion having liquid crystal elastomers substantially aligned in the second orientation.

Arriaga, Rodrigo Telles↗
DOE OSTI2024

Digital Light Process 3D Printing of Magnetically Aligned Liquid Crystalline Elastomer Free–forms

Liquid crystalline elastomers (LCEs) are anisotropic soft materials capable of large dimensional changes when subjected to a stimulus. The magnitude and directionality of the stimuli-induced thermomechanical response is associated with the alignment of the LCE. Recent reports detail the preparation of LCEs by additive manufacturing (AM) techniques, predominately using direct ink write printing. Another AM technique, digital light process (DLP) 3D printing, has generated significant interest as it affords LCE free-forms with high fidelity and resolution. However, one challenge of printing LCEs using vat polymerization methods such as DLP is enforcing alignment. Here, we document the preparation of aligned, main-chain LCEs via DLP 3D printing using a 100 mT magnetic field. Systematic examination isolates the contribution of magnetic field strength, alignment time, and build layer thickness on the degree of orientation in 3D printed LCEs. Informed by this fundamental understanding, DLP is used to print complex LCE free-forms with through-thickness variation in both spatial orientations. Further, the hierarchical variation in spatial orientation within LCE free-forms is used to produce objects that exhibit mechanical instabilities upon heating. DLP printing of aligned LCEs opens new opportunities to fabricate stimuli-responsive materials in form factors optimized for functional use in soft robotics and energy absorption.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Downwind pre-aligned rotors for extreme-scale wind turbines

Downwind force angles are small for current turbines systems (1-5 MW) such that they may be readily accommodated by conventional upwind configurations. However, analysis indicates that extreme-scale systems (10-20 MW) will have larger angles that may benefit from downwind-aligned configurations. To examine potential rotor mass reduction, the pre-alignment concept was investigated a two-bladed configuration by keeping the structural and aerodynamic characteristics of each blade fixed (to avoids a complete blade re-design). Simulations for a 13.2 MW rated rotor at steady-state conditions show that this concept-level two-bladed design may yield 25% rotor mass savings while also reducing average blade stress over all wind speeds. These results employed a pre-alignment on the basis of a wind speed of 1.25 times the rated wind speed. The downwind pre-aligned concept may also reduce damage equivalent loads on the blades by 60% for steady rated wind conditions. Even higher mass and damage equivalent load savings (relative to conventional upwind designs) may be possible for larger systems (15-20 MW) for which load-alignment angles become even larger. Furthermore, much more work is needed to determine whether this concept can be translated into a practical design that must meet a wide myriad of other criteria.

17 WIND ENERGY↗
DOE OSTI2017

Injectable Anisotropic Nanocomposite Hydrogels Direct in Situ Growth and Alignment of Myotubes

Here, while injectable in situ cross-linking hydrogels have attracted increasing attention as minimally invasive tissue scaffolds and controlled delivery systems, their inherently disorganized and isotropic network structure limits their utility in engineering oriented biological tissues. Traditional methods to prepare anisotropic hydrogels are not easily translatable to injectable systems given the need for external equipment to direct anisotropic gel fabrication and/or the required use of temperatures or solvents incompatible with biological systems. Herein, we report a new class of injectable nanocomposite hydrogels based on hydrazone cross-linked poly(oligoethylene glycol methacrylate) and magnetically aligned cellulose nanocrystals (CNCs) capable of encapsulating skeletal muscle myoblasts and promoting their differentiation into highly oriented myotubes in situ. CNC alignment occurs on the same time scale as network gelation and remains fixed after the removal of the magnetic field, enabling concurrent CNC orientation and hydrogel injection. The aligned hydrogels show mechanical and swelling profiles that can be rationally modulated by the degree of CNC alignment and can direct myotube alignment both in two- and three-dimensions following coinjection of the myoblasts with the gel precursor components. As such, these hydrogels represent a critical advancement in anisotropic biomimetic scaffolds that can be generated noninvasively in vivo following simple injection.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Implications of grain size variation in magnetic field alignment of block copolymer blends

Recent experiments have highlighted the intrinsic magnetic anisotropy in coil–coil diblock copolymers, specifically in poly(styrene- block -4-vinylpyridine) (PS- b -P4VP), that enables magnetic field alignment at field strengths of a few tesla. We consider here the alignment response of two low molecular weight (MW) lamallae-forming PS- b -P4VP systems. Cooling across the disorder–order transition temperature (T odt ) results in strong alignment for the higher MW sample (5.5K), whereas little alignment is discernible for the lower MW system (3.6K). This disparity under otherwise identical conditions of field strength and cooling rate suggests that different average grain sizes are produced during slow cooling of these materials, with larger grains formed in the higher MW material. Blending the block copolymers results in homogeneous samples which display T odt , d-spacings, and grain sizes that are intermediate between the two neat diblocks. Similarly, the alignment quality displays a smooth variation with the concentration of the higher MW diblock in the blends, and the size of grains likewise interpolates between limits set by the neat diblocks, with a factor of 3.5× difference in the grain size observed in high vs low MW neat diblocks. Finally, these results highlight the importance of grain growth kinetics in dictating the field response in block copolymers and suggests an unconventional route for the manipulation of such kinetics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