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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 OSTI2024

Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C

The yeast SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a ‘pincer-like’ conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5–nucleosome complex suggests that promoter proximal, histone H2B ubiquitylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Chlamydomonas violaxanthin de-epoxidase enzyme and its uses

This disclosure provides Chlamydomonas violaxanthin de-epoxidase (CVDE) gene, polypeptides, and variants thereof as well as host cells that are genetically modified to express a CVDE polypeptide or variant. The disclosure additionally provides methods of producing such a genetically modified host cell and methods of using the cells , e.g., to increase zeaxanthin production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Methods related to a structure of high-affinity human PD-1/PD-L2 complex

Variants of human PD-1 comprising one or more of amino acid substitutions in residues corresponding to N74, T76 and A132 of SEQ ID NO:1 are described. Also described are structures, obtained using X-ray crystallography, of the human PD-1/PD-L2 complex and mutant PD-1 variants. The structures of human PD-1 described in the present disclosure are useful in drug discovery, including small-molecule drug discovery. Accordingly, methods of using the structures in drug discovery are also described.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Side-channel Leakage Assessment Metrics: A Case Study of GIFT Block Ciphers

Determination of an adequate level of security and providing subsequent mechanisms to achieve it, is one of the most pressing problems regarding embedded computing devices. While there are some solutions available for resource-rich computer systems, direct application of these solutions to resource-constrained environments are often unfeasible. The fundamental problem for such resource-constrained systems is the fact that current cryptographic algorithms utilize significant energy consumption and storage overhead. Both the cryptographic algorithm and its physical implementation affect the resilience of a cryptosystem against side-channel attacks. A side-channel attack represents a process that exploits leakages in order to extract sensitive information such as the key. This paper focuses on Correlation Power Analysis (CPA) which is side-channel attack based on the power consumption leakage. In 2016 the U.S. Commerce Department’s National Institute of Standards and Technology (NIST) initiated the call for proposals of new cryptographic algorithms to strengthen the cryptographic defense of networked devices against cyberattacks and to protect the data created by those innumerable device. This work evaluates S-boxes used by NIST candidates PICCOLO, GIFT, and PRESENT, as well as several S-box variants that demonstrated sufficient weaknesses against classical cryptanalysis, for a quantitative comparison in terms of resiliency to CPA attack. Three well-known theoretical metrics are evaluated: transparency order (TO and RTO), nonlinearity, and signal-to-noise (SNR) ratio, aiming to characterize the resistance of these S-boxes against adversaries exploiting physical leakages. Experimental results from attacks on an 8- bit XMEGA were obtained via the ChipWhisperer platform and of all the S-boxes evaluated, GIFT64 with a PICCOLO S-box was found to be the most susceptible to CPA. Results showed that variations in TO and RTO were not sufficient to ensure practical CPA resistance and that among S-boxes with equal non-linearity there were no significant differences in the TO and SNR variants.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Side-channel Leakage Assessment Metrics: A Case Study of GIFT Block Ciphers

Determination of an adequate level of security and providing subsequent mechanisms to achieve it, is one of the most pressing problems regarding embedded computing devices. While there are some solutions available for resource-rich computer systems, direct application of these solutions to resource-constrained environments are often unfeasible. The fundamental problem for such resource-constrained systems is the fact that current cryptographic algorithms utilize significant energy consumption and storage overhead. Both the cryptographic algorithm and its physical implementation affect the resilience of a cryptosystem against side-channel attacks. A side-channel attack represents a process that exploits leakages in order to extract sensitive information such as the key. This paper focuses on Correlation Power Analysis (CPA) which is side-channel attack based on the power consumption leakage. In 2016 the U.S. Commerce Department’s National Institute of Standards and Technology (NIST) initiated the call for proposals of new cryptographic algorithms to strengthen the cryptographic defense of networked devices against cyberattacks and to protect the data created by those innumerable device. This work evaluates S-boxes used by NIST candidates PICCOLO, GIFT, and PRESENT, as well as several S-box variants that demonstrated sufficient weaknesses against classical cryptanalysis, for a quantitative comparison in terms of resiliency to CPA attack. Three well-known theoretical metrics are evaluated: transparency order (TO and RTO), nonlinearity, and signal-to-noise (SNR) ratio, aiming to characterize the resistance of these S-boxes against adversaries exploiting physical leakages. Experimental results from attacks on an 8- bit XMEGA were obtained via the ChipWhisperer platform and of all the S-boxes evaluated, GIFT64 with a PICCOLO S-box was found to be the most susceptible to CPA. Results showed that variations in TO and RTO were not sufficient to ensure practical CPA resistance and that among S-boxes with equal non-linearity there were no significant differences in the TO and SNR variants.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Recent Advances in Analysis and Design of Axial Flux Permanent Magnet Electric Machines

Axial flux permanent magnet machines (AFPM) are popular for applications that benefit from high torque density and an axially compact form factor, such as in-wheel traction drives. Although the radial flux permanent magnet machine (RFPM) and the AFPM work based on the same underlying principle, the differences in their geometry introduce complexities in analysis of the AFPM. In this paper, the different AFPM design variants, their sizing approaches, computationally efficient design optimization techniques, and manufacturing techniques reported in literature are reviewed. In addition to classical AFPM machines, emerging variants and research opportunities with potential to push the boundaries of electric machine technology are reviewed. These include bearingless AFPMs, magnetically geared AFPMs, and combined radial-axial flux machines.

