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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 OSTI2025

Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir

We investigate the effects of two naturally selected substitution and deletion (Δ) mutations, constituting part of the substrate binding subsites S2 and S4, on the structure, function, and inhibition of SARS CoV-2 main protease. Comparable to wild-type, MPro D48Y/ΔP168 undergoes N-terminal autoprocessing essential for stable dimer formation and mature-like catalytic activity. The structures are similar, but for an open active site conformation in MPro D48Y/ΔP168 and increased dynamics of the S2 helix, S5 loop, and the helical domain. Some dimer interface contacts exhibit shorter H bond distances corroborating the ~40-fold enhanced dimerization of the mutant although its thermal sensitivity to unfolding is 8 °C lower, relative to wild-type. ITC reveals a 3- and 5-fold decrease in binding affinity for nirmatrelvir and ensitrelvir, respectively, and similar GC373 affinity, to MPro D48Y/ΔP168 relative to wild-type. Structural differences in four inhibitor complexes of MPro D48Y/ΔP168 compared to wild-type are described. Consistent with enhanced dynamics, the S2 helix and S5 loop adopting a more open conformation appears to be a unique feature of MPro D48Y/ΔP168 both in the inhibitor-free and bound states. Our results suggest that mutational effects are compensated by changes in the conformational dynamics and thereby modulate N-terminal autoprocessing, K dimer , catalytic efficiency, and inhibitor binding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

The influence of nitrogen and nitrides on the structure and properties of proton irradiated ferritic/martensitic steel

The 12Cr1MoWV (wt%) ferritic/martensitic steel HT9 is a candidate material for fuel cladding in advanced nuclear reactors, such as the Versatile Test Reactor currently under development. As such, understanding the relationship between microstructure and mechanical properties in the context of irradiation environments for these steels is critical. N content, and more specifically interstitial N, has been hypothesized to be detrimental to irradiated properties at lower temperatures (less than 0.3T m ) to a total of 6 dpa; however, in this work at a dose of 1 dpa the irradiated microstructure was improved with added N, leading to less irradiation hardening. Three variants of HT9 were irradiated with 1.5 MeV protons to a dose of 1 dpa at 300°C. The HT9 variants included Low (10 ppm), Mid (190 ppm), and High (440 ppm) N alloys that were otherwise nearly identical. Changing the N content had a variety of effects on the irradiated defect structures. As N content increased, the average dislocation loop diameter decreased, while the number density of loops increased. Additionally, extensive Ni clustering was observed on dislocations and interfaces. The Mid and High N specimens exhibited significantly less hardening (ΔHV≃100) relative to the Low N specimen (ΔHV≃160). The decrease in hardening is attributed to vanadium carbonitride acting as a sink for Ni clusters that would otherwise form on dislocations. Under the irradiation conditions used, these results suggest increasing the N content in HT9 may have a desirable effect on the irradiated structure and properties at the dose studied, as well as the swelling resistance at higher doses. In other words, N content appears to be a powerful tool for tailoring the self-interstitial atom cluster mobility in F/M steels for different temperature and dose applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a ‘poor man’s crop’, finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21 st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Material Control & Accountancy for Molten Salt Reactors (FY2021 Report)

