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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Substrate-Wide Confined Shear Alignment of Carbon Nanotubes for Thin Film Transistors

To exploit their charge transport properties in transistors, semiconducting carbon nanotubes must be assembled into aligned arrays comprised of individualized nanotubes at optimal packing densities. However, achieving this control on the wafer-scale is challenging. Here, solution-based shear in substrate-wide, confined channels is investigated to deposit continuous films of well-aligned, individualized, semiconducting nanotubes. Polymer-wrapped nanotubes in organic ink are forced through sub-mm tall channels, generating shear up to 10 000 s -1 uniformly aligning nanotubes across substrates. The ink volume and concentration, channel height, and shear rate dependencies are elucidated. Optimized conditions enable alignment within a ±32° window, at 50 nanotubes µm-1, on 10 × 10 cm 2 substrates. Transistors (channel length of 1–5 µm) are fabricated parallel and perpendicular to the alignment. The parallel transistors perform with 7× faster charge carrier mobility (101 and 49 cm 2 V -1 s -1 assuming array and parallel-plate capacitances, respectively) with high on/off ratio of 105. The spatial uniformity varies ±10% in density, ±2° in alignment, and ±7% in mobility. Deposition occurs within seconds per wafer, and further substrate scaling is viable. Compared to random networks, aligned nanotube films promise to be a superior platform for applications including sensors, flexible/stretchable electronics, and light emitting and harvesting devices.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Bioinspired aligned magnetic features in aerogels for humidity sensing

Many natural plant tissues, such as pinecones, utilize structures to transduce changes in humidity into movement or strain. These often employ layered structures with aligned features in order to create differential stress across the material as different portions swell at different rates. Here, by replicating these types of structures in synthetic materials we can create structures that respond to humidity in a similar manner. Taking these aligned features as inspiration, silica aerogels with tailored humidity reactive properties were created. This behavior was achieved by creating aligned features in these aerogels using a Helmholtz coil to produce a uniform magnetic field that aligned ferrofluid droplets into chains and needle like features. These magnetite-based structures were shown to retain their superparamagnetic properties, allowing them to easily be removed from the aerogels, leaving a large number of aligned channels. Aerogels with the removed needles experienced significantly different strains than both unmodified aerogels and aerogels with the aligned features still in place. Aerogels with these tunable aligned features could be used in humidity sensors that can transduce changes in humidity into strain and could be used in applications such as volatile organic compound capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Design of practical alignment device in KSTAR Thomson diagnostic

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak’s Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR’s Thomson scattering diagnostics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

Cosmological information in the intrinsic alignments of luminous red galaxies

The intrinsic alignments of galaxies are usually regarded as a contaminant to weak gravitational lensing observables. The alignment of Luminous Red Galaxies, detected unambiguously in observations from the Sloan Digital Sky Survey, can be reproduced by the linear tidal alignment model of Catelan, Kamionkowski and Blandford (2001) on large scales. In this work, we explore the cosmological information encoded in the intrinsic alignments of red galaxies. We make forecasts for the ability of current and future spectroscopic surveys to constrain local primordial non-Gaussianity and Baryon Acoustic Oscillations (BAO) in the cross-correlation function of intrinsic alignments and the galaxy density field. For the Baryon Oscillation Spectroscopic Survey, we find that the BAO signal in the intrinsic alignments is marginally significant with a signal-to-noise ratio of 1.8 and 2.2 with the current LOWZ and CMASS samples of galaxies, respectively, and increasing to 2.3 and 2.7 once the survey is completed. For the Dark Energy Spectroscopic Instrument and for a spectroscopic survey following the EUCLID redshift selection function, we find signal-to-noise ratios of 12 and 15, respectively. Local type primordial non-Gaussianity, parametrized by f{sub NL} = 10, is only marginally significant in the intrinsic alignments signal with signal-to-noise ratios < 2 for the three surveys considered.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

THE DETECTION OF THE LARGE-SCALE ALIGNMENT OF MASSIVE GALAXIES AT z {approx} 0.6

We report on the detection of the alignment between galaxies and large-scale structure at z {approx} 0.6 based on the CMASS galaxy sample from the Baryon Oscillation Spectroscopy Survey Data Release 9. We use two statistics to quantify the alignment signal: (1) the alignment two-point correlation function that probes the dependence of galaxy clustering at a given separation in redshift space on the projected angle ({theta}{sub p}) between the orientation of galaxies and the line connecting to other galaxies, and (2) the cos (2{theta})-statistic that estimates the average of cos (2{theta}{sub p}) for all correlated pairs at a given separation s. We find a significant alignment signal out to about 70 h {sup -1} Mpc in both statistics. Applications of the same statistics to dark matter halos of mass above 10{sup 12} h {sup -1} M{sub Sun} in a large cosmological simulation show scale-dependent alignment signals similar to the observation, but with higher amplitudes at all scales probed. We show that this discrepancy may be partially explained by a misalignment angle between central galaxies and their host halos, though detailed modeling is needed in order to better understand the link between the orientations of galaxies and host halos. In addition, we find systematic trends of the alignment statistics with the stellar mass of the CMASS galaxies, in the sense that more massive galaxies are more strongly aligned with the large-scale structure.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A general Bayesian algorithm for the autonomous alignment of beamlines

