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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 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Orthogonal spatial coding with stimulated parametric down-conversion

Orthogonal optical coding is widely used in classical multi-user communication networks. Using the phase conjugation property of stimulated parametric down-conversion, we extend the current time-domain orthogonal optical coding scheme to the spatial domain to encode and decode image information. In this process, the idler beam inherits the complex conjugate of the field information encoded in the seed beam. An encoding phase mask introduced onto the input seed beam blurs the image transferred to the idler. The original image is restored by passing the coded transferred image through a corrective phase mask placed in the momentum space of the idler beam. We expect that this scheme can also inspire new techniques in secure image transmission, aberration cancellation, and frequency conversion imaging.

Xu, Yang↗
DOE OSTI2021

Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii

Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4 . The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas , land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery

Arboviruses are a diverse group of insect-transmitted pathogens that pose global public health challenges. Identifying evolutionarily conserved host factors that combat arbovirus replication in disparate eukaryotic hosts is important as they may tip the balance between productive and abortive viral replication, and thus determine virus host range. Here, we exploit naturally abortive arbovirus infections that we identified in lepidopteran cells and use bacterial effector proteins to uncover host factors restricting arbovirus replication. Bacterial effectors are proteins secreted by pathogenic bacteria into eukaryotic hosts cells that can inhibit antimicrobial defenses. Since bacteria and viruses can encounter common host defenses, we hypothesized that some bacterial effectors may inhibit host factors that restrict arbovirus replication in lepidopteran cells. Thus, we used bacterial effectors as molecular tools to identify host factors that restrict four distinct arboviruses in lepidopteran cells. By screening 210 effectors encoded by seven different bacterial pathogens, we identify several effectors that individually rescue the replication of all four arboviruses. We show that these effectors encode diverse enzymatic activities that are required to break arbovirus restriction. We further characterize Shigella flexneri-encoded IpaH4 as an E3 ubiquitin ligase that directly ubiquitinates two evolutionarily conserved proteins, SHOC2 and PSMC1, promoting their degradation in insect and human cells. We show that depletion of either SHOC2 or PSMC1 in insect or human cells promotes arbovirus replication, indicating that these are ancient virus restriction factors conserved across invertebrate and vertebrate hosts. Collectively, our study reveals a novel pathogen-guided approach to identify conserved antimicrobial machinery, new effector functions, and conserved roles for SHOC2 and PSMC1 in virus restriction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fungal community and functional responses to soil warming are greater than for soil nitrogen enrichment

Soil fungi are key regulators of forest carbon cycling and their responses to global change have effects that ripple throughout ecosystems. Global changes are expected to push many fungi beyond their environmental niches, but there are relatively few studies involving multiple, simultaneous global change factors. Here, we studied soil fungal diversity, community composition, co-occurrence patterns, and decomposition gene responses to 10 years of soil warming and nitrogen addition, alone and in combination. We specifically examined whether there were fungal community characteristics that could explain changes in soil carbon storage and organic matter chemistry in chronically warmed and fertilized soil. We found that fungal communities in warmed soils are less diverse and shift in composition. Warming also favored hyperdominance by a few mycorrhizal fungal species and lowered manganese peroxidase but increased hydrolytic enzyme encoding gene potentials. Nitrogen addition did not significantly affect fungal community composition but, like warming, did reduce fungal diversity and favored overdominance by a unique set of mycorrhizal taxa. Warming alone and in combination with nitrogen addition also reduced negative but increased positive fungal co-occurrence probabilities, promoting species coexistence. Negative fungal co-occurrence was positively correlated to soil carbon content, while the proportion of fungal hydrolytic enzyme encoding genes was negatively correlated with soil carbon content. This may reflect fungal life history trade-offs between competition (e.g., reduced negative co-occurrence) and resource acquisition (e.g., higher abundance of hydrolytic enzyme encoding genes) with implications for carbon storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

XMark: Reliable Multi-Bit Watermarking for LLM-Generated Texts

Multi-bit watermarking has emerged as a promising solution for embedding imperceptible binary messages into Large Language Model (LLM)-generated text, enabling reliable attribution and tracing of malicious usage of LLMs. Despite recent progress, existing methods still face key limitations: some become computationally infeasible for large messages, while others suffer from a poor trade-off between text quality and decoding accuracy. Moreover, the decoding accuracy of existing methods drops significantly when the number of tokens in the generated text is limited, a condition that frequently arises in practical usage. To address these challenges, we propose XMark, a novel method for encoding and decoding binary messages in LLM-generated texts. The unique design of XMark’s encoder produces a less distorted logit distribution for watermarked token generation, preserving text quality, and also enables its tailored decoder to reliably recover the encoded message with limited tokens. Extensive experiments across diverse downstream tasks show that XMark significantly improves decoding accuracy while preserving the quality of watermarked text, outperforming prior methods. The code will be made publicly available upon acceptance.

