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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment

Abstract Background Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or computing alignments in the presence of sequence length heterogeneity. Although this is a natural problem, only a few tools have been developed to use this information with high fidelity. Results We present EMMA (Extending Multiple alignments using MAFFT--add) for the problem of adding a set of unaligned sequences into a multiple sequence alignment (i.e., a constraint alignment). EMMA builds on MAFFT--add, which is also designed to add sequences into a given constraint alignment. EMMA improves on MAFFT--add methods by using a divide-and-conquer framework to scale its most accurate version, MAFFT-linsi--add, to constraint alignments with many sequences. We show that EMMA has an accuracy advantage over other techniques for adding sequences into alignments under many realistic conditions and can scale to large datasets with high accuracy (hundreds of thousands of sequences). EMMA is available at https://github.com/c5shen/EMMA . Conclusions EMMA is a new tool that provides high accuracy and scalability for adding sequences into an existing alignment.

Shen, Chengze↗
NASA NTRS2003

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Non-NASA Center↗
NASA NTRS2011

Backup Alignment Devices on Shuttle: Heads-Up Display or Crew Optical Alignment Sight

NASA s Space Shuttle was built to withstand multiple failures while still keeping the crew and vehicle safe. Although the design of the Space Shuttle had a great deal of redundancy built into each system, there were often additional ways to keep systems in the best configuration if a failure were to occur. One such method was to use select pieces of hardware in a way for which they were not primarily intended. The primary function of the Heads-Up Display (HUD) was to provide the crew with a display of flight critical information during the entry phase. The primary function of the Crew Optical Alignment Sight (COAS) was to provide the crew an optical alignment capability for rendezvous and docking phases. An alignment device was required to keep the Inertial Measurement Units (IMUs) well aligned for a safe Entry; nominally this alignment device would be the two on-board Star Trackers. However, in the event of a Star Tracker failure, the HUD or COAS could also be used as a backup alignment device, but only if the device had been calibrated beforehand. Once the HUD or COAS was calibrated and verified then it was considered an adequate backup to the Star Trackers for entry IMU alignment. There were procedures in place and the astronauts were trained on how to accurately calibrate the HUD or COAS and how to use them as an alignment device. The calibration procedure for the HUD and COAS had been performed on many Shuttle missions. Many of the first calibrations performed were for data gathering purposes to determine which device was more accurate as a backup alignment device, HUD or COAS. Once this was determined, the following missions would frequently calibrate the HUD in order to be one step closer to having the device ready in case it was needed as a backup alignment device.

Chavez, Melissa A.↗
DOE OSTI2023

Pattern of global spin alignment of ϕ and K*0 mesons in heavy-ion collisions

The strong force, as one of the four fundamental forces at work in the universe, governs interactions of quarks and gluons, and binds together the atomic nucleus. Notwithstanding decades of progress since Yukawa first developed a description of the force between nucleons in terms of meson exchange 1 , a full understanding of the strong interaction remains a major challenge in modern science. One remaining difficulty arises from the non-perturbative nature of the strong force, which leads to the phenomenon of quark confinement at distance scales on the order of the size of the proton. Here we show that in relativistic heavy-ion collisions, where quarks and gluons are set free over an extended volume, two species of produced vector (spin-1) mesons, namely φ and K∗0 , emerge with a surprising pattern of global spin alignment. In particular, the global spin alignment for φ is unexpectedly large, while that for K∗0 is consistent with zero. The observed spin-alignment pattern and magnitude for the φ cannot be explained by conventional mechanisms, while a model with strong force fields2, 3 accommodates the current data. This is the first time that the strong force field is experimentally supported as a key mechanism that leads to global spin alignment. We extract a quantity proportional to the intensity of the field of the strong force. Within the framework of the Standard Model, where the strong force is typically described in the quark and gluon language of Quantum Chromodynamics, the field being considered here is an effective proxy description. This is a qualitatively new class of measurement, which opens a new avenue for studying the behaviour of strong force fields via their imprint on spin alignment.

