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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

A novel FPCL model producing directional contraction through induction of fibroblast alignment by biphasic pulse direct current electric field

Although parallel alignment of fibroblasts to the tension lines of scar has been evidenced in vivo, how scar contracture generates directional contraction remains largely unclear due to the lack of effective in vitro model. Fibroblast populated collagen lattice (FPCL), a widely used in vitro model, fails to mimic scar contracture since it produces concentric contraction with the random orientation of fibroblast. We hypothesized that a novel FPCL model with fibroblast alignment might produce directional contraction and then simulate scar contracture better. Here, we showed that although direct current electric fields (DCEFs) enabled fibroblasts aligned perpendicularly to the field vector, it also promoted electrotactic migration of fibroblast in FPCL. By contrast, biphasic pulse direct current electric fields (BPDCEFs), featured by reversal of the EF direction periodically, abolished the electrotactic migration, but induced fibroblast alignment in a pulse frequency dependent manner. Specifically, BPDCEF at a pulse frequency of 0.0002 Hz induced fibroblast alignment comparable to that induced by DCEF under the same field strength (300 mV/mm), leading to an enhanced contraction of FPCL along the direction of cell alignment. FPCL pretreated by BPDCEF showed an elliptical contraction whereas it was concentric in control FPCL. Further study revealed that F-actin redistributions acted as a key mechanism for the induction of fibroblasts alignment by BPDCEF. Cytochalasin D, an inhibitor of actin dynamics, abolished F-actins redistribution, and significantly suppressed the fibroblasts alignment and the directional contraction of FPCL. Importantly, BPDCEF significantly increased RhoA activity in fibroblasts, while this response was attenuated by C3 transferase pre-treatment, a potent inhibitor of RhoA, caused F-actin depolymerization and actin filament bundle randomly distributed. Taken together, our study suggests a crucial role for fibroblast orientation in scar contracture, and provides a novel FPCL model that may be feasible and effective for investigating scar contracture in vitro.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Alignments in the orientation of radio jets from AGN and their host galaxies

It is well established that active galactic nuclei (AGNs) play an important role in the evolution of galaxies. These AGNs can be linked to the accretion processes onto massive black holes and past merger events in their host galaxies, which may lead to different alignments of the jets with respect to the host galaxies. This paper presents a study of the position angle (PA) differences between radio and optical images of radio-AGNs based on the second data release (DR2) of the Low Frequency Array (LOFAR) Two-Meter Sky Survey (LoTSS), theKarl G. JanskyVery Large Array Faint Images of the Radio Sky at Twenty-Centimeters Survey (FIRST), the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys, and the Sloan Digital Sky Survey (SDSS). We assessed PA measurement biases in the data and classified the radio-AGNs based on the radio luminosity and infrared colour from the Wide-field Infrared Survey Explorer (WISE). This resulted in the largest sample of radio AGNs with reliable radio and optical PA measurements published to date, with a total of 3682 AGNs. The PA difference (dPA) distributions for the radio-AGN sample show a prominent minor-axis alignment tendency. Based on some simple assumptions, we simulated the projection effect to estimate the intrinsic jet-galaxy alignment. The observed dPA distribution can be well described by a two-component jet-alignment model in which one component is more aligned with the minor axis of the host galaxy than the other. The fitting results indicate that the jet alignment is dependent on radio luminosity and the shape of the host galaxies, with the jets being more likely to be aligned with the minor axis of the galaxy for lower radio luminosity and for optically more elongated radio-AGNs. The minor-axis alignment of the entire sample may suggest a coherent accretion model present in most AGN host galaxies, while a considerable number of luminous radio-AGNs with massive host galaxies might have undergone accretion – according to the chaotic model – or past merger events.

Astronomy & Astrophysics↗
DOE OSTI2012

MODELING THE ALIGNMENT PROFILE OF SATELLITE GALAXIES IN CLUSTERS

Analyzing the halo and galaxy catalogs from the Millennium Simulations at redshifts z = 0, 0.5, 1, we determine the alignment profiles of cluster galaxies by measuring the average alignments between the major axes of the pseudo inertia tensors from all satellites within a cluster's virial radius and from only those satellites within some smaller radius as a function of the top-hat scale difference. The alignment profiles quantify how well the satellite galaxies retain the memory of the external tidal fields after merging into their host clusters and how fast they lose the initial alignment tendency as the cluster's relaxation proceeds. It is found that the alignment profile drops faster at higher redshifts and on smaller mass scales. This result is consistent with the picture that the faster merging of the satellites and earlier onset of the nonlinear effect inside clusters tend to break the preferential alignments of the satellites with the external tidal fields. Modeling the alignment profile of cluster galaxies as a power law of the density correlation coefficient that is independent of the power spectrum normalization ({sigma}{sub 8}) and demonstrating that the density correlation coefficient varies sensitively with the density parameter ({Omega}{sub m}) and neutrino mass fraction (f{sub {nu}}), we suggest that the alignment profile of cluster galaxies might be useful for breaking the {Omega}{sub m}-{sigma}{sub 8} and f{sub {nu}}-{sigma}{sub 8} degeneracies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