There is significant domestic and international interest, investment, and research and development momentum to pursue advanced nuclear reactor technologies. Molten salt reactor (MSR) concepts display the largest variability in fuel type and design features among the current advanced concepts. MSRs have been proposed with various core designs, sizes (power), and fuel cycles. Salt-fueled molten salt systems represent the only advanced reactor type with fuel that is not in a solid form during operation. These “liquid-fueled” MSRs are unique from perspectives of fuel fabrication, spent irradiated fuel and waste components, licensing, and material control and accountability (MC&A) including the potential of fissile material holdup. The liquid fuel salt is the defining distinction in comparison to other advanced reactors that propose TRI-structural ISOtropic particle fuel pebbles, various coolant options (e.g., molten salts or metals, high temperature gas), or small modular alternatives using solid fuel variants including both light water reactors and non-light water reactors. MSRs are appealing to the nuclear energy industry because of the diverse reactor characteristics they can support including various neutron energy spectra, fueling requirements, fuel cycles, and/or fuel utilization. However, because of the significant deviation and diversity of a salt-fueled system compared to traditional solid fuel light water-cooled reactors (LWRs), the history, regulatory licensing framework, modeling capabilities, and supporting engineering technology are either lacking or, in some cases, nonexistent. Therefore, the research community is actively supporting advanced MSR development on many of these fronts in particular to assist MSR vendors with licensing requirements. ORNL is leading the research and development of respective MC&A approaches for salt-fueled MSRs. This report summarizes the research performed at Oak Ridge National Laboratory (ORNL) under the US Department of Energy, Office of Nuclear Energy, Advanced Reactor Safeguards (ARS) program to investigate safeguards and security by design concepts, licensing and regulatory considerations, and dynamic system-level modeling to understand radioisotope concentrations for salt-fueled MSRs. The report builds upon the previous research and literature, identifies the MC&A challenges inherent to a salt-fueled MSR, reviews current regulatory frameworks for LWRs and their applicability towards salt-fueled MSRs, summarizes the status and progress of an MSR dynamic modeling tool, and discusses a prospective MC&A approach based on the Molten Salt Demonstration Reactor (MSDR) model.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
NASA NTRS1998

Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA

Bovine seminal ribonuclease (RNase) binds, melts, and (in the case of RNA) catalyzes the hydrolysis of double-stranded nucleic acid 30-fold better under physiological conditions than its pancreatic homologue, the well-known RNase A. Reported here are site-directed mutagenesis experiments that identify the sequence determinants of this enhanced catalytic activity. These experiments have been guided in part by experimental reconstructions of ancestral RNases from extinct organisms that were intermediates in the evolution of the RNase superfamily. It is shown that the enhanced interactions between bovine seminal RNase and double-stranded nucleic acid do not arise from the increased number of basic residues carried by the seminal enzyme. Rather, a combination of a dimeric structure and the introduction of two glycine residues at positions 38 and 111 on the periphery of the active site confers the full catalytic activity of bovine seminal RNase against duplex RNA. A structural model is presented to explain these data, the use of evolutionary reconstructions to guide protein engineering experiments is discussed, and a new variant of RNase A, A(Q28L K31C S32C D38G E111G), which contains all of the elements identified in these experiments as being important for duplex activity, is prepared. This is the most powerful catalyst within this subfamily yet observed, some 46-fold more active against duplex RNA than RNase A.

Non-NASA Center↗
NASA NTRS1996

Test Structures for Rapid Prototyping of Gas and Pressure Sensors

A multi-project ceramic substrate was used in developing a gas sensor and pressure sensor. The ceramic substrate cantained 36 chips with six variants including sensors, process control monitors, and an interconnect ship. Tha gas sensor is being developed as an air quality monitor and the pressure gauge as a barometer.

ceramics ceramic substrate gas sensor pressure sen↗
DOE OSTI2024

Efficient real space formalism for hybrid density functionals

We present an efficient real space formalism for hybrid exchange-correlation functionals in generalized Kohn–Sham density functional theory (DFT). In particular, we develop an efficient representation for any function of the real space finite-difference Laplacian matrix by leveraging its Kronecker product structure, thereby enabling the time to solution of associated linear systems to be highly competitive with the fast Fourier transform scheme while not imposing any restrictions on the boundary conditions. We implement this formalism for both the unscreened and range-separated variants of hybrid functionals. We verify its accuracy and efficiency through comparisons with established planewave codes for isolated as well as bulk systems. In particular, we demonstrate up to an order-of-magnitude speedup in time to solution for the real space method. We also apply the framework to study the structure of liquid water using ab initio molecular dynamics, where we find good agreement with the literature. Overall, the current formalism provides an avenue for efficient real-space DFT calculations with hybrid density functionals.

