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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Synthetic proteins for COVID-19 diagnostics

There is an urgent need for inexpensive, rapid and specific antigen-based assays to test for vaccine efficacy and detect infection with SARS-CoV-2 and its variants. We have identified a small, synthetic protein (JS7), representing a region of maximum variability within the receptor binding domain (RBD), which binds antibodies in sera from nine patients with PCR-verified COVID-19 of varying severity. Antibodies binding to either JS7 or the SARS-CoV-2 recombinant RBD, as well as those that disrupt binding between a fragment of the ACE2 receptor and the RBD, are proportional to disease severity and clinical outcome. Binding to JS7 was inhibited by linear peptides from the RBD interface with ACE2. Variants of JS7, such as E484K or N501Y, can be quickly synthesized in pure form in large quantities by automated methods. JS7 and related synthetic antigens can provide a basis for specific diagnostics for SARS-CoV-2 infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Protein data bank: From two epidemics to the global pandemic to mRNA vaccines and Paxlovid

Structural biologists and the open-access Protein Data Bank (PDB) played decisive roles in combating the COVID-19 pandemic. Global biostructure data were turned into global knowledge, allowing scientists and engineers to understand the inner workings of coronaviruses and develop effective countermeasures. Two mRNA vaccines, initially designed with guidance from PDB structures of the SARS-CoV-1 and MERS-CoV spike proteins, prevented infections entirely or reduced the likelihood of morbidity and mortality for more than five billion individual recipients worldwide. Structure-guided drug discovery by Pfizer, Inc (facilitated by PDB structures), initiated in the 2000s in response to SARS-CoV-1 and resumed in 2020, yielded nirmatrelvir (the active ingredient of Paxlovid) -- a potent, orally-bioavailable inhibitor of the SARS-CoV-2 main protease. You've got to love the Protein Data Bank!

Burley, Stephen K.↗
DOE OSTI2024

Pronounced reduction in the regeneration energy of potassium sarcosinate CO 2 capture solvent using TiO 2

Absorption-based CO 2 capture technologies face economic feasibility concerns due to the exceedingly high energy requirements of solvent regeneration. Among various proposed solutions, solid acid-aided solvent regeneration stands out as a promising approach. Studies have shown that solid materials containing Lewis and Brønsted acid sites can facilitate deprotonation of protonated amine and breakdown of carbamate molecules, which significantly increases CO 2 desorption rate and decreases regeneration energy of common solvents such as MEA and DEA. However, the influence of solid acids on alternate solvents such as amino acids is not well known. Here, we report the performance of TiO 2 for the regeneration of CO 2 -loaded aqueous potassium sarcosinate (K-Sar) solvent. K-Sar is an environmentally friendly amino-acid salt that provides high CO 2 absorption rates, making it a good candidate for both point-source and direct-air capture. TiO 2 is hydrothermally stable and contains high surface acid site concentration. Desorption of CO 2 from K-Sar starts at room temperature in the presence of TiO 2 , while such onset temperature is greater than 70°C for regeneration without TiO 2 . Further, at a temperature of 95°C, the maximum CO 2 desorption rate and cumulative CO 2 removal increase by 128% and 91%, respectively, in the presence of TiO 2 compared to the no TiO 2 case. The total regeneration energy could be reduced by ~ 50% with TiO 2 , showcasing the significant role this process can take in improving the commercial competitiveness of absorption-based CO 2 capture. Further characterization with XRD, SEM, and NMR concluded that neither the TiO 2 powder nor the solvent undergoes any physical or chemical degradation in the regeneration process, suggesting the potential of their long-term usability.

