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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Noise and drift analysis of non-equally spaced timing data

Generally, it is possible to obtain equally spaced timing data from oscillators. The measurement of the drifts and noises affecting oscillators is then performed by using a variance (Allan variance, modified Allan variance, or time variance) or a system of several variances (multivariance method). However, in some cases, several samples, or even several sets of samples, are missing. In the case of millisecond pulsar timing data, for instance, observations are quite irregularly spaced in time. Nevertheless, since some observations are very close together (one minute) and since the timing data sequence is very long (more than ten years), information on both short-term and long-term stability is available. Unfortunately, a direct variance analysis is not possible without interpolating missing data. Different interpolation algorithms (linear interpolation, cubic spline) are used to calculate variances in order to verify that they neither lose information nor add erroneous information. A comparison of the results of the different algorithms is given. Finally, the multivariance method was adapted to the measurement sequence of the millisecond pulsar timing data: the responses of each variance of the system are calculated for each type of noise and drift, with the same missing samples as in the pulsar timing sequence. An estimation of precision, dynamics, and separability of this method is given.

Vernotte, F.↗
NASA NTRS1988

Time evolution of surface chlorophyll patterns from cross-spectrum analysis of satellite color images

The rate of decorrelation of surface chlorophyll patterns as a function of the time separation between pairs of images was determined from two sequences of CZCS images of the Pacific Ocean area adjacent to Vancouver Island, Canada; cloud-free subareas were selected that were common to several images separated in time by 1-17 days. Image pairs were subjected to two-dimensional autospectrum and cross-spectrum analysis in an array processor, and squared coherence estimates found for several wave bands were plotted against time separation, in analogy with a time-lagged cross correlation function. It was found that, for wavelengths of 50-150 km, significant coherence was lost after 7-10 days, while for wavelengths of 25-50 km, significant coherence was lost after only 5-7 days. In both cases, offshore regions maintained coherence longer than coastal regions.

Denman, Kenneth L.↗
NASA NTRS1976

Interpretation of broad-band polarimetry of solar coronal transients - Importance of H-alpha emission

An eruptive prominence and coronal transient was observed in H-alpha, He II 304-A, and coronal white light (3700-7000 A). This event was generically similar to many other coronal transients associated with eruptive prominences in that loops of material propagated outward through the corona. It differed in that some of the prominence material was observed above 1.75 solar radii in both coronal white light and He II. Polarization analysis of the white-light data shows that the observed radiance from the loop-like transient was entirely due to free electron or Thomson scattering, whereas the white-light radiance from the prominence material was dominated by H-alpha emission. By comparing the white-light observations with model calculations, the densities along the loop and limits on the temperature and density of the prominence are obtained. Material observed in both white light and He II is shown to be cool prominence material, whereas analysis indicates that the transient-loop material is hot and coronal in origin. The time sequence of observations leads to the hypothesis that the prominence material is heated as it is ejected from the sun.

Poland, A. I.↗
NASA NTRS1991

Parallel computation of manipulator inverse dynamics

In this article, parallel computation of manipulator inverse dynamics is investigated. A hierarchical graph-based mapping approach is devised to analyze the inherent parallelism in the Newton-Euler formulation at several computational levels, and to derive the features of an abstract architecture for exploitation of parallelism. At each level, a parallel algorithm represents the application of a parallel model of computation that transforms the computation into a graph whose structure defines the features of an abstract architecture, i.e., number of processors, communication structure, etc. Data-flow analysis is employed to derive the time lower bound in the computation as well as the sequencing of the abstract architecture. The features of the target architecture are defined by optimization of the abstract architecture to exploit maximum parallelism while minimizing architectural complexity. An architecture is designed and implemented that is capable of efficient exploitation of parallelism at several computational levels. The computation time of the Newton-Euler formulation for a 6-degree-of-freedom (dof) general manipulator is measured as 187 microsec. The increase in computation time for each additional dof is 23 microsec, which leads to a computation time of less than 500 microsec, even for a 12-dof redundant arm.

Fijany, Amir↗
NASA NTRS2016

Crash Testing and Simulation of a Cessna 172 Aircraft: Pitch Down Impact Onto Soft Soil

During the summer of 2015, NASA Langley Research Center conducted three full-scale crash tests of Cessna 172 (C-172) aircraft at the NASA Langley Landing and Impact Research (LandIR) Facility. The first test represented a flare-to-stall emergency or hard landing onto a rigid surface. The second test, which is the focus of this paper, represented a controlled-flight-into-terrain (CFIT) with a nose-down pitch attitude of the aircraft, which impacted onto soft soil. The third test, also conducted onto soil, represented a CFIT with a nose-up pitch attitude of the aircraft, which resulted in a tail strike condition. These three crash tests were performed for the purpose of evaluating the performance of Emergency Locator Transmitters (ELTs) and to generate impact test data for model validation. LS-DYNA finite element models were generated to simulate the three test conditions. This paper describes the model development and presents test-analysis comparisons of acceleration and velocity time-histories, as well as a comparison of the time sequence of events for Test 2 onto soft soil.