Chemistry↗
DOE OSTI2022

Structure of Offshore Low-Level Jet Turbulence and Implications to Mesoscale-to-Microscale Coupling

This paper explores realistic nonstationary atmospheric boundary layer (ABL) turbulence arising from nonstationarity at the mesoscale, particularly within offshore low-level jets with implications to offshore wind farms, using high-fidelity multiscale large-eddy simulations (LES). To this end, we analyzed the single-point turbulence statistical structure of a North-Atlantic offshore LLJ event simulated using high-resolution LES (AMR-Wind). The nonstationary LLJ is simulated using a mesoscale-to-microscale coupled (MMC) simulation procedure involving data assimilation of mesoscale velocity and temperature data from the Weather Research and Forecasting (WRF) model. Unlike the assimilation of mesoscale velocity data into the LES, the direct assimilation of temperature profiles had a strong impact on turbulence stratification, thereby causing erroneous predictions of turbulence both above and within the jet layer. Various approaches to mitigate this effect have resulted in multiple (four) variants of this MMC strategy. Outcomes from this work clearly show that the turbulence within the low-level jet is a strong function of the MMC approach as the turbulence structure within the low-level jet is dependent on the flux of residual turbulence from outside the jet, which in turn depends on the temperature forcing history. Additionally, the turbulence predicted by all these different methods (as well as the observation data) show similar deviations from equilibrium as evidenced by comparisons with idealized atmospheric turbulence structure obtained using the same numerical method. In general, we observe that the predicted LLJ turbulence tends to differ from canonical ABL turbulence with comparable shear. Particularly, the combination of shear and turbulence observed in such nonstationary low-level turbulence cannot be matched using equilibrium settings and therefore, represents a critical use-case for both testing and leveraging meso–micro coupling strategies.

17 WIND ENERGY↗
DOE OSTI2025

Allosteric inhibition of the IZUMO1–JUNO fertilization complex by the naturally occurring antisperm antibody OBF13

Sperm IZUMO1 binds to egg JUNO, and this interaction is essential for mammalian fertilization. Isolated from a female mouse immunized with syngeneic sperm, the antisperm antibody OBF13 recognizes IZUMO1 and inhibits murine fertilization. How OBF13 interferes with sperm–egg interactions was unknown. Here, we present the X-ray crystal structure of IZUMO1 in complex with OBF13. OBF13 binds to the apex of the four-helix domain of IZUMO1, distant from the JUNO-binding site. Our crystal structure of OBF13-bound IZUMO1 resembles apo-IZUMO1 and differs from the structure of IZUMO1 in complex with JUNO. We identify that OBF13 carries a low level of somatic hypermutation, and through deep mutational scanning, we engineer an affinity-enhanced OBF13 variant. This OBF13 variant single-chain fragment variable decreases the apparent affinity of IZUMO1 for membrane-bound murine JUNO and blocks the binding of acrosome-reacted sperm to eggs, thereby preventing fertilization. We propose allostery between the OBF13 epitope and the JUNO-binding site. OBF13 inhibits a conformational change in IZUMO1, preventing fusion-competent sperm from adhering to murine eggs during fertilization. Surprisingly, murine IZUMO1 binds to hamster JUNO with an affinity ~20-fold higher than to murine JUNO. The decreased affinity caused by OBF13 of murine IZUMO1 for hamster JUNO is sufficient for murine sperm to bind to and fuse with hamster eggs. Our studies provide a structural and mechanistic framework for species-specific, allosteric inhibition of IZUMO1 by a naturally occurring antisperm antibody and offer insights into the development of immunocontraceptives.

