Engineering Papers⌕ Search

SEARCH · Engineering Papers

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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

On the Impact of Widening Vector Registers on Sequence Alignment

Vector extensions, such as SSE, have been part of the x86 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. In this paper, we demonstrate that the trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. We present a practically efficient SIMD implementation of a parallel scan based sequence alignment algorithm that can better exploit wider SIMD units. We conduct comprehensive workload and use case analyses to characterize the relative behavior of the striped and scan approaches and identify the best choice of algorithm based on input length and SIMD width.

Needleman-Wunsch↗
DOE OSTI2023

1 kV Self-Aligned Vertical GaN Superjunction Diode

This work demonstrates vertical GaN superjunction (SJ) diodes fabricated via a novel self-aligned process. The SJ comprises n-GaN pillars wrapped by the charge-balanced p-type nickel oxide (NiO). After the NiO sputtering around GaN pillars, the self-aligned process exposes the top pillar surfaces without the need for additional lithography or a patterned NiO etching which is usually difficult. The GaN SJ diode shows a breakdown voltage (B V) of 1100 V, a specific on-resistance (R ON ) of 0.4 mΩ· cm2, and a SJ drift-region resistance ( R dr ) of 0.13 mΩ· cm2. Further, the device also exhibits good thermal stability with B V retained over 1 kV and R ON dropped to 0.3 mΩ· cm2 at 125°C. The trade-off between B V and R dr is superior to the 1D GaN limit. These results show the promise of vertical GaN SJ power devices. The self-aligned process is applicable for fabricating the heterogeneous SJ based on various wide- and ultra-wide bandgap semiconductors.

42 ENGINEERING↗
DOE OSTI2014

SU-E-J-94: Positioning Errors Resulting From Using Bony Anatomy Alignment for Treating SBRT Lung Tumor

Purpose: To quantify patient setups errors based on bony anatomy registration rather than 3D tumor alignment for SBRT lung treatments. Method: A retrospective study was performed for patients treated with lung SBRT and imaged with kV cone beam computed tomography (kV-CBCT) image-guidance. Daily CBCT images were registered to treatment planning CTs based on bony anatomy alignment and then inter-fraction tumor movement was evaluated by comparing shift in the tumor center in the medial-lateral, anterior-posterior, and superior-inferior directions. The PTV V100% was evaluated for each patient based on the average daily tumor displacement to assess the impact of the positioning error on the target coverage when the registrations were based on bony anatomy. Of the 35 patients studied, 15 were free-breathing treatments, 10 used abdominal compression with a stereotactic body frame, and the remaining 10 were performed with BodyFIX vacuum bags. Results: For free-breathing treatments, the range of tumor displacement error is between 1–6 mm in the medial-lateral, 1–13 mm in the anterior-posterior, and 1–7 mm in the superior-inferior directions. These positioning errors lead to 6–22% underdose coverage for PTV - V100% . Patients treated with abdominal compression immobilization showed positional errors of 0–4mm mediallaterally, 0–3mm anterior-posteriorly, and 0–2 mm inferior-superiorly with PTV - V100% underdose ranging between 6–17%. For patients immobilized with the vacuum bags, the positional errors were found to be 0–1 mm medial-laterally, 0–1mm anterior-posteriorly, and 0–2 mm inferior-superiorly with PTV - V100% under dose ranging between 5–6% only. Conclusion: It is necessary to align the tumor target by using 3D image guidance to ensure adequate tumor coverage before performing SBRT lung treatments. The BodyFIX vacuum bag immobilization method has the least positioning errors among the three methods studied when bony anatomy is used for registration.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Alignment of RNA molecules: Binding energy and statistical properties of random sequences

A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energy between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies as well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Benchmarking of alignment-free sequence comparison methods

Background: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Results: Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. Conclusion: The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Linac Alignment Algorithm: Analysis on 1-to-1 Steering

In a linear accelerator, it is important to achieve a good alignment between all of its components (such as quadrupoles, RF cavities, beam position monitors et al.), in order to better preserve the beam quality during acceleration. After the survey of the main linac components, there are several beam-based alignment (BBA) techniques to be applied, to further optimize the beam trajectory and calculate the corresponding steering magnets strength. Among these techniques the most simple and straightforward one is the one-to-one (1-to-1) steering technique, which steers the beam from quad center to center, and removes the betatron oscillation from quad focusing. For a future linear collider such as the International Linear Collider (ILC), the initial beam emittance is very small in the vertical plane (flat beam with {gamma}{epsilon}{sub y} = 20-40nm), which means the alignment requirement is very tight. In this note, we evaluate the emittance growth with one-to-one correction algorithm employed, both analytically and numerically. Then the ILC main linac accelerator is taken as an example to compare the vertical emittance growth after 1-to-1 steering, both from analytical formulae and multi-particle tracking simulation. It is demonstrated that the estimated emittance growth from the derived formulae agrees well with the results from numerical simulation, with and without acceleration, respectively.