Xu, Jiahao [University of Nevada, Reno]↗
DOE OSTI2023

Moore Machine Motion Controls Refurbishment Statement of Work and Specification

Diamond Turning Machines known as “Moore” machines are used in the production of Potassium diHydrogen Phosphate (KDP) optics required for the National Ignition Facility (NIF). These machines are owned by the Department of Energy, as provided by Lawrence Livermore National Security LLC (LLNS). Moore Machines 1 and 2 are located at the Gooch & Housego (G&H) facility in Highland Heights, OH. The existing Aerotech motion controllers, motor drivers/amplifiers, input/output (I/O) hardware, control computer, software user interface, human machine interface (HMI), cabling, and encoders are beyond service life and require replacement. This Statement of Work (SoW) defines the motion control system refurbishment requirements for the Moore diamond turning machines designated Moore 1 and Moore 2. The motion controls system design shall include a motion control computer, control software, motor drive amplifiers and controllers, linear scale encoders, rotary encoders, HMI, power distribution, emergency stop (E-Stop) and interlocks, cabling, switches, solenoids, transducers, sensors, actuators, ancillary system interfaces, and related components necessary for a complete machine tool control system. The Subcontractor shall include effort to standardize systems between the two machines if reasonably possible.

42 ENGINEERING↗
DOE OSTI2023

ARENA: Adversary-Resistant Evolving Neural Architectures

Neural networks are becoming the cornerstone for national security prediction tasks. However, designing them requires significant research and trial/error, as they have many hyperparameters, including their computation graph (“architecture”). Neural architecture search (NAS) employs secondary optimizers to search for architectures maximizing objectives like accuracy. Evolutionary algorithms (EAs) are the most used class of optimizer for NAS. However, existing Python libraries for writing EAs limit the complexity of experiments a user can design. In this project, we built ARENA, a Python framework that encodes complex, hyper-realistic EAs. ARENA collects detailed information as it runs and is flexible enough to encode non-EA search algorithms. We tested ARENA on 4 toy optimization problems by encoding 3 search algorithms for each—random search, an EA, and simulated annealing. We also designed an EA that performs NAS on the MNIST dataset. Our experiments suggest the potential for immediate mission impact through solving lab-wide optimization problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Hierarchical memories: Simulating quantum LDPC codes with local gates

Constant-rate low-density parity-check (LDPC) codes are promising candidates for constructing efficient fault-tolerant quantum memories. However, if physical gates are subject to geometric-locality constraints, it becomes challenging to realize these codes. In this paper, we construct a new family of [[N,K,D]] codes, referred to as hierarchical codes, that encode a number of logical qubits K=Ω(N/log(N) 2 ). The N th element of this code family is obtained by concatenating a constant-rate quantum LDPC code with a surface code; nearest-neighbor gates in two dimensions are sufficient to implement the corresponding syndrome-extraction circuit and achieve a threshold. Below threshold the logical failure rate vanishes superpolynomially as a function of the distance D(N). We present a bilayer architecture for implementing the syndrome-extraction circuit, and estimate the logical failure rate for this architecture. Under conservative assumptions, we find that the hierarchical code outperforms the basic encoding where all logical qubits are encoded in the surface code.