Science & Technology - Other Topics↗
DOE OSTI2023

Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains

Peptoids are a class of highly customizable biomimetic foldamers that retain properties from both proteins and polymers. It has been shown that peptoids can adopt peptide-like secondary structures through the careful selection of sidechain chemistries, but the underlying conformational landscapes that drive these assemblies at the molecular level remain poorly understood. Given the high flexibility of the peptoid backbone, it is essential that methods applied to study peptoid secondary structure formation possess the requisite sensitivity to discriminate between structurally similar yet energetically distinct microstates. In this work, a generalizable simulation scheme is used to robustly sample the complex folding landscape of various 12mer polypeptoids, resulting in a predictive model that links sidechain chemistry with preferential assembly into one of 12 accessible backbone motifs. Using a variant of the metadynamics sampling method, four peptoid dodecamers are simulated in water: sarcosine, N-(1-phenylmethyl)glycine (Npm), (S)-N-(1-phenylethyl)glycine (Nspe), and (R)-N-(1-phenylethyl)glycine (Nrpe)–to determine the underlying entropic and energetic impacts of hydrophobic and chiral peptoid sidechains on secondary structure formation. Our results indicate that the driving forces to assemble Nrpe and Nspe sequences into polyproline type-I helices in water are found to be enthalpically driven, with small benefits from an entropic gain for isomerization and steric strain due to the presence of the chiral center. The minor entropic gains from bulky chiral sidechains in Nrpe- and Nspe-containing peptoids can be explained through increased configurational entropy in the cis state. However, overall assembly into a helix is found to be overall entropically unfavorable. Furthermore, these results highlight the importance of considering the many various competing interactions in the rational design of peptoid secondary structure building blocks.

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

Catalytic Dynamic Kinetic Resolutions in Tandem to Construct Two-Axis Terphenyl Atropisomers

The defined structure of molecules bearing multiple stereogenic axes is of increasing relevance to materials science, pharmaceuticals, and catalysis. However, catalytic enantioselective approaches to control multiple stereogenic axes remain synthetically challenging. Here, we report the catalytic synthesis of two-axis terphenyl atropisomers, with complementary strategies to both chlorinated and brominated variants, formed with high diastereo- and enantioselectivity. The chemistry proceeds through a sequence of two distinct dynamic kinetic resolutions: first, an atroposelective ring opening of Bringmann-type lactones produces a product with one established axis of chirality, and second, a stereoselective arene halogenation delivers the product with the second axis of chirality established. In order to achieve these results, a class of Brønsted basic guanidinylated peptides, which catalyze an efficient atroposelective chlorination, is reported for the first time. In addition, a complementary bromination is reported, which also establishes the second stereogenic axis. These bromo-terphenyls are accessible following the discovery that chiral anion phase transfer catalysis by C 2 -symmetric phosphoric acids allows catalyst control in the second stereochemistry-determining event. Accordingly, we established the fully catalyst-controlled stereodivergent synthesis of all possible chlorinated stereoisomers while also demonstrating diastereodivergence in the brominated variants, with significant levels of enantioselectivity in all cases.

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

CaMn 3 IV O 4 Cubane Models of the Oxygen‐Evolving Complex: Spin Ground States S <9/2 and the Effect of Oxo Protonation

Abstract We report the single crystal XRD and MicroED structure, magnetic susceptibility, and EPR data of a series of CaMn 3 IV O 4 and YMn 3 IV O 4 complexes as structural and spectroscopic models of the cuboidal subunit of the oxygen‐evolving complex (OEC). The effect of changes in heterometal identity, cluster geometry, and bridging oxo protonation on the spin‐state structure was investigated. In contrast to previous computational models, we show that the spin ground state of CaMn 3 IV O 4 complexes and variants with protonated oxo moieties need not be S =9/2. Desymmetrization of the pseudo ‐ C 3 ‐symmetric Ca(Y)Mn 3 IV O 4 core leads to a lower S =5/2 spin ground state. The magnitude of the magnetic exchange coupling is attenuated upon oxo protonation, and an S =3/2 spin ground state is observed in CaMn 3 IV O 3 (OH). Our studies complement the observation that the interconversion between the low‐spin and high‐spin forms of the S 2 state is pH‐dependent, suggesting that the (de)protonation of bridging or terminal oxygen atoms in the OEC may be connected to spin‐state changes.

