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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

GenomePeek—an online tool for prokaryotic genome and metagenome analysis

As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Here, using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1976

Considerations to achieve directionality for gamma ray lasers

A method of alignment of nuclei for a gamma ray laser and a means of achieving preferential emission of radiation along the crystal axis are discussed. The proposed method of preferential emission of radiation along the aligned needles is to have a symmetric field gradient at the nucleus and a sequence of excited levels of spin and parity 2(+) and C(+). The proposed scheme reduces the density of excited states required for lasing and reduces the linewidth due to inhomogeneous broadening. Mossbauer absorption experiments intended to test these ideas are outlined.

Jha, S.↗
NASA NTRS1976

Considerations to achieve directionality for gamma ray lasers

A method of alignment of nuclei for a gamma ray laser and a means of achieving preferential emission of radiation along the crystal axis are studied. Atomic alignment was achieved by materials researchers who made composite structures composed of needle-like single crystals all with the same orientation and all pointing in the same direction contained in a matrix of cobalt or nickel. The proposed method of preferential emission of radiation along the aligned needles is to have a symmetric field gradient at the nucleus and a sequence of excited levels of spin and parity 2(+) and 0(+). The proposed scheme reduces the density of excited states required for lasing and reduces the linewidth due to inhomogenous broadening. Mossbauer absorption experiments intended to test these ideas are outlined.

Jha, S.↗
DOE OSTI2015

Charge Transport across DNA-Based Three-Way Junctions

DNA-based molecular electronics will require charges to be transported from one site within a 2D or 3D architecture to another. While this has been shown previously in linear, π-stacked DNA sequences, the dynamics and efficiency of charge transport across DNA three-way junction (3WJ) have yet to be determined. Here, we present an investigation of hole transport and trapping across a DNA-based three-way junction systems by a combination of femtosecond transient absorption spectroscopy and molecular dynamics simulations. Hole transport across the junction is proposed to be gated by conformational fluctuations in the ground state which bring the transiently populated hole carrier nucleobases into better aligned geometries on the nanosecond time scale, thus modulating the π–π electronic coupling along the base pair sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

FASTERp: A Feature Array Search Tool for Estimating Resemblance of Protein Sequences

Metagenome sequencing efforts have provided a large pool of billions of genes for identifying enzymes with desirable biochemical traits. However, homology search with billions of genes in a rapidly growing database has become increasingly computationally impractical. Here we present our pilot efforts to develop a novel alignment-free algorithm for homology search. Specifically, we represent individual proteins as feature vectors that denote the presence or absence of short kmers in the protein sequence. Similarity between feature vectors is then computed using the Tanimoto score, a distance metric that can be rapidly computed on bit string representations of feature vectors. Preliminary results indicate good correlation with optimal alignment algorithms (Spearman r of 0.87, ~;;1,000,000 proteins from Pfam), as well as with heuristic algorithms such as BLAST (Spearman r of 0.86, ~;;1,000,000 proteins). Furthermore, a prototype of FASTERp implemented in Python runs approximately four times faster than BLAST on a small scale dataset (~;;1000 proteins). We are optimizing and scaling to improve FASTERp to enable rapid homology searches against billion-protein databases, thereby enabling more comprehensive gene annotation efforts.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1974

Second heated jettison test on the Centaur standard shroud

The second in a planned series of heated jettison tests on the Centaur Standard Shroud was conducted on January 16, 1974. The first 250-second portion of the test sequence involved heating the shroud with a specially-built fixture designed to provide a simulation of the heating environment encountered by the shroud during its ascent through the earth's atmosphere. The two heater halves, which were mounted on a rail system, were then retracted. This was followed by the jettison of the two shroud halves into catch nets positioned at 90 deg to the heater rails. The condition which made this test unique compared to the others in the test series was the alignment of the maximum thermal line with the shroud separation plane. Information on the test hardware, configuration, and sequence is presented. Shroud thermal and deflection data encountered during the heating portion of the test sequence are compared with free-skin design temperatures in various graphical formats.

