Search NASA⌕ Search

SEARCH · Search NASA

Results for “ALIGNMENT”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7

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↗

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↗

Optical tools and techniques for aligning solar payloads with the SPARCS control system

The success of a rocket-borne experiment depends not only on the pointing of the attitude control system, but on the alignment of the attitude control system to the payload. To ensure proper alignment, special optical tools and alignment techniques are required. Those that were used in the SPARCS program are described and discussed herein. These tools include theodolites, autocollimators, a 38-cm diameter solar simulator, a high-performance 1-m heliostat to provide a stable solar source during the integration of the rocket payload, a portable 75-cm sun tracker for use at the launch site, and an innovation called the Solar Alignment Prism. Using the real sun as the primary reference under field conditions, the Solar Alignment Prism facilitates the coalignment of the attitude sun sensor with the payload. The alignment techniques were developed to ensure the precise alignment of the solar payloads to the SPARCS attitude sensors during payload integration and to verify the required alignment under field conditions just prior to launch.

Thomas, N. L.↗

Orbit IMU alignment: Error analysis

A comprehensive accuracy analysis of orbit inertial measurement unit (IMU) alignments using the shuttle star trackers was completed and the results are presented. Monte Carlo techniques were used in a computer simulation of the IMU alignment hardware and software systems to: (1) determine the expected Space Transportation System 1 Flight (STS-1) manual mode IMU alignment accuracy; (2) investigate the accuracy of alignments in later shuttle flights when the automatic mode of star acquisition may be used; and (3) verify that an analytical model previously used for estimating the alignment error is a valid model. The analysis results do not differ significantly from expectations. The standard deviation in the IMU alignment error for STS-1 alignments was determined to the 68 arc seconds per axis. This corresponds to a 99.7% probability that the magnitude of the total alignment error is less than 258 arc seconds.

Corson, R. W.↗

Optical Alignment of the JWST ISIM to the OTE Simulator (OSIM): Current Concept and Design Studies

The James Webb Space Telescope's (JWST) Integrated Science Instrument Module (ISIM) contains the observatory's four science instruments and their support subsystems. During alignment and test of the integrated ISIM at NASA's Goddard Space Flight Center (GSFC), the Optical'telescope element SIMulator (OSIM) will be used to optically stimulate the science instruments to verify their operation and performance. In this paper we present the design of two cryogenic alignment fixtures that will be used to determine and verify the proper alignment of OSIM to ISIM during testing at GSFC. These fixtures, the Master Alignment Target Fixture (MAW) and the ISIM Alignment Target Fixture (IATF), will provide continuous, six degree of freedom feedback to OSIM during initial ambient alignment as well as during cryogenic vacuum testing. These fixtures will allow us to position the OSIM and maintain OSIM-ISIM alignment to better than 10 microns in translation and 250 micro-radians in rotation. We will provide a brief overview of the OSIM system and calibration and we will also discuss the relevance of these fixtures in the context of the overall ISIM alignment and verification plan.

Frey, Bradley J.↗

Alignment Pins for Assembling and Disassembling Structures

Simple, easy-to-use, highly effective tooling has been devised for maintaining alignment of bolt holes in mating structures during assembly and disassembly of the structures. The tooling was originally used during removal of a body flap from the space shuttle Atlantis, in which misalignments during removal of the last few bolts could cause the bolts to bind in their holes. By suitably modifying the dimensions of the tooling components, the basic design of the tooling can readily be adapted to other structures that must be maintained in alignment. The tooling includes tapered, internally threaded alignment pins designed to fit in the bolt holes in one of the mating structures, plus a draw bolt and a cup that are used to install or remove each alignment pin. In preparation for disassembly of two mating structures, external supports are provided to prevent unintended movement of the structures. During disassembly of the structures, as each bolt that joins the structures is removed, an alignment pin is installed in its place. Once all the bolts have been removed and replaced with pins, the pins maintain alignment as the structures are gently pushed or pulled apart on the supports. In assembling the two structures, one reverses the procedure described above: pins are installed in the bolt holes, the structures are pulled or pushed together on the supports, then the pins are removed and replaced with bolts. The figure depicts the tooling and its use. To install an alignment pin in a bolt hole in a structural panel, the tapered end of the pin is inserted from one side of the panel, the cup is placed over the pin on the opposite side of the panel, the draw bolt is inserted through the cup and threaded into the pin, the draw bolt is tightened to pull the pin until the pin is seated firmly in the hole, then the draw bolt and cup are removed, leaving the pin in place. To remove an alignment pin, the cup is placed over the pin on the first-mentioned side of the panel, the draw bolt is inserted through the cup and threaded into the pin, then the draw bolt is tightened to pull the pin out of the hole.