Lee, Heui Beom↗
DOE OSTI2021

CaMn 3 IV O 4 Cubane Models of the Oxygen‐Evolving Complex: Spin Ground States S <9/2 and the Effect of Oxo Protonation

Abstract We report the single crystal XRD and MicroED structure, magnetic susceptibility, and EPR data of a series of CaMn 3 IV O 4 and YMn 3 IV O 4 complexes as structural and spectroscopic models of the cuboidal subunit of the oxygen‐evolving complex (OEC). The effect of changes in heterometal identity, cluster geometry, and bridging oxo protonation on the spin‐state structure was investigated. In contrast to previous computational models, we show that the spin ground state of CaMn 3 IV O 4 complexes and variants with protonated oxo moieties need not be S =9/2. Desymmetrization of the pseudo ‐ C 3 ‐symmetric Ca(Y)Mn 3 IV O 4 core leads to a lower S =5/2 spin ground state. The magnitude of the magnetic exchange coupling is attenuated upon oxo protonation, and an S =3/2 spin ground state is observed in CaMn 3 IV O 3 (OH). Our studies complement the observation that the interconversion between the low‐spin and high‐spin forms of the S 2 state is pH‐dependent, suggesting that the (de)protonation of bridging or terminal oxygen atoms in the OEC may be connected to spin‐state changes.

Lee, Heui Beom↗
DOE OSTI2022

Structural and functional analysis of the human cone‐rod homeobox transcription factor

Abstract The cone‐rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone‐rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high‐resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small‐angle X‐ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX‐HD). We find that the CRX‐HD is a compact, globular monomer in solution that can specifically bind functional cis‐regulatory elements encoded upstream of retina‐specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease‐causing mutant protein variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The congenital APOA1 K107del mutation disrupts the lipid-free conformation of monomeric APOA1 and impairs oligomerization

Apolipoprotein A-I (APOA1) oligomerization is thought to be essential for high-density lipoprotein (HDL) formation and metabolism. Naturally occurring mutations can disrupt normal APOA1 folding and self-association, leading to dysfunctional HDL formation and cardiovascular disease. The congenital APOA1 variant p.K131del (APOA1 K107del ) has been associated with cardiovascular pathologies such as low HDL-cholesterol levels and aortic amyloidosis, and multiple studies indicate structural changes in APOA1 conformation underlie associated dysfunction. In the current study, we confirmed that APOA1 K107del exhibits no notable defect in lipid-binding. However, using polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC), we found that loss of lysine 107 resulted in a remarkable shift in the distribution of APOA1 oligomers with a much higher proportion of monomers present in APOA1 K107del compared to wild-type APOA1. Further investigation using quantitative cross-linking revealed a major disruption of interactions in helical regions reported to participate in domain swaps necessary for proper self-association. This structural disruption appears to impair N- and C-termini interactions and dynamics that lead to non-specific aggregation. In conclusion, these findings support the hypothesis that lysine 107 is critical for proper folding and self-association of lipid-free APOA1 which could impact HDL biogenesis.

APOA1 (p.K131del)↗
DOE OSTI2022

The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition

The ongoing SARS-CoV-2 pandemic continues to be a significant threat to global health. First reported in November 2021, the Omicron variant (B.1.1.529) is more transmissible and can evade immunity better than previous SARS-CoV-2 variants, fueling an unprecedented surge in cases. To produce functional proteins from its polyprotein, SARS-CoV-2 relies on the cysteine proteases Nsp3/papain-like protease (PL pro ) and Nsp5/main protease (M pro )/3C-like protease to cleave at three and more than 11 sites, respectively. Therefore, M pro and PL pro inhibitors are considered to be one of the most promising SARS-CoV-2 antivirals. On December 22, 2021, the Food and Drug Administration (FDA) issued an Emergency Use Authorization (EUA) for PAXLOVID, a ritonavir-boosted formulation of nirmatrelvir. Nirmatrelvir is a first-in-class orally bioavailable SARS-CoV-2 M pro inhibitor. Thus, the scientific community must vigilantly monitor potential mechanisms of drug resistance, especially because SARS-CoV-2 is naïve to M pro inhibitors. Mutations have been well identified in variants to this point. Notably, Omicron M pro (OM pro ) harbors a single mutation—P132H. Here, we characterized the enzymatic activity, drug inhibition, and structure of OM pro while evaluating the past and future implications of M pro mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Multiplexed profiling of transcriptional regulators in plant cells

Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear trans-elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.

Alamos, Simon↗