Abdallah, M. S.↗
DOE OSTI2022

Genetic-algorithm retrieval of the molecular alignment distribution with high-order harmonics generated from transiently aligned CO 2 molecules

Using genetic algorithm, we propose a method to retrieve the alignment distribution of transiently aligned CO 2 molecules from the high-order harmonic generation (HHG) spectra. The retrieval method is based on the quantitative rescattering (QRS) model where averaged photorecombination transition dipole can be factored out from the parallel (or perpendicular) harmonic spectra after the propagation of the harmonic fields in the gas medium. We examine how the retrieved alignment distributions are affected by uncertainty in alignment dependent ionization probability and on multiple orbital contribution to the HHG. We further confirm that alignment distribution is more accurately retrieved by using the minima in the HHG spectra driven by a long-wavelength laser. In addition, we show that earlier experimental data on the ratios between the perpendicular and the parallel HHG components of aligned CO 2 molecules are in better agreement with the QRS model if the macroscopic propagation and multiple orbital interference are included in the theoretical calculation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Are You Philanthropy-Ready? How to Work with Foundations on Mission-Aligned Community Solar

Community solar is emerging as a popular way to deliver a range of economic and social benefits that go beyond clean energy. The US Department of Energy (DOE) has set a goal for America to deploy enough community solar projects to power the equivalent of five million households by 2025 and create $1 billion in energy bill savings. To reach the goal, DOE has created the Community Power Accelerator, as part of the National Community Solar Partnership (NCSP). The Accelerator is an online ecosystem bringing together developers, lenders, foundations, community organizations, and other stakeholders to support the deployment of mission-aligned community solar. The Accelerator is especially focused on projects that deliver "meaningful benefits" to customers and communities, including: access by low- to moderate-income households; greater bill savings; resilience and grid benefits; community ownership; and local workforce development. Many philanthropic organizations are looking at community solar as a way to capture these benefits in their grant-making and investment programs, while also reducing pollution and promoting environmental justice. To help community-based organizations (CBOs), non-profit organizations, and mission-aligned developers seeking philanthropic support, Berkeley Lab and the National Renewable Energy Lab prepared Are You Philanthropy-Ready? How to Work with Foundations on Mission-Aligned Community Solar. The guide provides an overview of how foundations work, gives tips on what they seek in a fundable project, and provides guidance on crafting effective proposals. In short, this guide aims to help the fund-seeker become philanthropy-ready.

14 SOLAR ENERGY↗
NASA NTRS2010

Pupil Alignment Measuring Technique and Alignment Reference for Instruments or Optical Systems

A technique was created to measure the pupil alignment of instruments in situ by measuring calibrated pupil alignment references (PARs) in instruments. The PAR can also be measured using an alignment telescope or an imaging system. PAR allows the verification of the science instrument (SI) pupil alignment at the integrated science instrument module (ISIM) level of assembly at ambient and cryogenic operating temperature. This will allow verification of the ISIM+SI alignment, and provide feedback to realign the SI if necessary.

Hagopian, John G.↗
NASA NTRS2010

Aligning for Innovation - Alignment Strategy to Drive Innovation

With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

Johnson, Hurel↗
DOE OSTI2020

Robust control of the minima of high-order harmonics by fine-tuning the alignment of CO 2 molecules for shaping attosecond pulses and probing molecular alignment

In a recent paper, we reported that the position and depth of the minima in the harmonic spectra of CO 2 molecules can be dramatically manipulated by a slight change of the degree of alignment, thus providing a convenient method of shaping attosecond pulses which could lead to the splitting of a typical single attosecond burst into two. Here, we demonstrate that harmonic minima can also be dramatically controlled by changing the pump-probe angles to shape attosecond pulses. In the meanwhile, since the pump-probe angle-dependent harmonic spectra are very sensitive to the degree of alignment, harmonic spectra can also be used to calibrate the alignment distribution of molecules. In this work we identify such robust control of harmonic generation is due to the optical property of CO 2 and the coherent harmonic emission from the oriented molecules. The photoionization transition dipoles (PITDs) of CO 2 exhibit deep minima that change rapidly with molecular orientations accompanied by large phase changes of π in PITDs, thus leading to strong interference when the dipoles are added up coherently.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Giant terahertz polarization rotation in ultrathin films of aligned carbon nanotubes

For easy manipulation of polarization states of light for applications in communications, imaging, and information processing, an efficient mechanism is desired for rotating light polarization with a minimum interaction length. Here, we report giant polarization rotations for terahertz (THz) electromagnetic waves in ultrathin ( ∼ <#comment/> 45 n m ), high-density films of aligned carbon nanotubes. We observed polarization rotations of up to ∼ <#comment/> 20 ∘ <#comment/> and ∼ <#comment/> 110 ∘ <#comment/> for transmitted and reflected THz pulses, respectively. The amount of polarization rotation was a sensitive function of the angle between the incident THz polarization and the nanotube alignment direction, exhibiting a “magic” angle at which the total rotation through transmission and reflection becomes exactly 90°. Our model quantitatively explains these giant rotations as a result of extremely anisotropic optical constants, demonstrating that aligned carbon nanotubes promise ultrathin, broadband, and tunable THz polarization devices.