Pattison, Christopher A. [California Institute of ↗
DOE OSTI2021

The Hyperthermophilic Restriction-Modification Systems of Thermococcus kodakarensis Protect Genome Integrity

Thermococcus kodakarensis (T. kodakarensis), a hyperthermophilic, genetically accessible model archaeon, encodes two putative restriction modification (R-M) defense systems, TkoI and TkoII. TkoI is encoded by TK1460 while TkoII is encoded by TK1158. Bioinformative analysis suggests both R-M enzymes are large, fused methyltransferase (MTase)-endonuclease polypeptides that contain both restriction endonuclease (REase) activity to degrade foreign invading DNA and MTase activity to methylate host genomic DNA at specific recognition sites. In this work, we demonsrate T. kodakarensis strains deleted for either or both R-M enzymes grow more slowly but display significantly increased competency compared to strains with intact R-M systems, suggesting that both TkoI and TkoII assist in maintenance of genomic integrity in vivo and likely protect against viral- or plasmid-based DNA transfers. Pacific Biosciences single molecule real-time (SMRT) sequencing of T. kodakarensis strains containing both, one or neither R-M systems permitted assignment of the recognition sites for TkoI and TkoII and demonstrated that both R-M enzymes are TypeIIL; TkoI and TkoII methylate the N 6 position of adenine on one strand of the recognition sequences GTGAAG and TTCAAG, respectively. Further in vitro biochemical characterization of the REase activities reveal TkoI and TkoII cleave the DNA backbone GTGAAG(N) 20 /(N) 18 and TTCAAG(N) 10 /(N) 8 , respectively, away from the recognition sequences, while in vitro characterization of the MTase activities reveal transfer of tritiated S-adenosyl methionine by TkoI and TkoII to their respective recognition sites. Together these results demonstrate TkoI and TkoII restriction systems are important for protecting T. kodakarensis genome integrity from invading foreign DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression

Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F430. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

EdgeAI: Machine learning via direct attached accelerator for streaming data processing at high shot rate x-ray free-electron lasers

We present a case for low batch-size inference with the potential for adaptive training of a lean encoder model. We do so in the context of a paradigmatic example of machine learning as applied in data acquisition at high data velocity scientific user facilities such as the Linac Coherent Light Source-II x-ray Free-Electron Laser. We discuss how a low-latency inference model operating at the data acquisition edge can capitalize on the naturally stochastic nature of such sources. We simulate the method of attosecond angular streaking to produce representative results whereby simulated input data reproduce high-resolution ground truth probability distributions. By minimizing the mean-squared error between the decoded output of the latent representation and the ground truth distributions, we ensure that the encoding layers and resulting latent representation maintains full fidelity for any downstream task, be it classification or regression. We present throughput results for data-parallel inference of various batch sizes, some with throughput exceeding 100 k images per second. We also show in situ training below 10 s per epoch for the full encoder–decoder model as would be relevant for streaming and adaptive real-time data production at our nation’s scientific light sources.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa

Brown-rot fungi lack many enzymes associated with complete wood degradation, such as lignin-attacking peroxidases, and have developed alternative mechanisms for rapid wood breakdown. To identify the effects of culture conditions and wood substrates on gene expression, we grew Fibroporia radiculosa in submerged cultures containing Wiley milled wood (5 days) and solid wood wafers (30 days), using aspen, pine, and spruce as a substrate. The comparative analysis revealed that wood species had a limited effect on the transcriptome: <3% of genes were differentially expressed between different wood species substrates. The comparison between gene expression during growth on milled wood and wood wafer conditions, however, indicated that the genes encoding plant cell wall-degrading enzymes, such as glycoside hydrolases and peptidases, were activated during growth on wood wafers, confirming previous reports. On the other hand, it was shown for the first time that the genes encoding Fenton chemistry enzymes, such as hydroquinone biosynthesis enzymes and oxidoreductases, were activated during submerged growth on ground wood. This illustrates the diversity of wood-decay reactions encoded in fungi and activated at different stages of this process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Contrastive Machine Learning with Gamma Spectroscopy Data Augmentations for Detecting Shielded Radiological Material Transfers

