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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Marker Exchange Mutagenesis of mxaF , Encoding the Large Subunit of the Mxa Methanol Dehydrogenase, in Methylosinus trichosporium OB3b

Here, methanotrophs have remarkable redundancy in multiple steps of the central pathway of methane oxidation to carbon dioxide. For example, it has been known for over 30 years that two forms of methane monooxygenase, responsible for oxidizing methane to methanol, exist in methanotrophs, i.e., soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO), and that expression of these two forms is controlled by the availability of copper. Specifically, sMMO expression occurs in the absence of copper, while pMMO expression increases with increasing copper concentrations. More recently, it was discovered that multiple forms of methanol dehydrogenase (MeDH), Mxa MeDH and Xox MeDH, also exist in methanotrophs and that the expression of these alternative forms is regulated by the availability of cerium. That is, expression of Xox MeDH increases in the presence of cerium, while Mxa MeDH expression decreases in the presence of cerium. As it had been earlier concluded that pMMO and Mxa MeDH form a supercomplex in which electrons from Mxa MeDH are back donated to pMMO to drive the initial oxidation of methane, we speculated that Mxa MeDH could be rendered inactive through marker-exchange mutagenesis but growth on methane could still be possible if cerium was added to increase the expression of Xox MeDH under sMMO-expressing conditions. Here we report that mxaF, encoding the large subunit of Mxa MeDH, could indeed be knocked out in Methylosinus trichosporium OB3b, yet growth on methane was still possible, so long as cerium was added. Interestingly, growth of this mutant occurred in both the presence and the absence of copper, suggesting that Xox MeDH can replace Mxa MeDH regardless of the form of MMO expressed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain

Structural characterization of infection- and vaccination-elicited antibodies in complex with antigen provides insight into the evolutionary arms race between the host and the pathogen and informs rational vaccine immunogen design. We isolated a germ line-encoded monoclonal antibody (mAb) from plasmablasts activated upon mRNA vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and determined its structure in complex with the spike glycoprotein by electron cryomicroscopy (cryo-EM). We show that the mAb engages a previously uncharacterized neutralizing epitope on the spike N-terminal domain (NTD). The high-resolution structure reveals details of the intermolecular interactions and shows that the mAb inserts its heavy complementarity-determining region 3 (HCDR3) loop into a hydrophobic NTD cavity previously shown to bind a heme metabolite, biliverdin. We demonstrate direct competition with biliverdin and that, because of the conserved nature of the epitope, the mAb maintains binding to viral variants B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta), and B.1.1.529 (omicron). Our study describes a novel conserved epitope on the NTD that is readily targeted by vaccine-induced antibody responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Quantum Key Distribution with Nonbinary Phase–Time Encoding That Admits an Exact Proof of Secrecy

A quantum key distribution (QKD) protocol with nonbinary encoding is proposed that admits an exact proof of secrecy. The protocol provides higher rate of key generation compared with the BB84 protocol and, moreover, has a simple experimental implementation without active elements on the receiver side, that does not require polarization matching at the output of the communication line.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Tencoder: tensor-product encoder-decoder architecture for predicting solutions of PDEs with variable boundary data

It is widely hoped that artificial intelligence will boost data-driven surrogate models in science and engineering. However, fundamental spatial aspects of AI surrogate models remain under-studied. We investigate the ability of neural-network surrogate models to predict solutions to PDEs under variable boundary values. We do not wish to retrain the model when the boundary values change but to make them inputs to the model and infer the solution of the PDE under those boundary conditions. Such a capability is essential to making AI-based surrogate models practically useful. While simple feedforward networks are used for one-dimensional (1D) Poisson equation, an encoder-decoder architecture with a tensor-product layer is developed for the two-dimensional Poisson equation posed on a rectangular domain. We show that it is indeed possible to infer solutions to PDEs from variable boundary data using neural networks in this relatively simple setting, and point to future directions.