Baydin, Andrey (ORCID:0000000225673506)↗
NASA NTRS2016

Silicon Alignment Pins: An Easy Way to Realize a Wafer-To-Wafer Alignment

A silicon alignment pin is used to align successive layers of components made in semiconductor chips and/or metallic components to make easier the assembly of devices having a layered structure. The pin is made as a compressible structure which can be squeezed to reduce its outer diameter, have one end fit into a corresponding alignment pocket or cavity defined in a layer of material to be assembled into a layered structure, and then allowed to expand to produce an interference fit with the cavity. The other end can then be inserted into a corresponding cavity defined in a surface of a second layer of material that mates with the first layer. The two layers are in registry when the pin is mated to both. Multiple layers can be assembled to create a multilayer structure. Examples of such devices are presented.

Jung-Kubiak, Cecile↗
NASA NTRS2013

Silicon Alignment Pins: An Easy Way to Realize a Wafer-to-Wafer Alignment

Submillimeter heterodyne instruments play a critical role in addressing fundamental questions regarding the evolution of galaxies as well as being a crucial tool in planetary science. To make these instruments compatible with small platforms, especially for the study of the outer planets, or to enable the development of multi-pixel arrays, it is essential to reduce the mass, power, and volume of the existing single-pixel heterodyne receivers. Silicon micromachining technology is naturally suited for making these submillimeter and terahertz components, where precision and accuracy are essential. Waveguide and channel cavities are etched in a silicon bulk material using deep reactive ion etching (DRIE) techniques. Power amplifiers, multiplier and mixer chips are then integrated and the silicon pieces are stacked together to form a supercompact receiver front end. By using silicon micromachined packages for these components, instrument mass can be reduced and higher levels of integration can be achieved. A method is needed to assemble accurately these silicon pieces together, and a technique was developed here using etched pockets and silicon pins to align two wafers together.

Jung-Kubiak, Cecile↗
DOE OSTI2022

Te/CdTe and Al/CdTe Interfacial Energy Band Alignment by Atomistic Modeling

A synergistic approach that incorporates first-principles atomistic modeling with numerical device simulations is used to systematically evaluate the role of heterointerfaces within metal-chalcogenide-based photovoltaic technologies. Two interfaces involving either a tellurium back contact or aluminum back electrode combined with a cadmium telluride absorber layer within cadmium-telluride-based thin-film solar cells are investigated on an atomic scale to determine the mechanisms contributing to variations in device performance. Electronic structures and predicted charge transport behavior with respect to cadmium and tellurium termination of the absorber layer are studied along the polar oriented CdTe{111} facets. The computational methodology reveals a noticeable contrast between the Schottky barrier forming Al/CdTe interface versus the Type I Te/CdTe heterojunction. Greater band bending features are exhibited by the cadmium termination as opposed to the tellurium termination for each interface case. Subsequent device modeling suggests that 3.6% higher photovoltaic conversion efficiency is achievable for the cadmium termination relative to the tellurium termination of the Te/CdTe interface. Based strictly on an idealistic representation, both interface models show the importance of atomic-scale interfacial properties for cadmium telluride solar cell device performance with their bulk properties being validated in comparison to published experimental data. Here, the synergistic approach offers a suitable method to analyze solar cell interfaces through a predictive computational framework for the engineering and optimization of metal-chalcogenide-based thin-film photovoltaic technologies.

Green’s function↗
DOE OSTI2023

Microstructure Alignment Effects from Engineered Cooling during Additive Manufacturing of Alnico Magnets from Prealloyed Powder

Alnico is a rare-earth free; permanent magnet (PM) which maintains its saturation magnetization while at temperatures up to 550°C but lacks the coercivity and energy product needed for a wide range of demanding applications. With an optimal set of processing and manufacturing techniques, Alnico could replace Dy-free Nd-Fe-B magnets in certain applications if the microstructure is textured in a $\langle$001$\rangle$ direction. Additive manufacturing (AM) of near-net-shape magnets may provide such texture. To investigate the possibility, directed-energy deposition (DED) in conjunction with an actively cooled substrate was used to build samples with a compositionally modified, gas-atomized, Alnico 8 alloy. The resulting samples were solutionized and quenched, followed by magnetic annealing and a heat treatment. Magnetic properties and microstructures are compared to previous work.

36 MATERIALS SCIENCE↗