Data analysis techniques can be powerful tools for rapidly analyzing data and extracting information that can be used in a latent space for categorizing observations between classes of data. Machine learning models that exploit learned data relationships can address a variety of nuclear nonproliferation challenges like the detection and tracking of shielded radiological material transfers. The high resource cost of manually labeling radiation spectra is a hindrance to the rapid analysis of data collected from persistent monitoring and to the adoption of supervised machine learning methods that require large volumes of curated training data. Instead, contrastive self-supervised learning on unlabeled spectra can enhance models that are built on limited labeled radiation datasets. This work demonstrates that contrastive machine learning is an effective technique for leveraging unlabeled data in detecting and characterizing nuclear material transfers demonstrated on radiation measurements collected at an Oak Ridge National Laboratory testbed, where sodium iodide detectors measure gamma radiation emitted by material transfers between the High Flux Isotope Reactor and the Radiochemical Engineering Development Center. Label-invariant data augmentations tailored for gamma radiation detection physics are used on unlabeled spectra to contrastively train an encoder, learning a complex, embedded state space with self-supervision. A linear classifier is then trained on a limited set of labeled data to distinguish transfer spectra between byproducts and tracked nuclear material using representations from the contrastively trained encoder. The optimized hyperparameter model achieves a balanced accuracy score of 80.30%. Any given model—that is, a trained encoder and classifier—shows preferential treatment for specific subclasses of transfer types. Regardless of the classifier complexity, a supervised classifier using contrastively trained representations achieves higher accuracy than using spectra when trained and tested on limited labeled data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

YPK9 and WHI2 Negatively Interact during Oxidative Stress

Yeast PARK9 (YPK9) shares homology with human ATP13A2, which encodes a polyamine transporter implicated in juvenile forms of Parkinson’s disease. We used YPK9 to gain insight into how ATP13A2 affects cell growth and sensitivity to oxidative stress. Surprisingly, the YPK9 deletion strain from the Saccharomyces cerevisiae deletion collection (YKO) in wildtype BY4741 (mating type a) grew faster and was more resistant to hydrogen peroxide than a commercial, putative parental BY4741 wildtype strain (BY4741 COM ). In contrast, deleting YPK9 from BY4741 COM rendered it very sensitive to hydrogen peroxide, suggesting its background is different from that of the deletion collection. Whole-genome sequencing revealed that BY4741 COM and BY4741 COM ypk9Δ contain a novel premature stop codon near the 3' end of WHI2 (WHI2 G1324T ), whereas the collection’s YPK9 deletion strain contains WHI2, which encodes a 486 amino acid protein, Whi2p. Replacing full-length WHI2 with the sequence coding for the predicted truncation (Whi2p E442* ) rendered strains more sensitive to hydrogen peroxide, whereas the converse replacement rendered them more resistant. The sequences of WHI2 in 20 randomly chosen strains from the collection encode the full-length protein, indicating that the putative parental BY4741 WHI2 G1324T strain’s genetic background differs from that of the deletion collection. Examination of WHI2 sequences in several commonly used wildtype S. cerevisiae strains and isolates revealed other Whi2p truncations that might yield altered phenotypes. Together, these results demonstrate a novel premature stop codon in WHI2 that renders yeast sensitive to hydrogen peroxide; they also reveal a negative genetic interaction between WHI2 and YPK9 in the presence of hydrogen peroxide in the BY4741 background.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Study of statistical coding for digital TV

The results are presented for a detailed study to determine a pseudo-optimum statistical code to be installed in a digital TV demonstration test set. Studies of source encoding were undertaken, using redundancy removal techniques in which the picture is reproduced within a preset tolerance. A method of source encoding, which preliminary studies show to be encouraging, is statistical encoding. A pseudo-optimum code was defined and the associated performance of the code was determined. The format was fixed at 525 lines per frame, 30 frames per second, as per commercial standards.

Gardenhire, L. W.↗
NASA NTRS1972

RAE-B antenna aspect system

The development of a facsimile camera to serve as the antenna aspect system for the second generation Radio Astronomy Explorer Satellite designated RAE-B is summarized. The camera system consists of two cameras and a data encoder. The program deliverables were two flight cameras, a flight encoder and one spare flight encoder. The RAE-B satellite was originally intended for an earth orbit mission and the facsimile subsystem characteristics were specified with this in mind. Subsequently the flight mission was changed to orbit the moon; however the change occurred too late to significantly influence the facsimile system design. Therefore, this report considers only compliance of the system to earth orbit requirements.

Source record↗
NASA NTRS1972

Radio astronomy Explorer B antenna aspect processor

The antenna aspect system used on the Radio Astronomy Explorer B spacecraft is described. This system consists of two facsimile cameras, a data encoder, and a data processor. Emphasis is placed on the discussion of the data processor, which contains a data compressor and a source encoder. With this compression scheme a compression ratio of 8 is achieved on a typical line of camera data. These compressed data are then convolutionally encoded.

Miller, W. H.↗