Kashi, Aditya↗
DOE OSTI2023

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations

Publicly available collections of drug-like molecules have grown to comprise tens of billions of compounds due to advances in combinatorial chemistry. Traditional methods for identifying "hit" molecules from a large collection of potential drug-like candidates have relied on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have the major drawback that they require exceptional computing capabilities for even relatively small collections of molecules. Hyperdimensional Computing (HDC) is a recently-proposed learning paradigm that represents data with high-dimension binary vectors; this allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas. We consider existing HDC approaches for molecular property classification and introduce two novel encodings of a commonly-used molecular representation, the extended connectivity fingerprint (ECFP). We show that HDC-based inference methods are as much as 91 times more efficient than traditional machine learning methods, and achieve an acceleration of nearly nine orders of magnitude compared to molecular docking. Our results show that HDC accelerated methods retain competitive accuracy on a number of well-studied tasks such as molecular property predictions using the MoleculeNet dataset, and bind/no-bind activity classification using the DUD-E and LIT-PCBA datasets. Our work thus motivates further investigation into molecular representation learning to develop ultraefficient pre-screening tools.

Jones, William↗
DOE OSTI2025

Enhancing Short-Range Weather Forecasts through Temporal Variation Encoding: A Multiperiod Embedding Approach

Machine learning (ML) techniques have emerged as promising approaches to improve regional weather forecast accuracy and reliability through data-driven methods. We propose a novel ML-based weather forecasting model, the Multiperiod Embed Net (MPENet). A key distinguishing feature of MPENet is its explicit utilization of the inherent cyclic nature in weather dynamics, unlike the autoregressive strategies commonly used in other ML weather forecasting approaches. Critical cyclic structures are identified via Fourier analyses of dynamic time series. Cyclicity in the convolutional representation is achieved by transforming one-dimensional time series of meteorological variables into two-dimensional tensors based on identified periods. This approach enables the model to leverage intrinsic weather patterns, enhancing regional forecast performance. To demonstrate the effectiveness of MPENet, we conduct a comparative analysis with Nvidia’s FourCastNet. Both models are trained on High-Resolution Rapid Refresh (HRRR) data from 2015 to 2022, over a 192 km × 192 km region in Tennessee. The comparisons are performed locally at two specific locations known to have different weather dynamics due to orographic effects: Crossville, on the relatively flat Cumberland Plateau with fewer topographic airflow disruptions, and Oak Ridge, in the ridge-and-valley region, where airflow is heavily influenced by surrounding valleys and mountains. Our results indicate that FourCastNet achieves strong accuracy at very short lead times, while MPENet maintains competitive skill and shows advantages in capturing temporal evolution over longer periods. Cross-correlation analyses of MPENet and FourCastNet predictions with the HRRR data suggest that encoding critical cyclicity into the network architecture leads to improvements in the forecasting skill.

Artificial intelligence↗
DOE OSTI2014

Deletion of a gene cluster encoding pectin degrading enzymes in Caldicellulosiruptor bescii reveals an important role for pectin in plant biomass recalcitrance

A major obstacle, and perhaps the most important economic barrier to the effective use of plant biomass for the production of fuels, chemicals, and bioproducts, is our current lack of knowledge of how to efficiently and effectively deconstruct wall polymers for their subsequent use as feedstocks. Plants represent the most desired source of renewable energy and hydrocarbons because they fix CO 2 , making their use carbon neutral. Their biomass structure, however, is a barrier to deconstruction, and this is often referred to as recalcitrance. Members of the bacterial genus Caldicellulosiruptor have the ability to grow on unpretreated plant biomass and thus provide an assay for plant deconstruction and biomass recalcitrance. Using recently developed genetic tools for manipulation of these bacteria, a deletion of a gene cluster encoding enzymes for pectin degradation was constructed, and the resulting mutant was reduced in its ability to grow on both dicot and grass biomass, but not on soluble sugars. The plant biomass from three phylogenetically diverse plants, Arabidopsis (a herbaceous dicot), switchgrass (a monocot grass), and poplar (a woody dicot), was used in these analyses. These biomass types have cell walls that are significantly different from each other in both structure and composition. While pectin is a relatively minor component of the grass and woody dicot substrates, the reduced growth of the mutant on all three biomass types provides direct evidence that pectin plays an important role in biomass recalcitrance. Glycome profiling of the plant material remaining after growth of the mutant on Arabidopsis biomass compared to the wild-type revealed differences in the rhamnogalacturonan I, homogalacturonan, arabinogalactan, and xylan profiles. In contrast, only minor differences were observed in the glycome profiles of the switchgrass and poplar biomass. In conclusion, the combination of microbial digestion and plant biomass analysis provides a new and important platform to identify plant wall structures whose presence reduces the ability of microbes to deconstruct plant walls and to identify enzymes that specifically deconstruct those structures.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Encoding the complete electric field of an ultraviolet ultrashort laser pulse in a near-infrared nonlinear-optical signal