Autonomous methods to align beamlines can decrease the amount of time spent on diagnostics, and also uncover better global optima leading to better beam quality. The alignment of these beamlines is a high-dimensional expensive-to-sample optimization problem involving the simultaneous treatment of many optical elements with correlated and nonlinear dynamics. Bayesian optimization is a strategy of efficient global optimization that has proved successful in similar regimes in a wide variety of beamline alignment applications, though it has typically been implemented for particular beamlines and optimization tasks. In this paper, we present a basic formulation of Bayesian inference and Gaussian process models as they relate to multi-objective Bayesian optimization, as well as the practical challenges presented by beamline alignment. We show that the same general implementation of Bayesian optimization with special consideration for beamline alignment can quickly learn the dynamics of particular beamlines in an online fashion through hyperparameter fitting with no prior information. We present the implementation of a concise software framework for beamline alignment and test it on four different optimization problems for experiments on X-ray beamlines at the National Synchrotron Light Source II and the Advanced Light Source, and an electron beam at the Accelerator Test Facility, along with benchmarking on a simulated digital twin. We discuss new applications of the framework, and the potential for a unified approach to beamline alignment at synchrotron facilities.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps

Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being potentially stuck in local minima, we propose here a new procedure, called AlignOT, which relies on the use of computational optimal transport (OT) to align EM maps in 3D space. By embedding a fast estimation of OT maps within a stochastic gradient descent algorithm, our method searches for a rotation that minimizes the Wasserstein distance between two maps, represented as point clouds. Here, we quantify the impact of various parameters on the precision and accuracy of the alignment, and show that AlignOT can outperform the standard local alignment methods, with an increased range of rotation angles leading to proper alignment. We further benchmark AlignOT on various pairs of experimental maps, which account for different types of conformational heterogeneities and geometric properties. As our experiments show good performance, we anticipate that our method can be broadly applied to align 3D EM maps.

3D alignment↗
DOE OSTI2024

metabCombiner 2.0: Disparate Multi-Dataset Feature Alignment for LC-MS Metabolomics

Liquid chromatography–high-resolution mass spectrometry (LC-HRMS), as applied to untargeted metabolomics, enables the simultaneous detection of thousands of small molecules, generating complex datasets. Alignment is a crucial step in data processing pipelines, whereby LC-MS features derived from common ions are assembled into a unified matrix amenable to further analysis. Variability in the analytical factors that influence liquid chromatography separations complicates data alignment. This is prominent when aligning data acquired in different laboratories, generated using non-identical instruments, or between batches from large-scale studies. Previously, we developed metabCombiner for aligning disparately acquired LC-MS metabolomics datasets. Here, we report significant upgrades to metabCombiner that enable the stepwise alignment of multiple untargeted LC-MS metabolomics datasets, facilitating inter-laboratory reproducibility studies. To accomplish this, a “primary” feature list is used as a template for matching compounds in “target” feature lists. We demonstrate this workflow by aligning four lipidomics datasets from core laboratories generated using each institution’s in-house LC-MS instrumentation and methods. We also introduce batchCombine, an application of the metabCombiner framework for aligning experiments composed of multiple batches. metabCombiner is available as an R package on Github and Bioconductor, along with a new online version implemented as an R Shiny App.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

We presented some considerations for achieving high degree of alignment in polymer bonded permanent magnets via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. Moreover, the thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees with an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Finally, manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Magnesium diboride (MgB2): An effective and novel precursor for the synthesis of vertically aligned BNNTs

Highlights: • Discovered Magnesium diboride (MgB{sub 2}) as an effective and novel precursor for the synthesis of BNNTs. • Synthesized vertically aligned BNNTs directly on SiO{sub 2} substrate at 1000{sup °}C. • Magnesium (Mg) from MgB{sub 2} in partially melted form diffuses on SiO{sub 2} substrate. • The adsorbed Boron with Mg reacts with Nitrogen from decomposed ammonia and synthesized vertically aligned BNNTs. - Abstract: Vertically aligned Boron nitride nanotubes (BNNTs) have exceptional electrical, mechanical and thermal properties suitable for its potential applications without any further purification. However, the synthesis of aligned BNNTs via previously reported techniques is not only complicated, lengthy and misleading but also result in useless impurities in the final product. Here, we report Magnesium diboride (MgB{sub 2}) as an effective and novel precursor for the synthesis of vertically aligned BNNTs directly on SiO{sub 2} substrate at 1000 {sup °}C. Magnesium (Mg) from MgB{sub 2} in partially melted form diffuses on SiO{sub 2} substrate whereas the adsorbed Boron with Mg reacts with Nitrogen from decomposed ammonia and synthesized vertically aligned BNNTs. The morphology, alignment, structure and compositions of the as-synthesized BNNTs are studied via field emission scanning electron microscope, high resolution transmission electron microscope, energy dispersive x-ray spectroscopy, x-ray diffraction, Raman spectroscopy and Fourier transform infrared spectroscopy.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Strain-induced alignment and phase behavior of blue phase liquid crystals confined to thin films