Nishanth, FNU↗
DOE OSTI2023

Data-Driven Whole-Genome Clustering to Detect Geospatial, Temporal, and Functional Trends in SARS-CoV-2 Evolution

Current methods for defining SARS-CoV-2 lineages ignore the vast majority of the SARS-CoV-2 genome. We develop and apply an exhaustive vector comparison method that directly compares all known SARS-CoV-2 genome sequences to produce novel lineage classifications. We utilize data-driven models that (i) accurately capture the complex interactions across the set of all known SARS-CoV-2 genomes, (ii) scale to leadership-class computing systems, and (iii) enable tracking how such strains evolve geospatially over time. We show that during the height of the original Omicron surge, countries across Europe, Asia, and the Americas had a spatially asynchronous distribution of Omicron sub-strains. Moreover, neighboring countries were often dominated by either different clusters of the same variant or different variants altogether throughout the pandemic. Analyses of this kind may suggest a different pattern of epidemiological risk than was understood from conventional data, as well as produce actionable insights and transform our ability to prepare for and respond to current and future biological threats.

Jacobson, Daniel↗
DOE OSTI2024

Microstructure and Mechanical Properties of Ni-Based Superalloy Nimonic 105 with Varying Carbon Content

High carbon levels have been found to improve the fabricability of high-strength cast and wrought Ni-based superalloys, enabling the development of superior cast/wrought materials. However, carbon also strongly influences the microstructure and mechanical properties of the alloys. Nimonic 105 variants with three different carbon concentrations were manufactured. A bimodal grain size was found in the intermediate carbon content variant, while the high (low) carbon resulted in fine (coarse) grains thereby significantly affecting creep performance. The variations in grain structure were attributed to the primary carbides. An intermediate carbon level showed the best combination of strength and ductility in tension at high-temperature but little improvement in, or even inferior, creep performance. Discussion of the results will establish an understanding of the influence of carbon on the microstructure and mechanical properties of high strength cast and wrought superalloys, providing insights into obtaining high-quality alloys for future high-temperature applications.

Fang, Xiaotian↗
DOE OSTI2024

Exploring gauge-fixing conditions with gradient-based optimization

Lattice gauge fixing is required to compute gauge-variant quantities, for example those used in RI-MOM renormalization schemes or as objects of comparison for model calculations. Recently, gauge-variant quantities have also been found to be more amenable to signal-to-noise optimization using contour deformations. These applications motivate systematic parameterization and exploration of gauge-fixing schemes. This work introduces a differentiable parameterization of gauge fixing which is broad enough to cover Landau gauge, Coulomb gauge, and maximal tree gauges. The adjoint state method allows gradient-based optimization to select gauge-fixing schemes that minimize an arbitrary target loss function.

Detmold, William↗
DOE OSTI2025

Ex-situ Heat Treatment of TEM Foils in a Custom Titanium Fixture: A Case Study on Ni-based Superalloy

The advancement of microstructural characterization at the nanoscale is critical to understanding the microstructural evolution and performance of engineering materials. Transmission electron microscopy (TEM) plays a vital role in such investigations, particularly when coupled with controlled ex- and in-situ experiments. In this study, we introduce a novel method for ex-situ heat treatment (HT) of TEM foils using a custom-designed fixture, made from pure titanium, and vacuum furnace to inhibit oxidation. This approach ensures precise temperature control and minimal sample contamination during HT, critical for substructural characterization and analysis of metallic materials. The fixture consists of a titanium base with three slits, for three sample foils, and a titanium cap for closure. The entire assembly is placed in a vacuum heat treatment furnace with high vacuum capability to prevent oxidation. To validate the effectiveness of the setup, precipitation behavior and microstructural changes were studied in an IN725 variant heat-treated at 500°C for 1 hour and 282 variant heat-treated at 700°C for 1 hour, as case studies.

electron microscopy↗
DOE OSTI2023

Structural and functional validation of a highly specific Smurf2 inhibitor

Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor‐β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross‐reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein‐based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2–E3 protein interaction interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Zika virus mutation enhances transmission potential and confers escape from protective dengue virus immunity