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

A 3.4-Å cryo-electron microscopy structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles

Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family Coronaviridae that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild upper respiratory symptoms in children, elderly and immunocompromised individuals. It has also been shown to cause severe lower respiratory illness. NL63 shares ACE2 as a receptor for viral entry with SARS-CoV-1 and SARS-CoV-2. Here we present the in situ structure of HCoV-NL63 spike (S) trimer at 3.4-Å resolution by single-particle cryo-EM imaging of vitrified virions without chemical fixative. It is structurally homologous to that obtained previously from the biochemically purified ectodomain of HCoV-NL63 S trimer, which displays a 3-fold symmetric trimer in a single conformation. In addition to previously proposed and observed glycosylation sites, our map shows density at other sites, as well as different glycan structures. The domain arrangement within a protomer is strikingly different from that of the SARS-CoV-2 S and may explain their different requirements for activating binding to the receptor. Overall, this structure provides the basis for future studies of spike proteins with receptors, antibodies, or drugs, in the native state of the coronavirus particles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Protein Surface Printer for Exploring Protein Domains

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces

The COVID-19 pandemic has claimed millions of lives worldwide, sickened many more, and has resulted in severe socio-economic consequences. As society returns to normal, understanding the spread and persistence of SARS CoV-2 on commonplace surfaces can help to mitigate future outbreaks of coronaviruses and other pathogens. We hypothesize that such an understanding can be aided from studying the binding and interaction of viral proteins with non-biological surfaces. Here, we propose a methodology for investigating the adhesion of the SARS CoV-2 spike glycoprotein on common inorganic surfaces such as aluminum-, copper-, iron-, silica-, and ceria-oxides as well as metallic gold. Quantitative adhesion was obtained from the analysis of measured forces at the nanoscale using an atomic force microscope operated under ambient conditions. Without imposing further constraints on the measurement conditions, our preliminary findings suggest that spike glycoproteins interact with similar adhesion forces across the majority of the metal oxides tested with the exception to gold, for which attraction forces ~10 times stronger than all other materials studied were observed. Ferritin, which was used as a reference protein, was found to exhibit similar adhesion forces as SARS CoV-2 spike protein. Further, this study results show that glycoprotein adhesion forces for similar ambient humidity, tip shape, and contact surface are non-specific to the properties of metal oxide surfaces, which are expected to be covered by a thin water film. The findings suggest that at ambient conditions glycoprotein adhesion to metal oxides is primarily controlled by the water capillary forces and they depend on the surface tension of the liquid (water). We discuss further strategies warranted to decipher the intricate nanoscale forces for improved quantification of the adhesion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike–antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

Science & Technology - Other Topics↗
DOE OSTI2020

Novel fisheries investigations by Harald Dannevig: some parallels with Johan Hjort on the other side of the world

Abstract Harald Dannevig was Australia’s first Director of fisheries research and Director of Australia’s first ocean-going research vessel. Dannevig’s initial contributions concerned hatchery technology, freshwater fisheries, and impacts of estuarine prawn trawling. Later, he revealed the growth and migration of sea mullet, the spawning of pelagic eggs in the coastal ocean, and he was the first to demonstrate the effect of onshore winds on recruitment to estuarine fisheries. Using plans of the first Norwegian research trawler Michael Sars, he advised on the construction and commissioning of Endeavour. He organized 99 research voyages over 6 years to determine suitable trawling grounds over ∼7000 km, discovering 263 new species, including 96 new fish species and ∼5000 catalogued specimens. Harald Dannevig’s significant achievements in Australia were soon forgotten after his death with the loss of Endeavour in the Southern Ocean at the beginning of World War I. Both Johan Hjort and Dannevig were numerate, loved natural history, and were keenly observant on the deck. As these two scientists did not correspond, their innovative and parallel thinking stems from the shared university environment with G.O. Sars, and the rapport between Sars and Harald’s father Gunder Dannevig, concerning the fish hatchery and stocking of larval cod.