Here, we report on the influence of surface confinement on the phase behavior and strain-induced alignment of thin films of blue phase liquid crystals (BPs). Confining surfaces comprised of bare glass, dimethyloctadecyl [3-(trimethoxysilyl)propyl] ammonium chloride (DMOAP)-functionalized glass, or polyvinyl alcohol (PVA)-coated glass were used with or without mechanically rubbing to influence the azimuthal anchoring of the BPs. These experiments reveal that confinement can change the phase behavior of the BP films. For example, in experiments performed with rubbed-PVA surfaces, we measured the elastic strain of the BPs to change the isotropic–BPII phase boundary, suppressing formation of BPII for film thicknesses incommensurate with the BPII lattice. In addition, we observed strain-induced alignment of the BPs to exhibit a complex dependence on both the surface chemistry and azimuthal alignment of the BPs. For example, when using bare glass surfaces causing azimuthally degenerate and planar anchoring, BPI oriented with (110) planes of the unit cell parallel to the contacting surfaces for thicknesses below 3 μm but transitioned to an orientation with (200) planes aligned parallel to the contacting surfaces for thicknesses above 4 μm. In contrast, BPI aligned with (110) planes parallel to confining surfaces for all other thicknesses and surface treatments, including bare glass with uniform azimuthal alignment. Complementary simulations based on minimization of the total free energy (Landau–de Gennes formalism) confirmed a thickness-dependent reorientation due to strain of BPI unit cells within a window of surface anchoring energies and in the absence of uniform azimuthal alignment. In contrast to BPI, BPII did not exhibit thickness-dependent orientations but did exhibit orientations that were dependent on the surface chemistry, a result that was also captured in simulations by varying the anchoring energies. Overall, the results in this paper reveal that the orientations assumed by BPs in thin films reflect a complex interplay of surface interactions and elastic energies associated with strain of the BP lattice. The results also provide new principles and methods to control the structure and properties of BP thin films, which may find use in BP-templated material synthesis, and BP-based optical and electronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Alignment of gold nanorods by angular photothermal depletion

In this paper, we demonstrate that a high degree of alignment can be imposed upon randomly oriented gold nanorod films by angular photothermal depletion with linearly polarized laser irradiation. The photothermal reshaping of gold nanorods is observed to follow quadratic melting model rather than the threshold melting model, which distorts the angular and spectral hole created on 2D distribution map of nanorods to be an open crater shape. We have accounted these observations to the alignment procedures and demonstrated good agreement between experiment and simulations. The use of multiple laser depletion wavelengths allowed alignment criteria over a large range of aspect ratios, achieving 80% of the rods in the target angular range. We extend the technique to demonstrate post-alignment in a multilayer of randomly oriented gold nanorod films, with arbitrary control of alignment shown across the layers. Photothermal angular depletion alignment of gold nanorods is a simple, promising post-alignment method for creating future 3D or multilayer plasmonic nanorod based devices and structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Ionization induced dynamic alignment of water

Two-body dissociation resulting from strong-field double ionization of water is investigated. Two distinct features are seen in the alignment of the fragment momenta with respect to the laser polarization. One feature shows alignment of the H–OH axis with the laser polarization, while the other indicates polarization alignment normal to the H–OH axis. By analyzing kinematic differences between the OH + /D + and OD + /H + channels of HOD, these two alignment features are shown to result from dissociation from different states in the dication. Only dissociation from one of these states has an alignment dependence consistent with predictions of sequential strong-field tunneling ionization models. Finally, the alignment dependence of dissociation from the other state can only be explained by dynamic alignment launched by the unbending of the molecule during ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Paramagnetic alignment of small grains: A novel method for measuring interstellar magnetic fields