Fasanella, Edwin L.↗
NASA NTRSDate not supplied

Method Development for In Situ Microbiome Profiling of the Water Recovery System’s Wastewater Tank Onboard the International Space Station

A distinctive microbial community has inhabited the wastewater tank within the International Space Station Water Recovery System (WRS) for over 14 years and experienced the stressors associated with the microgravity environment. The WRS generates potable water for the crew from urine distillate, humidity condensate, Sabatier product water, and the occasional off-loading of ground-supplied water. The reservoir for these products, the wastewater tank, does not have a means of microbial control. While samples are occasionally collected for analysis, the time between sample collection and the return to Earth, as well as the lack of preservation, results in a skewed depiction of the microbiome. Routinely observed from these returned samples are high counts (105 – 106 colony forming units per mL) and two prevailing genera, Burkholderia and Ralstonia. The wastewater tank likely contains a more diverse microbiome, as a higher diversity of bacteria and fungus has been noted upstream and downstream of the tank. To characterize the microbial profile of the tank, analysis needs to occur at the time of sample collection. Toward this goal, a method for in situ analysis based on nanopore sequencing was developed. The filter-to-sequencer method evolved from previous work that has been validated onboard the ISS (BEST payload and the BioMole Crew Health Care Systems Facility). The method, including filtration, DNA extraction, purification, amplification, library preparation, and nanopore sequencing will be described. Additionally, data collected with this method from both ISS and terrestrial samples will be detailed. The consumables needed to support in situ analysis of the tank are set to the launch to the ISS in the spring of 2023. This investigation will allow for the first accurate characterization of the microbiome of the tank providing insight for crew health, planetary protection, and has the potential to enable engineering controls for future space station water systems.

Sarah Stahl-Rommel↗
DOE OSTI2024

A General Materials Data Science Framework for Quantitative 2D Analysis of Particle Growth from Image Sequences

Abstract Phase transformations are a challenging problem in materials science, which lead to changes in properties and may impact performance of material systems in various applications. We introduce a general framework for the analysis of particle growth kinetics by utilizing concepts from machine learning and graph theory. As a model system, we use image sequences of atomic force microscopy showing the crystallization of an amorphous fluoroelastomer film. To identify crystalline particles in an amorphous matrix and track the temporal evolution of the particle dispersion, we have developed quantitative methods of 2D analysis. 700 image sequences were analyzed using a neural network architecture, achieving 0.97 pixel-wise classification accuracy as a measure of the correctly classified pixels. The growth kinetics of isolated and impinged particles were tracked throughout time using these image sequences. The relationship between image sequences and spatiotemporal graph representations was explored to identify the proximity of crystallites from each other. The framework enables the analysis of all image sequences without the requirement of sampling for specific particles or timesteps for various materials systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The emergence and transmission dynamics of HIV-1 CRF07_BC in Mainland China

A total of 1155 partial pol gene sequences of human immunodeficiency virus (HIV)-1 CRF07_BC were sampled between 1997 and 2015, spanning 13 provinces in Mainland China and risk groups [heterosexual, injecting drug users (IDU), and men who have sex with men (MSM)] to investigate the evolution, adaptation, spatiotemporal and risk group dynamics, migration patterns, and protein structure of HIV-1 CRF07_BC. Due to the unequal distribution of sequences across time, location, and risk group in the complete dataset (‘full1155’), subsampling methods were used. Maximum-likelihood and Bayesian phylogenetic analysis as well as discrete trait analysis of geographical location and risk group were carried out. To study mutations of a cluster of HIV-1 CRF07_BC (CRF07-1), we performed a comparative analysis of this cluster to the other CRF07_BC sequences (‘backbone_295’) and mapped the mutations observed in the respective protein structure. Our findings showed that HIV-1 CRF07_BC most likely originated among IDU in Yunnan Province between October 1992 to July 1993 [95 per cent hightest posterior density (HPD): May 1989–August 1995] and that IDU in Yunnan Province and MSM in Guangdong Province likely served as the viral sources during the early and more recent spread in Mainland China. We also revealed that HIV-1 CRF07-1 has been spreading for roughly 20 years and continues to cause local transmission in Mainland China and worldwide. Overall, our study sheds light on the dynamics of HIV-1 CRF07_BC distribution patterns in Mainland China. Our research may also be useful in formulating public health policies aimed at controlling acquired immune deficiency syndrome in Mainland China and globally.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2018