43 PARTICLE ACCELERATORS↗
DOE OSTI2012

Laboratory Guide for Residual Stress Sample Alignment and Experiment Planning-October 2011 Version

The December 2010 version of the guide, ORNL/TM-2008/159, by Jeff Bunn, Josh Schmidlin, Camden Hubbard, and Paris Cornwell, has been further revised due to a major change in the GeoMagic Studio software for constructing a surface model. The Studio software update also includes a plug-in module to operate the FARO Scan Arm. Other revisions for clarity were also made. The purpose of this revision document is to guide the reader through the process of laser alignment used by NRSF2 at HFIR and VULCAN at SNS. This system was created to increase the spatial accuracy of the measurement points in a sample, reduce the use of neutron time used for alignment, improve experiment planning, and reduce operator error. The need for spatial resolution has been driven by the reduction in gauge volumes to the sub-millimeter level, steep strain gradients in some samples, and requests to mount multiple samples within a few days for relating data from each sample to a common sample coordinate system. The first step in this process involves mounting the sample on an indexer table in a laboratory set up for offline sample mounting and alignment in the same manner it would be mounted at either instrument. In the shared laboratory, a FARO ScanArm is used to measure the coordinates of points on the sample surface ('point cloud'), specific features and fiducial points. A Sample Coordinate System (SCS) needs to be established first. This is an advantage of the technique because the SCS can be defined in such a way to facilitate simple definition of measurement points within the sample. Next, samples are typically mounted to a frame of 80/20 and fiducial points are attached to the sample or frame then measured in the established sample coordinate system. The laser scan probe on the ScanArm can then be used to scan in an 'as-is' model of the sample as well as mounting hardware. GeoMagic Studio 12 is the software package used to construct the model from the point cloud the scan arm creates. Once a model, fiducial, and measurement files are created, a special program, called SScanSS combines the information and by simulation of the sample on the diffractometer can help plan the experiment before using neutron time. Finally, the sample is mounted on the relevant stress measurement instrument and the fiducial points are measured again. In the HFIR beam room, a laser tracker is used in conjunction with a program called CAM2 to measure the fiducial points in the NRSF2 instrument's sample positioner coordinate system. SScanSS is then used again to perform a coordinate system transformation of the measurement file locations to the sample positioner coordinate system. A procedure file is then written with the coordinates in the sample positioner coordinate system for the desired measurement locations. This file is often called a script or command file and can be further modified using excel. It is very important to note that this process is not a linear one, but rather, it often is iterative. Many of the steps in this guide are interdependent on one another. It is very important to discuss the process as it pertains to the specific sample being measured. What works with one sample may not necessarily work for another. This guide attempts to provide a typical work flow that has been successful in most cases.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Impact of Lateral Alignment for Cooling Airflow during Heavy-Truck Platooning

A truck platooning system was tested using two heavy-duty tractor-trailer trucks on a closed test track to investigate the thermal control/heat rejection system sensitivity to intentional lateral offsets over a range of intervehicle spacings. Previous studies have shown the following vehicle can experience elevated temperatures and reduced airflow through the cooling package as a result of close-formation platooning. Four anemometers positioned across the grille of the following trucks as well as aligned and multiple offset positions are used to evaluate the sensitivity of the impact. Straight sections of the track are isolated for the most accurate airflow impact measurements and to be most representative of on-highway driving. An intentional lateral offset in truck platooning is considered as a controls approach to mitigate reduced cooling efficacy at close following scenarios where the highest platoon savings are achieved. The truck platooning system was tested at four gap distances from 9 to 23 meters and the following truck was either aligned with the lead or offset with a 25% width (0.65 m) or 50% width (1.3 m) lateral distance. The experimental results clearly show that offset driving is effective at bringing cooling airflow from 56% with an aligned platoon back up to 75%-80% with minimal impact to fuel savings. In addition, the offset driving can also reduce the trailing truck’s engine coolant temperature by 2°C and the corresponding underhood temperature rise by 10°C. The test outcomes indicate a plausible controls strategy to mitigate reduced cooling flow during hot-weather truck platooning while still enabling the highest-energy-saving, close-following scenarios.

