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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Abstract Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Local cation order and ferrimagnetism in compositionally complex spinel ferrites

We present an exploration of a family of compositionally complex cubic spinel ferrites featuring combinations of Mg, Fe, Co, Ni, Cu, Mn, and Zn cations, systematically investigating the average and local atomic structures, chemical short-range order, magnetic spin configurations, and magnetic properties. All compositions result in ferrimagnetic average structures with extremely similar local bonding environments; however, the samples display varying degrees of cation inversion and, therefore, differing apparent bulk magnetization. Additionally, first-order reversal curve analysis of the magnetic reversal behavior indicates varying degrees of magnetic ordering and interactions, including potentially local frustration. Finally, reverse Monte Carlo modeling of the spin orientation demonstrates a relationship between the degree of cation inversion and the spin collinearity. Collectively, these observations correlate with differences in synthesis procedures. This work provides a framework for understanding magnetic behavior reported for “high-entropy spinels,” revealing many are likely compositionally complex oxides with differing degrees of chemical short-range order—not meeting the community established criteria for high or medium entropy compounds. Moreover, this work highlights the importance of reporting complete sample processing histories and investigating local to long-range atomic arrangements when evaluating potential entropic mixing effects and assumed property correlations in high entropy materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

Science & Technology - Other Topics↗
DOE OSTI2024

Noncoplanar magnetic order in the breathing kagome lattice compound Pb⁡(OF)⁢Cu 3 ⁢(SeO 3 ) 2⁢ (NO 3 )

We report a comprehensive study investigating the magnetic ordering properties of the quasi-two-dimensional breathing kagome lattice compound Pb⁡(OF)⁢Cu 3 ⁢(SeO 3 ) 2 ⁢(NO 3 ) using neutron diffraction and thermodynamic measurements. A long-range magnetic order emerges below the Néel temperature, T N = 18K, characterized by a propagating vector k = (0,0,1.5). Refinement analysis reveals that the copper moments display a noncoplanar arrangement, with the c components parallelly aligned within the breathing kagome plane and antiparallelly aligned between the layers. In-plane moment components form a chiral “tail-chase” structure. The magnetic order is quickly suppressed under moderate external fields applied both within and perpendicular to the kagome plane. Potential magnetic interactions that may be associated with the noncoplanar chiral magnetic structure are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Local Markers for Crystalline Topology

Over the last few years, crystalline topology has been used in photonic crystals to realize edge- and corner-localized states that enhance light-matter interactions for potential device applications. However, the band-theoretic approaches currently used to classify bulk topological crystalline phases cannot predict the existence, localization, or spectral isolation of any resulting boundary-localized modes. While interfaces between materials in different crystalline phases must have topological states at some energy, these states need not appear within the band gap, and thus may not be useful for applications. Here, we derive a class of local markers for identifying material topology due to crystalline symmetries, as well as a corresponding measure of topological protection. As our real-space-based approach is inherently local, it immediately reveals the existence and robustness of topological boundary-localized states, yielding a predictive framework for designing topological crystalline heterostructures. In conclusion, beyond enabling the optimization of device geometries, we anticipate that our framework will also provide a route forward to deriving local markers for other classes of topology that are reliant upon spatial symmetries.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Origin of surface and subband states at the InAs(111)A surface

The atomic structure of surfaces and interfaces plays a vital role in the electronic quality and properties of quantum devices. The interplay between the surface and confined bulk subband states in terms of their susceptibility has been investigated in relation to crystal defects on an InAs(111)A-(2×2) reconstructed surface, using low-temperature scanning tunneling microscopy and spectroscopy. We measure the two-dimensional quantized subband states arising from the confined potential imposed by downward bending of the conduction band edge. Furthermore, we show evidence of the existence of surface Bloch states within the confined bulk band gap projected on the surface spectrum which have originated from the surface reconstruction. As expected, larger confined bulk band gaps at the surface and conduction band offset are measured to be 0.58 and 0.31 eV, respectively. Here we further show the scattering of these quantum states at different surface defects and demonstrate that surface states are more susceptible to the defect potential when compared with the corresponding subband states. This apparent contrast follows from the length scale at which these defect potentials actively interact on or near the surface. Our observed experimental results are supported by empirical tight-binding simulations for the subband states and first-principles density functional theory simulations for the surface states present on the surface.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Synergistic Effects of a Chalkophore, Methanobactin, on Microbial Methylation of Mercury