Campbell, Oliver C.↗

Aligning Three Off-Axis Mirrors with Help of a DOE

A proposed method based on the use of a special-purpose diffractive optical element (DOE) would simplify (relative to prior methods) the alignment of three off-axis mirrors that constitute an imaging optical system. The method would exploit the fact that a DOE can be fabricated lithographically with high accuracy by electron-beam lithography in a thin film of poly(methyl methacrylate). The method would effectively transfer much of the problem of obtaining the needed accuracy from the mechanical-mirror-alignment domain to the lithographic domain. Unlike other methods that depend on specific symmetries (e.g., sphericity and/or concentricity), this method is expected to apply with equal ease and accuracy to mirrors of any configuration including aspherical, decentered mirrors. Assuming that one of the mirrors of a general three-mirror imaging optical system can serve as a reference for the alignment of the other two mirrors, such a system has 12 degrees of freedom in alignment. In the proposed method, one would use an interferometer in combination with a DOE to effect precise and relatively rapid and easy alignment of two of the mirrors with respect to each other, thus reducing the alignment task to that of the six degrees of freedom of the remaining mirror. The figure depicts a representative three-mirror off-axis imaging system, wherein the primary and tertiary mirrors (M1 and M3, respectively) are concave and the secondary mirror (M2) is convex. The DOE for aligning this system would be fabricated on the right surface of an optical flat and could be made to have either negative or positive focusing power, depending on the requirements of the specific application. The DOE could be designed to be placed at any convenient distance from M1 and M3 - again, depending on the application. The DOE would be illuminated with light coming from the left, generated by an interferometer. First, assuming the optical flat is of high quality, the plane of the DOE would be aligned perpendicular to the collimated beam by use of light reflected from the left face of the optical flat. The DOE would comprise two independent areas: one dedicated to M1, the other to M3. The portions of the collimated beam passing through those areas would be diffracted towards the corresponding mirrors. A mask, not shown in the figure, could be used to prevent light from passing through the rest of the area of the optical flat. Light rays reflected from M1 and M3 would retrace their paths through the DOE and would propagate leftward to the interferometer.

Mouroulis, Pantazis↗

Optical Performance Prediction of the Thirty Meter Telescope after Initial Alignment Using Optical Modeling

We present an estimate of the optical performance of the Thirty Meter Telescope (TMT) after execution of the full telescope alignment plan. The TMT alignment is performed by the Global Metrology System (GMS) and the Alignment and Phasing System (APS). The GMS first measures the locations of the telescope optics and instruments as a function of elevation angle. These initial measurements will be used to adjust the optics positions and build initial elevation look-up tables. Then the telescope is aligned using starlight as the input for the APS at multiple elevation angles. APS measurements are used to refine the telescope alignment to build elevation and temperature dependent look-up tables. Due to the number of degrees of freedom in the telescope (over 10,000), the ability of the primary mirror to correct aberrations on other optics, the tight optical performance requirements and the multiple instrument locations, it is challenging to develop, test and validate these alignment procedures. In this paper, we consider several GMS and APS operational scenarios. We apply the alignment procedures to the model-generated TMT, which consists of various quasi-static errors such as polishing errors, passive supports errors, thermal and gravity deformations and installation position errors. Using an integrated optical model and Monte-Carlo framework, we evaluate the TMT’s aligned states using optical performance metrics at multiple instrument and field of view locations. The optical performance metrics include the Normalized Point Source Sensitivity (PSSN), RMS wavefront error before and after Adaptive Optics (AO) correction, pupil position change, and plate scale distortion.

Rogers, John↗

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↗

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↗

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↗

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 ↗

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↗

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↗

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↗

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↗

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↗

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↗