Columbus IFHX Ammonia Leak Analysis

After the Columbus Moderate Temperature Loop (MTL) InterFace Heat eXchanger (IFHX) low temperature event of GMT 345-2013, NASA investigated relevant transient scenarios involving IFHX rupture after water freezing and subsequent thawing. NASA recommended development of a Fault Detection Isolation and Recovery (FDIR) plan that would, in the event of a heat exchanger freeze event, close the Water On/Off Valves (WOOVs) to isolate the heat exchanger and prevent ammonia from the external flow loops from spreading into the cabin. NASA performed a preliminary simplified analysis for the reference case of IFHX rupture, but for a deeper understanding TAS developed detailed SINDA-FLUINT models of the Columbus ITCS that were built and run through the SINAPS GUI. This allowed simulation of the ammonia leakage physics including the variation of environmental parameters, thus providing more accurate and specific input to the FDIR under development. The result was finalization of the IFHX WOOVs closure sequence and wait times to contain the ammonia propagation to Columbus and allow identification of the leaking IFHX. In addition, the analysis results provided reference pressure profiles to be used on console and by the Engineering as support for the telemetry data assessment in case of failure.This paper gives an overview on the issue and focuses on the analytical aspects of the multiphase fluid dynamics involved.

Tilloca, A.↗
DOE OSTI2022

pnnl/memgaze

MemGaze is a memory analysis toolset that combines high-resolution trace analysis and low overhead measurement, both with respect to time and space. It provides high-resolution by collecting world-level memory access traces, where the highest resolution supported is back-to-back sequences. It achieves low-overhead in space and time by leveraging sampling and various methods of hardware support for collecting traces. Its post-mortem trace processing provides multiresolution analysis for locations vs. operations; accesses vs. spatio-temporal reuse, and reuse (distance, rate, volume) vs. access patterns.

Central, PNNL Developer↗
DOE OSTI2025

Sequencing and analysis of 131 SARS-CoV-2 isolates in previously sampled and unsampled regions of Jordan from 2020 to 2023

The Hashemite Kingdom of Jordan remains an understudied country for next generation sequencing analysis of SARS-CoV-2 genomes collected during the 2019 pandemic. Here we provide 131 additional reference genomes collected between 2020–2023 from SARS-CoV-2-positive patients across Jordan. Phylogenetic analysis supports existing pandemic narratives of changing clade dominance over time and adds genomes in novel Jordanian locations and timepoints to make Jordan SARS-CoV-2 databases more comprehensive. Samples from the less-sequenced cities of Ajloun, Jaresh, Karak, and Madaba identified previously unreported lineages while Amman, Irbid, and Zarqa have existing sequencing efforts bolstered. Despite many incomplete patient records and a relatively small sample size, we observe interesting symptom patterns that support existing global and Jordanian pandemic narratives. We note how in-country COVID-19 pandemic genomic studies showcase Jordan’s efforts to expand next generation sequencing capabilities, especially through the leveraging of EDGE COVID-19, a bioinformatics platform for performing rapid, batched analysis of SARS-CoV-2 sequencing that streamlines sample processing prepared from a network of hospital locations.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2014

Preliminary Analysis of Aircraft Loss of Control Accidents: Worst Case Precursor Combinations and Temporal Sequencing

Aircraft loss of control (LOC) is a leading cause of fatal accidents across all transport airplane and operational classes, and can result from a wide spectrum of hazards, often occurring in combination. Technologies developed for LOC prevention and recovery must therefore be effective under a wide variety of conditions and uncertainties, including multiple hazards, and their validation must provide a means of assessing system effectiveness and coverage of these hazards. This requires the definition of a comprehensive set of LOC test scenarios based on accident and incident data as well as future risks. This paper defines a comprehensive set of accidents and incidents over a recent 15 year period, and presents preliminary analysis results to identify worst-case combinations of causal and contributing factors (i.e., accident precursors) and how they sequence in time. Such analyses can provide insight in developing effective solutions for LOC, and form the basis for developing test scenarios that can be used in evaluating them. Preliminary findings based on the results of this paper indicate that system failures or malfunctions, crew actions or inactions, vehicle impairment conditions, and vehicle upsets contributed the most to accidents and fatalities, followed by inclement weather or atmospheric disturbances and poor visibility. Follow-on research will include finalizing the analysis through a team consensus process, defining future risks, and developing a comprehensive set of test scenarios with correlation to the accidents, incidents, and future risks. Since enhanced engineering simulations are required for batch and piloted evaluations under realistic LOC precursor conditions, these test scenarios can also serve as a high-level requirement for defining the engineering simulation enhancements needed for generating them.