We present a novel method to measure the strength of interstellar magnetic fields using ultraviolet (UV) polarization of starlight that is in part produced by weakly aligned, small dust grains. We begin with calculating the degrees of the paramagnetic alignment of small (size a ∼ 0.01 μm) and very small (a ∼ 0.001 μm) grains in the interstellar magnetic field due to the Davis-Greenstein relaxation and resonance relaxation. To calculate the degrees of paramagnetic alignment, we use Langevin equations and take into account various interaction processes essential for the rotational dynamics of small grains. We find that the alignment of small grains is necessary to reproduce the observed polarization in the UV, although the polarization arising from these small grains is negligible at the optical and infrared (IR) wavelengths. Based on fitting theoretical models to observed extinction and polarization curves, we find that the best-fit model for the case with the peak wavelength of polarization λ{sub max} < 0.55 μm requires a higher degree of alignment of small grains than for the typical case with λ{sub max} = 0.55 μm. We interpret the correlation between the systematic increase of the UV polarization relative to maximum polarization (i.e., of p(6 μm{sup –1})/p{sub max}) with λ{sub max}{sup −1} for cases of low λ{sub max} by appealing to the higher degree of alignment of small grains. We utilize the correlation of the paramagnetic alignment of small grains with the magnetic field strength B to suggest a new way to measure B using the observable parameters λ{sub max} and p(6 μm{sup –1})/p{sub max}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

The shapes and alignments of dark matter halos

We present measurements of the triaxial dark matter halo shapes and alignment correlation functions in the Millennium and Millennium-2 dark matter N-body simulations. These two simulations allow us to measure the distributions of halo shapes down to 10% of the virial radius over a halo mass range of 6 × 10{sup 9}–2 × 10{sup 14} h{sup −1}M{sub s}un. We largely confirm previous results on the distributions of halo axis ratios as a function of halo mass, but we find that the median angle between halo major axes at different halo radii can vary by a factor of 2 between the Millennium-1 and 2 simulations because of the different mass resolution. Thus, error in the shape determinations from limited resolution is potentially degenerate with the misalignment of halo inner and outer shapes used to constrain Brightest Cluster Galaxy alignments in previous works. We also present simplifying parameterizations for the 3-D halo-mass alignment correlation functions that are necessary ingredients for triaxial halo models of large-scale structure and models of galaxy intrinsic alignments as contaminants for cosmic shear surveys. We measure strong alignments between halos of all masses and the surrounding dark matter overdensities out to several tens of h{sup −1} Mpc, in agreement with observed shear-galaxy and cluster shape correlations. We use these measurements to forecast the contribution to the weak lensing signal around galaxy clusters from correlated mass along the line-of-sight. For prolate clusters with major axes aligned with the line-of-sight the fraction of the weak lensing signal from mass external to the cluster can be twice that predicted if the excess halo alignment correlation is assumed to be zero.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The alignment between brightest cluster galaxies and host clusters

The alignment between the brightest cluster galaxies (BCGs) and host clusters can reveal the mystery of the formation and evolution of galaxy clusters. We measure cluster orientations in optical based on the projected distribution of member galaxies and in X-ray by fitting the morphology of intracluster medium (ICM). Cluster orientations determined in the two wavelengths are generally consistent. The orientation alignment between BCGs and host clusters is confirmed and more significant than in previous works. We find that BCGs are more aligned with cluster orientations measured in X-ray than those from optical data. Clusters with a brighter BCG generally show a stronger alignment. We argue that the detected redshift evolution of the alignment is probably caused by observational bias rather than intrinsic evolution. The alignment is not related to the ellipticity of BCGs, and the richness, ellipticity, and dynamical state of host clusters. As a result, the strong alignment between BCGs and the morphology of ICMs may be the consequence of the co-evolution between the central massive galaxy and host clusters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Increasing the power of weak lensing data with multipole-based intrinsic alignment estimators

ABSTRACT It has long been known that galaxy shapes align coherently with the large-scale density field. Characterizing this effect is essential to interpreting measurements of weak gravitational lensing, the deflection of light from distant galaxies by matter overdensities along the line of sight, as it also produces coherent galaxy alignments that we wish to interpret in terms of a cosmological model. Existing direct measurements of intrinsic alignments using galaxy samples with high-quality shape and redshift measurements typically use well-understood but sub-optimal projected estimators, which do not make good use of the information in the data when comparing those estimators to theoretical models. We demonstrate a more optimal estimator, based on a multipole expansion of the correlation functions or power spectra, for direct measurements of galaxy intrinsic alignments. We show that even using the lowest order multipole alone increases the significance of inferred model parameters using simulated and real data, without any additional modelling complexity. We apply this estimator to measurements of parameters of the non-linear alignment model using data from the Sloan Digital Sky survey, demonstrating consistent results with a factor of ∼2 greater precision in parameter fits to intrinsic alignments models. This result is functionally equivalent to quadrupling the survey area, but without the attendant costs – thereby demonstrating the value in using this new estimator in current and future intrinsic alignments measurements using spectroscopic galaxy samples.

Astronomy & Astrophysics↗