27 ARPA - Advanced Research Projects Agency-Energy↗
NASA NTRSDate not supplied

PACE OCI Short-Wave Infrared Detection Assembly Optical System Design, Alignment, and Environmental Test

The Ocean Color Instrument (OCI), which will be integrated with the Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) satellite, will collect science data that will be used to monitor the health of Earth’s oceans and atmosphere. The Short-Wave Infrared (SWIR) Detection Assembly (SDA), built and characterized by Utah State University Space Dynamics Laboratory (SDL), is a subsystem of OCI consisting of 32 channels covering seven discrete optical bands of interest. A total of 16 SWIR Detection Subassemblies (SDSs) compose the SDA and house the cold optical system. The science data optical input for each SDS is supplied by a 0.22 NA multimode fiber interfacing with a fiber adapter. The diverging light from the fiber is collimated, split by a dichroic beamsplitter to two separate channels, filtered by the science filter, and then reimaged onto the single-element detectors with a final 0.76 NA. Aspheric, diamond-turned powered elements are used throughout the optical design. Fabrication and alignment tolerance analysis/budgets are balanced to ensure the optical system meets throughput requirements. All systems are aligned at ambient temperature using an InSb camera and an in-line illumination microscope system to directly image the active detector area through the science filters. Compensators used during alignment are detector focus and decenter, which are adjusted via photoetched shims in increments of 25 µm. Average focus and centering errors were less than 8 µm among all 32 flight and 10 flight spare detectors. Each SDS spectral response and conversion gain was verified at operational temperature of -65°C in vacuum.

OCI↗
NASA NTRS2024

CODEX Optical Design and Alignment

The COronal Diagnostic EXperiment (CODEX) is a Heliophysics mission to measure the density, temperature, and velocity of the electrons in the solar corona with the primary goal of improving our understanding of the physical conditions of the solar wind in the acceleration region. The temperature and velocity measurement requires much higher signal-to-noise ratio than the density measurements. In solar coronagraphs, the diffraction of the solar disk light due to the occulting element is the dominant source of noise. Therefore, to further suppress the diffracted sun light with respect to the existing coronagraphs is a critical element of the CODEX design. To minimize the stray light due to diffraction, the selected optical design is a two-stage standard coronagraph with an external occulter, an internal occulter, and a Lyot stop. What is unique for this design is that a focal mask was inserted at the telescope focal plane. It works together with the field lens suppressing the stray light down by ~ another order of magnitude as compared to a traditional three-stage approach. During the optical design, a Fourier Transform based beam propagation software, i.e., GLAD, was used to model the beam path through the full coronagraph, from the external occulter to the detector array. All diffraction sensitive elements: external occulter, internal occulter, focal mask, and Lyot stop were carefully modeled and optimized. As a result, the requirement of achieving a stray light level which is one order of magnitude lower than F-corona was satisfied. On the other hand, to achieve the final suppression, a precision optical alignment is another must. This paper also presents our creative alignment procedure: using the combination of metrology, precision alignment equipment, and real time diffraction ring monitoring to minimize the diffraction. The final test results show that the suppression ratio (B/B 0 ) reaches 10 -11 level, which is equivalent to one order of magnitude lower than F-corona.

CODEX optical design and alignment↗
DOE OSTI2013

Strategies and Lessons-Learned for the Successful Alignment of Contract Cost with the Contract Budget Base (CBB) within the First Year of Contract Award - 13154

In order to provide a sound basis and foundation for integrated Project and Contract change management, it is imperative to ensure the alignment of the Negotiated Contract Costs (NCC) with the Contract Budget Base (CBB), where CBB is defined as the Performance Measurement Baseline (PMB) plus Management Reserve (MR). The achievement of this alignment assures customer and contractor agreement on scope, requirements, quantities, schedule and cost, which facilitates the identification of change conditions and ultimate agreement on the value of changes to the NCC and the CBB. Delays in contract/CBB true up/reconciliation can negatively effect measurement of project progress, limiting owner understanding of liability, and may result in increased contract disagreements and potential claims. The Department of Energy Oak Ridge Office of Environmental Management (OR-EM) and URS - CH2M Oak Ridge LLC (UCOR) achieved alignment of the NCC with the CBB within 10 months of UCOR taking over work on the East Tennessee Technology Park (ETTP) cleanup contract by: 1. Managing as a discrete project; 2. Establishing expectations and setting tone of interactions; 3. Using personnel experienced with Federal Acquisition Regulation (FAR); 4. Partnering; 5. Establishing ombudsmen. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2015

On the field‐aligned electric field in the polar cap

Abstract The Johns Hopkins University Applied Physics Laboratory open‐field line particle precipitation model predicts downward field‐aligned electric field to maintain charge quasi‐neutrality. Previous studies confirmed the existence of such electric fields. However, the present study shows that upward field‐aligned electric field can be found within upward field‐aligned current (FAC) region. In the upward FAC region, upward electric field that accelerates electron downward is seen with the occurrence rates of 82%–96%. In contrast, the occurrence rates in the downward FAC regions are 3%–11%. Polar rain electrons located in the upward FAC region adjacent to closed field lines often show a ramping up of energy with increasing latitude before reaching a plateau. This plateau may be attributed to the magnetosheath electrons that progressively have higher antisunward velocity and lower density with increasing distance from the subsolar point before they asymptotically reach the solar wind values.