Source record↗
DOE OSTI2026

Governing in Time: Temporal Capacity and the Feasibility of Energy Transitions

Energy systems function as both technological systems and temporal institutions that shape how societies coordinate, justify, and support collective choices over time. This paper introduces the concept of governance horizons to explain why energy transitions can remain morally supported yet become institutionally weak under increasing pressure. We argue that governability depends on institutions' capacity to synchronize across multiple timeframes - aligning short-term decisions with intermediate coordination and long-term commitments. When this synchronization fails, transitions struggle not because their goals are dismissed, but because governance lacks sufficient time to justify, coordinate, and uphold decisions. Comparative analysis of San Antonio, Texas, and Interior Alaska reveals how energy system pressures generate distinct temporal configurations: San Antonio exhibits governance horizon stretching, where institutions must simultaneously meet near-term reliability demands and long-term transformation goals, while Interior Alaska exhibits horizon compression, where extreme environmental constraints force decision-making into short stabilization cycles. In both contexts, public support for sustainability goals coexists with institutional strain because evaluative judgments are unevenly distributed over time. A temporal configuration analysis is introduced as a diagnostic analytic stance for identifying these patterns. By treating temporal alignment as an explanatory variable rather than a background condition, this approach clarifies how feasibility, sequencing, and legitimacy are shaped by constraints on institutional time. The analysis demonstrates that successful energy transitions depend not only on technological innovation or institutional support, but on governance systems’ ability to sustain credible coordination across multiple time horizons.

Comparative case study↗
DOE OSTI2018

New science in plain sight: Citizen scientists lead to the discovery of optical structure in the upper atmosphere

A glowing ribbon of purple light running east-west in the night sky has recently been observed by citizen scientists. This narrow, subauroral, visible structure, distinct from the traditional auroral oval, was largely undocumented in the scientific literature and little was known about its formation. Amateur photo sequences showed colors distinctly different from common types of aurora and occasionally indicated magnetic field–aligned substructures. Observations from the Swarm satellite as it crossed the arc have revealed an unusual level of electron temperature enhancement and density depletion, along with a strong westward ion flow, indicating that a pronounced subauroral ion drift (SAID) is associated with this structure. These early results suggest the arc is an optical manifestation of SAID, presenting new opportunities for investigation of the dynamic SAID signatures from the ground. On the basis of the measured ion properties and original citizen science name, we propose to identify this arc as a Strong Thermal Emission Velocity Enhancement (STEVE).

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2018

Image Station Matching, Preprocessing, Spatial Registration and Change Detection with Multi-Temporal Remotely-Sensed Imagery

A method for collecting and processing remotely sensed imagery in order to achieve precise spatial co-registration (e.g., matched alignment) between multi-temporal image sets is presented. Such precise alignment or spatial co-registration of imagery can be used for change detection, image fusion, and temporal analysis/modeling. Further, images collected in this manner may be further processed in such a way that image frames or line arrays from corresponding photo stations are matched, co-aligned and if desired merged into a single image and/or subjected to the same processing sequence. A second methodology for automated detection of moving objects within a scene using a time series of remotely sensed imagery is also presented. Specialized image collection and preprocessing procedures are utilized to obtain precise spatial co-registration (image registration) between multitemporal image frame sets. In addition, specialized change detection techniques are employed in order to automate the detection of moving objects.

Coulter, Lloyd Lawrence Arthur↗
NASA NTRS2018

New Science in Plain Sight: Citizen Scientists Lead to the Discovery of Optical Structure in the Upper Atmosphere

A glowing ribbon of purple light running east-west in the night sky has recently been observed by citizen scientists. This narrow, subauroral, visible structure, distinct from the traditional auroral oval, was largely undocumented in the scientific literature and little was known about its formation. Amateur photo sequences showed colors distinctly different from common types of aurora and occasionally indicated magnetic field aligned substructures. Observations from the Swarm satellite as it crossed the arc have revealed an unusual level of electron temperature enhancement and density depletion, along with a strong westward ion flow, indicating that a pronounced subauroral ion drift (SAID) is associated with this structure. These early results suggest the arc is an optical manifestation of SAID, presenting new opportunities for investigation of the dynamic SAID signatures from the ground. On the basis of the measured ion properties and original citizen science name, we propose to identify this arc as a Strong Thermal Emission Velocity Enhancement (STEVE).