Suthers, Iain M.↗
DOE OSTI2022

Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity

Coronaviruses (Coronaviridae) such as SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus) and MERS‐CoV (Middle East respiratory syndrome coronavirus) have been the source of recent outbreaks and global health concerns. While vaccines have been essential for controlling the SARS‐CoV‐2 (COVID‐19) pandemic, it is uncertain whether they will be effective against future coronavirus strains. Therefore, identification or design of a broad‐spectrum drug that targets highly conserved regions of the main protease of multiple coronavirus strains is essential in the long term. As part of a virtual summer research experience with the RCSB PDB, bioinformatics tools were employed to predict and construct 3D models of the coronavirus main protease (MPro) using SARS‐CoV‐2 as the template, with a focus on mutational trends and active sites. This study focused on the active sites of MPro, a cysteine protease essential for viral assembly and replication. Sequence alignments and structure modeling of MPro structures has identified conserved regions across multiple coronavirus strains. Inhibition of MPro halts coronavirus replication, making it an ideal drug target, and studies of MPro may foster and accelerate the discovery of high affinity broad‐spectrum drugs.

Wu Wu, Amy↗
DOE OSTI2026

Practical Three-Dimensional Curvilinear Aperture Monopulse Synthetic Aperture Radar

When collected over a curved path, Synthetic Aperture Radar (SAR) contains information about the three-dimensional content of a scene that can aid interpretation of this difficult imaging modality. In a point scatterer simulation with amplitudes and heights derived from a real SAR image pair, we supplement confocal processing with a monopulse-based algorithm to compute heights of certain bright points, which we find automatically. In SAR, bright points often reflect man-made infrastructure central to scene interpretation.

Story, Mark [ORNL] (ORCID:0000000289148911)↗
DOE OSTI2022

An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses

The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)–directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Thermal Evaluation of the SAVY-4000 1 Quart Container at High Heat Loads

The SAVY-4000 Safety Analysis Report (SAR) was published in 2013 which established the design life of the container series through physical testing that meets applicable requirements from DOE M 441.1-1, Nuclear Material Packaging Manual. One critical requirement in DOE M 441.1-1 is to set a maximum heat load for the entire series to ensure that throughout the lifetime of the container, each of the components still performs within manufacture specifications. The original maximum decay heat limit has been defined within the SAVY-4000 SAR, which was accomplished by completing a series of tests that heat loaded the SAVY-4000 series and measured the steady state temperature and graded it against manufacture specifications. The container series is comprised of a corrosion resistant 316L stainless steel containment boundary, ceramic composite filter for the prevention of radiological particulate release and a chemically stable O-ring made of Viton ® . Currently, the SAVY 4000 maximum decay heat load is set at 25 Watts and the heat load expected during normal handling and storage is considered sufficient that the SAVY 4000 container requirements will not be the limiting factor for storage of most common material in use at TA-55, e.g. weapons grade oxide, americium, Pu-238 oxide and encapsulated heat sources. The SAVY 4000 lifetime was originally set as 5 years within the SAVY-4000 SAR, but in July 2019 the lifetime was extended to 15 years through a technical basis justification approved by the Department of Energy (DOE) Los Alamos Field Office. The 25 Watt limit applies to all SAVY 4000 container sizes; 1-quart, 2-quart, 3-quart, 5-quart, 8-quart, 12-quart, 5-gallon, and 10-gallon.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

National Technology & Engineering Solutions of Sandia, LLC Technical Assistance With Energy Cloud (Final CTAP Report)

Sandia provided technical assistance to Energy Cloud to support the assessment of Energy Cloud’s technology for air filtration of the SARS-CoV-2 virus. The Energy Cloud system was developed to filter the SARS-CoV-2 virus from commercial HVAC systems, ducts, and enclosed rooms without generating ozone. The project included a 3-week experimental series with aerosolized SARS-CoV-2 virus at the University of Southern California’s biosafety level 3 (BSL-3) laboratory. USC provided the facility as well as experimentally derived measurements and assessment of the Energy Cloud system efficacy for SARSCoV-2 filtration from air handling systems.