The intrinsic alignment of red galaxies in DES Y1 redMaPPer galaxy clusters

ABSTRACT Clusters of galaxies trace the most non-linear peaks in the cosmic density field. The weak gravitational lensing of background galaxies by clusters can allow us to infer their masses. However, galaxies associated with the local environment of the cluster can also be intrinsically aligned due to the local tidal gradient, contaminating any cosmology derived from the lensing signal. We measure this intrinsic alignment in Dark Energy Survey (DES) Year 1 redMaPPer clusters. We find evidence of a non-zero mean radial alignment of galaxies within clusters between redshifts 0.1–0.7. We find a significant systematic in the measured ellipticities of cluster satellite galaxies that we attribute to the central galaxy flux and other intracluster light. We attempt to correct this signal, and fit a simple model for intrinsic alignment amplitude (AIA) to the measurement, finding AIA = 0.15 ± 0.04, when excluding data near the edge of the cluster. We find a significantly stronger alignment of the central galaxy with the cluster dark matter halo at low redshift and with higher richness and central galaxy absolute magnitude (proxies for cluster mass). This is an important demonstration of the ability of large photometric data sets like DES to provide direct constraints on the intrinsic alignment of galaxies within clusters. These measurements can inform improvements to small-scale modelling and simulation of the intrinsic alignment of galaxies to help improve the separation of the intrinsic alignment signal in weak lensing studies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Alignment Thresholds of Molecules

Molecules have long been known to align in moderately intense, far off-resonance laser fields with a large variety of applications in physics and optics. Here, we illustrate and describe the physical origin of a previously unexplored phenomenon in the adiabatic alignment dynamics of molecules, which is fundamentally interesting and also has an important practical implication. Specifically, the intensity dependence of the degree of adiabatic alignment exhibits a threshold behavior, below which molecules are isotropically distributed rotationally and above which the alignment rapidly reaches a plateau. Furthermore, we show that both the intensity and the temperature dependencies of the alignment of all linear molecules exhibit universal curves and derive analytical forms to describe these dependencies. Finally, we illustrate that the alignment threshold occurs very generally at a lower intensity than the off-resonance ionization threshold, a numerical observation that is readily illustrated analytically. The threshold behavior is attributed to a tunneling mechanism that rapidly switches off at the threshold intensity, where tunneling between the potential wells corresponding to the two orientations of the aligned molecules becomes impossible. The universal threshold behavior of molecular alignment is a simple phenomenon, but one that was not realized before and can be readily tested experimentally.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

SU-E-T-484: A New Method of Aligning Patient Setup Lasers in Radiation Therapy

Purpose: To develop a new method to align the patient setup lasers in radiation therapy and examine its validity and effectiveness. Methods: The new laser alignment method was realized by a device composed of both a metallic base plate and few acrylic transparent plates with a cross hair line on each of them. The holders of radiochromic films were prepared in the device to find a radiation isocenter. The right laser positions could be found optically by matching the shadows of all the cross hairs in the gantry head and the device. The repeatability and reproducibility (R and R) of laser alignments and the dependency of the alignment on the position error of the light source were evaluated by comparing the standard deviations and the means of the measured laser positions. After aligning the lasers optically, a radiation isocenter was found by a collimator spoke shot and the gantry spoke shot, and then the lasers were parallely translated to the isocenter. Results: In the R and R test, the standard deviation was 1.14 mm for the new method whereas it was 1.49 mm or 2.76 mm for the conventional method with either high- or low-precision levels. In the test of the dependency on the position error of the light source, the mean laser position was shifted by 5.3 mm corresponding to the shift of the light source, 4.8 mm for the new method, but for the conventional method the laser position was shifted more than 7 times than that. The positional shift could be corrected by a parallel translation to the isocenter in the new method. Conclusion: A new laser alignment method was devised for radiation therapy and tested successfully. The method enabled us to align the lasers easily and accurately without repetition, and all lasers could be finally aligned to the radiation isocenter.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (BELLA) v1.0

BELLA is a long-read overlapper and read-to-read aligner that exploits novel approaches for selecting reliable k-mer seeds for filtering and for detecting overlapping read pairs to reconstruct the whole genome. BELLA uses a sparse matrix-matrix multiplication for high-performance overlap detection and then performs pairwise alignment on the overlapping read pairs. BELLA can be built with different pre-existing aligners to use on each read pair, so precision rates are determined by those aligners. Our evaluations include real and synthetic datasets with varying size and complexity and include recall, precision, and running time. BELLA's overlap detection retains nearly all true alignments, with recall rates that exceed other aligners, yet it filters enough read pairs that the running time, including pairwise alignments, is closer to tools that only perform overlapping and is significantly faster than tools that also perform alignment

Guidi, Giulia↗
DOE OSTI2014

Nuclear reactor alignment plate configuration

An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
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↗