We introduce a variation on the cross-correlation frequency-resolved optical gating (XFROG) technique that uses a near-infrared (NIR) nonlinear-optical signal to characterize pulses in the ultraviolet (UV). Using a transient-grating XFROG beam geometry, we create a grating using two copies of the unknown UV pulse and diffract a NIR reference pulse from it. We show that, by varying the delay between the UV pulses creating the grating, the UV pulse intensity-and-phase information can be encoded into a NIR signal. We also implemented a modified generalized-projections phase-retrieval algorithm for retrieving the UV pulses from these spectrograms. We performed proof-of-principle measurements of chirped pulses and double pulses, all at 400 nm. This approach should be extendable deeper into the UV and potentially even into the extreme UV or x-ray range.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

Robust spatial memory maps encoded by networks with transient connections

The spiking activity of principal cells in mammalian hippocampus encodes an internalized neuronal representation of the ambient space-a cognitive map. Once learned, such a map enables the animal to navigate a given environment for a long period. However, the neuronal substrate that produces this map is transient: the synaptic connections in the hippocampus and in the downstream neuronal networks never cease to form and to deteriorate at a rapid rate. How can the brain maintain a robust, reliable representation of space using a network that constantly changes its architecture? We address this question using a computational framework that allows evaluating the effect produced by the decaying connections between simulated hippocampal neurons on the properties of the cognitive map. Using novel Algebraic Topology techniques, we demonstrate that emergence of stable cognitive maps produced by networks with transient architectures is a generic phenomenon. The model also points out that deterioration of the cognitive map caused by weakening or lost connections between neurons may be compensated by simulating the neuronal activity. Lastly, the model explicates the importance of the complementary learning systems for processing spatial information at different levels of spatiotemporal granularity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma . A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Two Origins for the Gene Encoding α-Isopropylmalate Synthase in Fungi

The biosynthesis of leucine is a biochemical pathway common to prokaryotes, plants and fungi, but absent from humans and animals. The pathway is a proposed target for antimicrobial therapy. Here we identified the leuA gene encoding a-isopropylmalate synthase in the zygomycete fungus Phycomyces blakesleeanus using a genetic mapping approach with crosses between wild type and leucine auxotrophic strains. To confirm the function of the gene, Phycomyces leuA was used to complement the auxotrophic phenotype exhibited by mutation of the leu3 + gene of the ascomycete fungus Schizosaccharomyces pombe. Phylogenetic analysis revealed that the leuA gene in Phycomyces, other zygomycetes, and the chytrids is more closely related to homologs in plants and photosynthetic bacteria than ascomycetes or basidiomycetes, and suggests that the Dikarya have acquired the gene more recently. The identification of leuA in Phycomyces adds to the growing body of evidence that some primary metabolic pathways or parts of them have arisen multiple times during the evolution of fungi, probably through horizontal gene transfer events.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding Klebsiella pneumoniae Strain

Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious disease challenge. These strains can accumulate many antibiotic resistance genes though horizontal transfer of genetic elements, those for b-lactamases being of particular concern. Some b-lactamases are active on a broad spectrum of b-lactams including the last-resort carbapenems. The gene for the broad-spectrum and carbapenem-active metallo-b-lactamase NDM-1 is rapidly spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146, the first U.S. isolate found to encode NDM-1, and describe its repertoire of antibiotic-resistance genes and mutations, including genes for eight b-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the evolution of this rich repertoire, the mobile elements of the genome were characterized, including four plasmids with varying degrees of conservation and mosaicism and eleven chromosomal genomic islands. One island was identified by a novel phylogenomic approach, that further indicated the cps-lps polysaccharide synthesis locus, where operon translocation and fusion was noted. Unique plasmid segments and mosaic junctions were identified. Plasmid-borne blaCTX-M-15 was transposed recently to the chromosome by ISEcp1. None of the eleven full copies of IS26, the most frequent IS element in the genome, had the expected 8-bp direct repeat of the integration target sequence, suggesting that each copy underwent homologous recombination subsequent to its last transposition event. Comparative analysis likewise indicates IS26 as a frequent recombinational junction between plasmid ancestors, and also indicates a resolvase site. In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected. In a second novel use, circular transposition intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY family, suggesting that it uses the two-step transposition mechanism of IS3. Robust genome-based phylogeny showed that a unified Klebsiella cluster contains Enterobacter aerogenes and Raoultella, suggesting the latter genus should be abandoned.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans

Viral glycoproteins are a primary target for host antibody responses. However, glycans on viral glycoproteins can hinder antibody recognition since they are self glycans derived from the host biosynthesis pathway. During natural HIV-1 infection, neutralizing antibodies are made against glycans on HIV-1 envelope glycoprotein (Env). However, such antibodies are rarely elicited with vaccination. Previously, the vaccine-induced, macaque antibody DH501 was isolated and shown to bind to high mannose glycans on HIV-1 Env. Understanding how DH501 underwent affinity maturation to recognize glycans could inform vaccine induction of HIV-1 glycan antibodies. Here, we show that DH501 Env glycan reactivity is mediated by both germline-encoded residues that contact glycans, and somatic mutations that increase antibody paratope flexibility. Only somatic mutations in the heavy chain were required for glycan reactivity. The paratope conformation was fragile as single mutations within the immunoglobulin fold or complementarity determining regions were sufficient for eliminating antibody function. Taken together, the initial germline V H DJ H rearrangement generated contact residues capable of binding glycans, and somatic mutations were required to form a flexible paratope with a cavity conducive to HIV-1 envelope glycan binding. The requirement for the presence of most somatic mutations across the heavy chain variable region provides one explanation for the difficulty in inducing anti-Env glycan antibodies with HIV-1 Env vaccination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Tau and β-Amyloid Are Associated with Medial Temporal Lobe Structure, Function, and Memory Encoding in Normal Aging

Normal aging is associated with a decline in episodic memory and also with aggregation of the β-amyloid (Aβ) and tau proteins and atrophy of medial temporal lobe (MTL) structures crucial to memory formation. Although some evidence suggests that Aβ is associated with aberrant neural activity, the relationships among these two aggregated proteins, neural function, and brain structure are poorly understood. Using in vivo human Aβ and tau imaging, we demonstrate that increased Aβ and tau are both associated with aberrant fMRI activity in the MTL during memory encoding in cognitively normal older adults. This pathological neural activity was in turn associated with worse memory performance and atrophy within the MTL. A mediation analysis revealed that the relationship with regional atrophy was explained by MTL tau. These findings broaden the concept of cognitive aging to include evidence of Alzheimer’s disease-related protein aggregation as an underlying mechanism of age-related memory impairment.

amyloid↗
DOE OSTI2022

Deep Set Auto Encoders for Anomaly Detection in Particle Physics

There is an increased interest in model agnostic search strategies for physics beyond the standard model at the Large Hadron Collider. We introduce a Deep Set Variational Autoencoder and present results on the Dark Machines Anomaly Score Challenge. We find that the method attains the best anomaly detection ability when there is no decoding step for the network, and the anomaly score is based solely on the representation within the encoded latent space. This method was one of the top-performing models in the Dark Machines Challenge, both for the open data sets as well as the blinded data sets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Time Encoded Radiation Imaging

Passive detection of special nuclear material (SNM) at long range or under heavy shielding can only be achieved by observing the penetrating neutral particles that it emits: gamma rays and neutrons in the MeV energy range. The ultimate SNM standoff detector system would have sensitivity to both gamma and neutron radiation, a large area and high efficiency to capture as many signal particles as possible, and good discrimination against background particles via directional and energy information. Designing such a system is a daunting task. Using timemodulated collimators could be a transformative technique leading to practical gamma-neutron imaging detector systems that are highly efficient with the potential to exhibit simultaneously high angular and energy resolution. A new technique using time encoding to make a compact, high efficiency imaging detector was conceived. Design considerations using Monte Carlo modeling and the construction and demonstration of a prototype imager are described.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Results from field tests of the one-dimensional Time-Encoded Imaging System.

A series of field experiments were undertaken to evaluate the performance of the one dimensional time encoded imaging system. The significant detection of a Cf252 fission radiation source was demonstrated at a stand-off of 100 meters. Extrapolations to different quantities of plutonium equivalent at different distances are made. Hardware modifications to the system for follow on work are suggested.

Marleau, Peter↗
DOE OSTI2014

Time-Encoded Imagers

This report provides a short overview of the DNN R&D funded project, Time-Encoded Imagers. The project began in FY11 and concluded in FY14. The Project Description below provides the overall motivation and objectives for the project as well as a summary of programmatic direction. It is followed by a short description of each task and the resulting deliverables.

Marleau, Peter↗