MacDonald, Elizabeth A.↗
DOE OSTI2014

Conformation-independent structural comparison of macromolecules with ProSMART

The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods. The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing pool of structural data into a more readily accessible form, potentially offering biological insight or influencing subsequent experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men

Prospective molecular studies of HIV-1 pol region (2253–5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017–2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790–8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Using Biomimetic Polymers in Place of Noncollagenous Proteins to Achieve Functional Remineralization of Dentin Tissues

In calcified tissues such as bones and teeth, mineralization is regulated by an extracellular matrix, which includes non-collagenous proteins (NCP). This natural process has been adapted or mimicked to restore tissues following physical damage or demineralization by using polyanionic acids in place of NCPs, but the remineralized tissues fail to fully recover their mechanical properties. Here we show that pre-treatment with certain amphiphilic peptoids, a class of peptide-like polymers consisting of N-substituted glycines that have defined monomer sequences, enhances ordering and mineralization of collagen and induces functional remineralization of dentin lesions in vitro. In the vicinity of dentin tubules, the newly formed apatite nano-crystals are co-aligned with the c-axis parallel to the tubular periphery and recovery of tissue ultrastructure is accompanied by development of high mechanical strength. The observed effects are highly sequence-dependent with alternating polar and non-polar groups leading to positive outcomes while diblock sequences have no effect. The observations suggest aromatic groups interact with the collagen while the hydrophilic side chains bind the mineralizing constituents and highlight the potential of synthetic sequence-defined biomimetic polymers to serve as NCP mimics in tissue remineralization.

Chien, Yung-Ching↗
DOE OSTI2018

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA

Background: The application of genomic data and bioinformatics for the identification of restricted or illegally-sourced natural products is urgently needed. The taxonomic identity and geographic provenance of raw and processed materials have implications in sustainable-use commercial practices, and relevance to the enforcement of laws that regulate or restrict illegally harvested materials, such as timber. Improvements in genomics make it possible to capture and sequence partial-to-complete genomes from challenging tissues, such as wood and wood products. Results: In this paper, we report the success of an alignment-free genome comparison method, d 2; that differentiates different geographic sources of white oak (Quercus) species with a high level of accuracy with very small amount of genomic data. The method is robust to sequencing errors, different sequencing laboratories and sequencing platforms. Conclusions: This method offers an approach based on genome-scale data, rather than panels of pre-selected markers for specific taxa. The method provides a generalizable platform for the identification and sourcing of materials using a unified next generation sequencing and analysis framework.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Line-space description of resonant four-wave mixing: Theory for isotropic molecular states

Based on the quantum Liouville formalism, a theory of the two-color, triply resonant four-wave mixing is developed for molecules with isotropically oriented angular momenta. The approach allows to strictly incorporate the relaxation matrices Γ{sup (r)} (r = 0, 1, 2) into the third-order susceptibility χ{sup (3)} whose expression acquires therewith the form of a scalar product in the line space. Thanks to this representation, isolation of all resonance terms from χ{sup (3)} becomes a routine task. Some of these terms correspond to the case when a molecule initially interacts with two pump photons of the same frequency. Such interactions give rise to the grating line-space vectors which have the same (zero) eigenfrequency. Due to this degeneracy, the latter are easily mixed by rotationally inelastic collisions which shows up in a state-resolved coherence transfer. The satellite signals induced thereby provide a great scope to study the state-to-state inelastic rates in situ by purely optical means. If the diagonal form of Γ is assumed, the satellites become forbidden and our results reduce to conventional expressions for the main resonances. Polarization configurations are designed for direct measurements of the population (r = 0), orientation (r = 1), and alignment (r = 2) contributions to χ{sup (3)}. Finally, depending on the photon-molecule interaction sequence, the resonance terms of χ{sup (3)} are shown to be differently affected by velocity averaging, the effect which conspicuously manifests itself when Doppler broadening becomes paramount.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Explaining System-Level Prognostics with Established Machine Learning Methods