Wing, Simon↗
DOE OSTI2022

Surface‐Enforced Alignment of Reprogrammable Liquid Crystalline Elastomers

Abstract Liquid crystalline elastomers (LCEs) are stimuli‐responsive materials capable of undergoing large deformations. The thermomechanical response of LCEs is attributable to the coupling of polymer network properties and disruption of order between liquid crystalline mesogens. Complex deformations have been realized in LCEs by either programming the nematic director via surface‐enforced alignment or localized mechanical deformation in materials incorporating dynamic covalent chemistries. Here, the preparation of LCEs via thiol‐Michael addition reaction is reported that are amenable to surface‐enforced alignment. Afforded by the thiol‐Michael addition reaction, dynamic covalent bonds are uniquely incorporated in chemistries subject to surface‐enforce alignment. Accordingly, LCEs prepared with complex director profiles are able to be programmed and reprogrammed by (re)activating the dynamic covalent chemistry to realize distinctive shape transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Room-Temperature Phototransistor with Negative Photoresponsivity of 10 8 A W -1 Using Fullerene-Sensitized Aligned Carbon Nanotubes

Detection of low intensity light down to a few photons requires photodetectors with high gain. In this paper, a new photodetector is reported based on C 60 -sensitized aligned carbon nanotube (CNT) transistors with an extremely high responsivity of 10 8 A W -1 (gain > 10 8 ) in the ultraviolet and visible range, and 720 A W -1 (gain = 940) in the infrared range. In contrast to most sensitized phototransistors that operate on the photogating effect, the new photodetector operates on the modulation of the electrons scattering in the CNTs, leading to negative photoconductivity. Comparison with similar photodetectors using random CNT networks shows the benefit of using aligned CNTs. Finally, at room temperature, the aligned CNT photodetectors are demonstrated to detect a few tens of photons per CNT.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Analytic analysis of load alignment for coning extreme‐scale rotors

Abstract Extreme‐scale wind turbines (rated powers greater than 10 MW) with large rotor diameters and conventional upwind designs must resist extreme downwind and gravity loads. This can lead to significant structural design challenges and high blade masses that can impede the reduction of levelized cost of wind energy. Herein, the theoretical basis for downwind load alignment is developed. This alignment can be addressed with active downwind coning to reduce/eliminate flapwise bending loads by balancing the transverse components of thrust, centrifugal, and gravitational force. Equations are developed herein that estimates the optimal coning angle that reduces flapwise loads by a specified amount. This analysis is then applied to a 13.2‐MW scale with 100‐m‐level wind turbine blades, where it is found that a load alignment coning schedule can substantially reduce the root flapwise bending moments. This moment reduction in this example can allow the rotor mass to be decreased significantly when compared with a conventional upwind three‐bladed rotor while maintaining structural performance and annual energy output.

Noyes, Carlos↗
DOE OSTI2017

High scale flavor alignment in two-Higgs doublet models and its phenomenology

The most general two-Higgs doublet model (2HDM) includes potentially large sources of flavor changing neutral currents (FCNCs) that must be suppressed in order to achieve a phenomenologically viable model. The flavor alignment ansatz postulates that all Yukawa coupling matrices are diagonal when expressed in the basis of mass-eigenstate fermion fields, in which case tree-level Higgs-mediated FCNCs are eliminated. In this work, we explore models with the flavor alignment condition imposed at a very high energy scale, which results in the generation of Higgs-mediated FCNCs via renormalization group running from the high energy scale to the electroweak scale. Using the current experimental bounds on flavor changing observables, constraints are derived on the aligned 2HDM parameter space. In the favored parameter region, we analyze the implications for Higgs boson phenomenology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Residual symmetries and scalar multiplet vacuum alignment in non-Abelian flavour models

We demonstrate that, upon minimizing a renormalizable, single-scalar potential invariant under a non-Abelian symmetry, special orientations in the associated vacuum alignment of the scalar multiplet correspond to the preservation of a discrete residual flavour symmetry in the broken phase of the theory. Conversely, we show that these special scalar alignments are perturbed when additional Lagrangian operators (e.g. renormalizable, multi-flavon operators and/or effective, higher-dimensional operators) are present that break said residual symmetry, leading to a vacuum reorientation and phenomenological consequences. We therefore construct a one-to-one correspondence principle between broken residual symmetries and vacuum alignment corrections, providing a mechanism to identify (and correct) a subtle but persistent form of phenomenologically relevant fine-tuning embedded in — but often ignored by — most successful non-Abelian flavour models. We first establish this correspondence in a set of toy models based on the S4 permutation symmetry, and then apply the lessons learned to the more realistic A4 Altarelli-Feruglio and ∆(27) Universal Texture Zero models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