Zika virus (ZIKV) and dengue virus (DENV) are arthropod-borne pathogenic flaviviruses that co-circulate in many countries. To understand some of the pressures that influence ZIKV evolution, we mimic the natural transmission cycle by repeating serial passaging of ZIKV through cultured mosquito cells and either DENV-naive or DENV-immune mice. Compared with wild-type ZIKV, the strains passaged under both conditions exhibit increased pathogenesis in DENV-immune mice. Application of reverse genetics identifies an isoleucine-to-valine mutation (I39V) in the NS2B proteins of both passaged strains that confers enhanced fitness and escape from pre-existing DENV immunity. Introduction of I39V or I39T, a naturally occurring homologous mutation detected in recent ZIKV isolates, increases the replication of wild-type ZIKV in human neuronal precursor cells and laboratory-raised mosquitoes. Our data indicate that ZIKV strains with enhanced transmissibility and pathogenicity can emerge in DENV-naive or -immune settings, and that NS2B-I39 mutants may represent ZIKV variants of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses

Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5–1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

A tool and a methodology to use macros for abstracting variations in code for different computational demands

Scientific software used on high-performance computing platforms is in a phase of transformation because of the combined increase in the heterogeneity and complexity of models and hardware platforms. Having separate implementations for different platforms can easily lead to combinatorial explosions; therefore, the computational science community has been looking for mechanisms to express code through abstractions that can be specialized for different platforms. Most existing approaches use template meta-programming in C++, and are, therefore language specific. Here, we have developed a tool that uses customized expansion of macros to mimic some of C++ behavior in other languages. It enables unification of any code variants that may be necessary to run efficiently on different target architectures and different computational environments through use of macros with multiple alternative definitions and ability to arbitrate on definition selection for expansion. Combined with two other tools, a custom runtime, and a user specified recipe translator, our custom macroprocessor becomes a part of an overall performance portability solution that does not depend on any specific programming language. We also use macros as code-shorthand that lets code snippets become building blocks that allow variations in control flow to explore performance options. We demonstrate use of macros in Flash-X, a multiphysics multicomponent code with many Fortran legacy components derived from an earlier community code FLASH.

Heterogenous computing↗
DOE OSTI2023

Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease

Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against novel pandemic coronaviruses and to more effectively respond to SARS-CoV-2 variants. The emergence of Omicron and subvariants of SARS-CoV-2 illustrates the limitations of solely targeting the receptor-binding domain (RBD) of the spike (S) protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors, which targets a conserved S2 region in the betacoronavirus spike fusion machinery. Select bnAbs showed broad in vivo protection against all three deadly betacoronaviruses, SARS-CoV-1, SARS-CoV-2, and MERS-CoV, which have spilled over into humans in the past two decades. Structural studies of these bnAbs delineated the molecular basis for their broad reactivity and revealed common antibody features targetable by broad vaccination strategies. These bnAbs provide new insights and opportunities for antibody-based interventions and for developing pan-betacoronavirus vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Effective antiviral coatings for deactivating SARS-CoV-2 virus on N95 respirator masks or filters

The application of antiviral coatings to masks and respirators is a potential mitigating step toward reducing viral transmission during the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic. The use of appropriate masks, social distancing, and vaccines is the immediate solution for limiting the viral spread and protecting people from this virus. N95 respirator masks are effective in filtering the virus particles, but they cannot kill or deactivate the virus. We report a possible approach to deactivating SARS-CoV-2 by applying an antimicrobial coating (Goldshield 75) to masks and respirators, rendering them suitable for repeated use. Masks coated with Goldshield 75 demonstrated continuous inactivation of the Alpha and Beta variants of the SARS-CoV-2 over a 3-day period and no loss of inactivation when stored at temperatures at 50 °C.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Proteomic Characterization of Damaged Single Hairs Recovered after an Explosion for Protein-Based Human Identification

Evidence recovery is challenging where an explosion has occurred. Though hair evidence may be sufficiently robust to be recovered at the site, forensic analysis underutilizes the matrix by relying on morphological analysis. Where DNA is compromised, particularly in hair, protein-based human identification presents a promising alternative. Detection of amino acid polymorphisms in hair proteins as genetically variant peptides (GVPs) permits the inference of individualizing single nucleotide polymorphisms for identification. However, an explosive blast may damage hair proteins and compromise GVP identification. This work evaluates effects of an explosive blast on the hair proteome and GVP identification, investigates microscopy as a predictor of proteome profiling success in recovered hairs to improve analysis throughput, and quantifies discriminative power in damaged hairs. The proteomics dataset has been deposited into the ProteomeXchange Consortium (PXD017427). With the exception of degradation in keratins K75, K80, K40, and keratin-associated protein KAP10-11 as markers of hair cuticular damage, corroborated by scanning electron microscopic analysis, minimal hair proteome degradation following explosion allowed successful proteome profiling of single hairs regardless of morphological damage. Finally, GVP identification remained independent of explosion conditions, permitting similar discriminative power between exploded and undamaged hairs. These findings lend greater confidence to GVP analysis in one-inch hairs for forensic identification and provide information about hair protein localization.

59 BASIC BIOLOGICAL SCIENCES↗