42 ENGINEERING↗
DOE OSTI2021

Decontamination and Sterilization of Surfaces using Low Cost Ionic Liquids (CRADA Final Report)

The current study made a comprehensive literature review of the structure activity relationship (SAR) for microcidal and virucidal influence of ionic liquids. It summarized the key structure parameters that have close correlation to the antimicrobial and antiviral properties of the ILs. It proposed an experimental plan on developing and testing an effective ionic liquid from renewable lignocellulosic biomass. The goal is to understand the structure activity relationship (SAR) for virucidal influence of ionic liquids through comprehensive literature search and data analysis. A full experimental plan will be drafted based on the literature summary. Perform a comprehensive literature search to aid the development of an effective and easily deployable method to inactivate SARS-CoV-2 and decontaminate surfaces based on low-cost functional ionic liquids. These designer solvents have the potential to be a compelling and environmentally friendly alternative to common chemical disinfectants. Literature summary report including reported ionic liquid structures, synthesis and testing methods, and the structure activity relationship. Experimental plan on developing a low cost effective antiviral ionic liquid.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States

Although many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number ℛ0, the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of ℛ0 relates to a herd immunity threshold (HIT), which is given by 1−1/ℛ0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level ℛ0 estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. ℛ0 estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21 January 2020 to 21 June 2020. Our ℛ0 estimates characterize the infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we found that no state had achieved herd immunity as of 20 September 2021.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Apparatus, system and method for highlighting activity-induced change in multi-pass synthetic aperture radar imagery

Described herein are various technologies relating to constructing a differenced change product (DCP) image. A plurality of synthetic aperture radar (SAR) images of a scene are generated based upon radar signals directed towards and reflected off of the scene, and a plurality of coherence change detection (CCD) images of the scene are generated based upon the SAR images. The CCD images are registered with one another, and their pixel values re-scaled according to a monotonic mapping function. The DCP image is generated based upon a computed pixel-wise difference between a pair of the re-scaled CCD images. The DCP image identifies locations in the scene where human activity-induced change is likely to have occurred between a pair of SAR passes of the scene.

42 ENGINEERING↗
DOE OSTI2023

Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity

Novel therapeutic monoclonal antibodies (MAbs) must accommodate comprehensive breadth of activity against diverse sarbecoviruses and high neutralization potency to overcome emerging variants. Here, in this study, we report the crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD) in complex with MAb WRAIR-2063, a moderate-potency neutralizing antibody with exceptional sarbecovirus breadth, that targets the highly conserved cryptic class V epitope. This epitope overlaps substantially with the spike protein N-terminal domain (NTD) -interacting region and is exposed only when the spike is in the open conformation, with one or more RBDs accessible. WRAIR-2063 binds the RBD of SARS-CoV-2 WA-1, all variants of concern (VoCs), and clade 1 to 4 sarbecoviruses with high affinity, demonstrating the conservation of this epitope and potential resiliency against variation. We compare structural features of additional class V antibodies with their reported neutralization capacity to further explore the utility of the class V epitope as a pan-sarbecovirus vaccine and therapeutic target.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Continuous-variable quantum Boltzmann machine

Here, we propose a continuous-variable quantum Boltzmann machine (CVQBM) using a powerful energy-based neural network. It can be realized experimentally on a continuous-variable (CV) photonic quantum computer. We used a CV quantum imaginary time evolution (QITE) algorithm to prepare the essential thermal state and then designed the CVQBM to proficiently generate continuous probability distributions. We applied our method to both classical and quantum data. Using real-world classical data, such as synthetic-aperture radar (SAR) images, we generated probability distributions. For quantum data, we used the output of CV quantum circuits. We obtained high fidelity and low Kullback–Leibler (KL) divergence showing that our CVQBM learns distributions from given data well and generates data sampling from that distribution efficiently. We also discussed the experimental feasibility of our proposed CVQBM. Our method can be applied to a wide range of real-world problems by choosing an appropriate target distribution (corresponding to, e.g., SAR images, medical images, and risk management in finance). Moreover, our CVQBM is versatile and could be programmed to perform tasks beyond generation, such as anomaly detection.

SAR images↗