Belcastro, Christine M.↗
DOE OSTI2025

Differentiable hybrid neural network approach for enhancing reactor dynamics simulations

Reactor dynamics simulations provide essential insights into the time-dependent behavior of nuclear reactors under various operating conditions. However, high-fidelity simulations can be computationally intensive, requiring significant computational resources. Here, to address this challenge, this study employs a differentiable hybrid model that utilizes neural networks as a corrector to enhance the performance of a low-fidelity simulation, aligning its predictions with those of a high-fidelity simulation. Low-fidelity and high-fidelity simulations were obtained by adjusting the mesh size in the System Dynamics Analysis Tool. The differentiable hybrid model was trained in two approaches: time-step-wise and sequence-wise. It was then applied to simulate various transients in a molten salt reactor. Its performance was evaluated by comparing its responses to transients against those of the high-fidelity simulation. An additional approach was performed using a data-driven model to correct the low-fidelity simulation. In comparison, the differentiable hybrid model showed significant improvements in transient prediction, effectively addressing the limitations of the low-fidelity simulations. The results highlighted the robustness of the differentiable hybrid model in both training approaches. It delivered simulations that were at least 3.8 times faster than high-fidelity models. In the time-step-wise approach, it achieved at least a 39% improvement in accuracy. In the sequence-wise approach, it showed at least an 81% accuracy improvement over the full transient. This approach offers a promising path for improving computational efficiency without compromising accuracy in nuclear reactor simulations, making it suitable for real-time digital twin applications.

42 - ENGINEERING↗
NASA NTRS1980

Solar cells and modules from dentritic web silicon

Some of the noteworthy features of the processes developed in the fabrication of solar cell modules are the handling of long lengths of web, the use of cost effective dip coating of photoresist and antireflection coatings, selective electroplating of the grid pattern and ultrasonic bonding of the cell interconnect. Data on the cells is obtained by means of dark I-V analysis and deep level transient spectroscopy. A histogram of over 100 dentritic web solar cells fabricated in a number of runs using different web crystals shows an average efficiency of over 13%, with some efficiencies running above 15%. Lower cell efficiency is generally associated with low minority carrier time due to recombination centers sometimes present in the bulk silicon. A cost analysis of the process sequence using a 25 MW production line indicates a selling price of $0.75/peak watt in 1986. It is concluded that the efficiency of dentritic web cells approaches that of float zone silicon cells, reduced somewhat by the lower bulk lifetime of the former.

Campbell, R. B.↗
NASA NTRS1990

Integrated Communication and Control Systems. III - Nonidentical sensor and controller sampling

Networking in Integrated Communication and Control Systems (ICCS) introduces randomly varying delays which degrade the system dynamic performance and are a source of potential instability. In Part I of this sequence of papers, a discrete-time, finite-dimensional model of the delayed control system for analysis and design of ICCS was developed where the sensor and controller have identical sampling rates. In Part II, two alternate approaches for ICCS design, namely, identical and nonidentical sampling rates for sensor and controller were proposed. This Part III presents extended modeling of ICCS for nonidentical sensor and controller sampling rates. This model is also suitable for analyzing tracking problems, i.e., control systems with time-dependent reference inputs.

Liou, Luen-Woei↗
NASA NTRS1993

Well-resolved observations by ISEE 2 of ion dispersion in the magnetospheric cusp

During a prolonged period of southward IMF on October 30, 1978, the ISEE 2 spacecraft observed an unusually prolonged and distinct region of ion energy-time dispersion in the dayside dawn magnetosphere. Observed plasma features included the (1) presence of magnetosheath electrons and initial absence of magnetosheath ions and (2) subsequent arrival and energy-time dispersion of magnetosheath ions as the spacecraft transited outbound from 6.03 to 7.66 Earth radii. We use ISEE 2 ion measurements to illustrate these dispersive time-of-flight effects and to support our interpretation of a location in the north magnetospheric cusp. Ion energy dispersion persists for about 35 min and includes well-resolved sequences of magnetosheath and magnetospheric ion distributions. We focus primarily on observations and time-of-flight analysis of ions from the magnetosheath, which are observed simultaneously entering and exiting the cusp at different energies. We discuss the observational support and shortcomings of various ion injection locations and durations and conclude that quasi-steady merging at the dayside magnetopause, with ion dispersion caused by spacecraft motion away from the last closed field line, is the most likely scenario.

Phillips, J. L.↗