System-level prognostics is crucial for ensuring reliability and enabling predictive maintenance in complex systems with interconnected components. This study presents a framework that integrates data-driven methods to predict the remaining useful life (RUL) of a subsystem under multiple and concurrent faults within a nuclear power plant system with explainable artificial intelligence (XAI). A nuclear power plant (NPP) operation was simulated to model the degradation behavior of NPP components, and four machine learning models—Gradient Boosting Regressor (GBR), Support Vector Regressor (SVR), Fully Connected Neural Network (FCNN), and Long Short-Term Memory (LSTM)—were evaluated for prognostics with a novel system RUL parameter. The LSTM model demonstrated potential superior repeatability, while SHAP (SHapley Additive exPlanations) for explainability provided consistent and trustworthy global explanations. In contrast, LIME (Local Interpretable Model-agnostic Explanations) offered localized interpretability but showed reduced stability for sequential data. Key findings include the interplay between component-level degradation and system-wide performance, with LSTM effectively capturing these dynamics through sequence-level predictions. The XAI techniques enhanced transparency by identifying critical features influencing model predictions and aligning with domain knowledge. Furthermore, this framework has significant implications for improving trust and understanding in predictive maintenance, particularly in safety-critical industries like nuclear energy.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

An integrated model-driven method for in-treatment upper airway motion tracking using cine MRI in head and neck radiation therapy

Purpose: For the first time, MRI-guided radiation therapy systems can acquire cine images to dynamically monitor in-treatment internal organ motion. However, the complex head and neck (H&N) structures and low-contrast/resolution of on-board cine MRI images make automatic motion tracking a very challenging task. In this study, the authors proposed an integrated model-driven method to automatically track the in-treatment motion of the H&N upper airway, a complex and highly deformable region wherein internal motion often occurs in an either voluntary or involuntary manner, from cine MRI images for the analysis of H&N motion patterns. Methods: Considering the complex H&N structures and ensuring automatic and robust upper airway motion tracking, the authors firstly built a set of linked statistical shapes (including face, face-jaw, and face-jaw-palate) using principal component analysis from clinically approved contours delineated on a set of training data. The linked statistical shapes integrate explicit landmarks and implicit shape representation. Then, a hierarchical model-fitting algorithm was developed to align the linked shapes on the first image frame of a to-be-tracked cine sequence and to localize the upper airway region. Finally, a multifeature level set contour propagation scheme was performed to identify the upper airway shape change, frame-by-frame, on the entire image sequence. The multifeature fitting energy, including the information of intensity variations, edge saliency, curve geometry, and temporal shape continuity, was minimized to capture the details of moving airway boundaries. Sagittal cine MR image sequences acquired from three H&N cancer patients were utilized to demonstrate the performance of the proposed motion tracking method. Results: The tracking accuracy was validated by comparing the results to the average of two manual delineations in 50 randomly selected cine image frames from each patient. The resulting average dice similarity coefficient (93.28% ± 1.46%) and margin error (0.49 ± 0.12 mm) showed good agreement between the automatic and manual results. The comparison with three other deformable model-based segmentation methods illustrated the superior shape tracking performance of the proposed method. Large interpatient variations of swallowing frequency, swallowing duration, and upper airway cross-sectional area were observed from the testing cine image sequences. Conclusions: The proposed motion tracking method can provide accurate upper airway motion tracking results, and enable automatic and quantitative identification and analysis of in-treatment H&N upper airway motion. By integrating explicit and implicit linked-shape representations within a hierarchical model-fitting process, the proposed tracking method can process complex H&N structures and low-contrast/resolution cine MRI images. Future research will focus on the improvement of method reliability, patient motion pattern analysis for providing more information on patient-specific prediction of structure displacements, and motion effects on dosimetry for better H&N motion management in radiation therapy.

60 APPLIED LIFE SCIENCES↗