Microbial production of the neurotoxin methylmercury (MeHg) is a significant health and environmental concern, as it can bioaccumulate and biomagnify in the food web. A chalkophore or a copper-binding compound, termed methanobactin (MB), has been shown to form strong complexes with mercury [as Hg(II)] and also enables some methanotrophs to degrade MeHg. It is unknown, however, if Hg(II) binding with MB can also impede Hg(II) methylation by other microbes. Contrary to expectations, MB produced by the methanotroph Methylosinus trichosporium OB3b (OB3b-MB) enhanced the rate and efficiency of Hg(II) methylation more than that observed with thiol compounds (such as cysteine) by the mercury-methylating bacteria Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. Compared to no-MB controls, OB3b-MB decreased the rates of Hg(II) sorption and internalization, but increased methylation by 5- to 7-fold, suggesting that Hg(II) complexation with OB3b-MB facilitated exchange and internal transfer of Hg(II) to the HgcAB proteins required for methylation. Conversely, addition of excess amounts of OB3b-MB or a different form of MB from Methylocystis strain SB2 (SB2-MB) inhibited Hg(II) methylation, likely due to greater binding of Hg(II). Collectively, our results underscore the complex roles of microbial exogenous metal-scavenging compounds in controlling net production and bioaccumulation of MeHg in the environment. Some anaerobic microorganisms convert inorganic mercury (Hg) into the neurotoxin methylmercury, which can bioaccumulate and biomagnify in the food web. While the genetic basis of microbial mercury methylation is known, factors that control net methylmercury production in the environment are still poorly understood. Here, it is shown that mercury methylation can be substantially enhanced by one form of an exogenous copper-binding compound (methanobactin) produced by some methanotrophs, but not by another. This novel finding illustrates that complex interactions exist between microbes and that these interactions can potentially affect the net production of methylmercury in situ .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

BRCore: an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fitting

Identifying core taxa in microbial ecology highlights groups likely to participate in a broad range of potential ecological interactions. Here, we present BRCore, an R package to identify core taxa using abundance-occupancy distributions and beta-diversity contributions across ecological niches, and predict stochastic and deterministic taxa.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

EMC3 regulates trafficking and pulmonary toxicity of the SFTPC I73T mutation associated with interstitial lung disease

The most common mutation in surfactant protein C gene (SFTPC), SFTPC I73T , causes interstitial lung disease with few therapeutic options. We previously demonstrated that EMC3, an important component of the multiprotein endoplasmic reticulum membrane complex (EMC), is required for surfactant homeostasis in alveolar type 2 epithelial (AT2) cells at birth. In the present study, we investigated the role of EMC3 in the control of SFTPC I73T metabolism and its associated alveolar dysfunction. Using a knock-in mouse model phenocopying the I73T mutation, we demonstrated that conditional deletion of Emc3 in AT2 cells rescued alveolar remodeling/simplification defects in neonatal and adult mice. Proteomic analysis revealed that Emc3 depletion reversed the disruption of vesicle trafficking pathways and rescued the mitochondrial dysfunction associated with I73T mutation. Affinity mass spectrometry analysis identified potential EMC3 interacting proteins in lung AT2 cells, including Valosin Containing Protein (VCP) and its interactors. Treatment of Sftpc I73T knock-in mice and SFTPC I73T expressing iAT2 cells derived from SFTPC I73T patient-specific iPSCs with the specific VCP inhibitor CB5083 restored alveolar structure and SFTPC I73T trafficking respectively. Taken together, the present work identifies the EMC complex and VCP in the metabolism of the disease-associated SFTPC I73T mutant, providing novel therapeutical targets for SFTPC I73T -associated interstitial lung disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A polypeptide model for toxic aberrant proteins induced by aminoglycoside antibiotics

Aminoglycoside antibiotics interfere with the selection of cognate tRNAs during translation, resulting in the synthesis of aberrant proteins that are the ultimate cause of cell death. However, the toxic potential of aberrant proteins and how they avoid degradation by the cell’s protein quality control (QC) machinery are not understood. Here we report that levels of the heat shock (HS) transcription factor σ32 increased sharply following exposure of Escherichia coli to the aminoglycoside kanamycin (Kan), suggesting that at least some of the aberrant proteins synthesized in these cells were recognized as substrates by DnaK, a molecular chaperone that regulates the HS response, the major protein QC pathway in bacteria. To further investigate aberrant protein toxic potential and interaction with cell QC factors, we studied an acutely toxic 48-residue polypeptide (ARF48) that is encoded by an alternate reading frame in a plant cDNA. As occurred in cells exposed to Kan, σ32 levels were strongly elevated following ARF48 expression, suggesting that ARF48 was recognized as a substrate by DnaK. Paradoxically, an internal 10-residue region that was tightly bound by DnaK in vitro also was required for the ARF48 toxic effect. Despite the increased levels of σ32, levels of several HS proteins were unchanged following ARF48 expression, suggesting that the HS response had been aborted. Nucleoids were condensed and cell permeability increased rapidly following ARF48 expression, together suggesting that ARF48 disrupts DNA-membrane interactions that could be required for efficient gene expression. Our results are consistent with earlier studies showing that aberrant proteins induced by aminoglycoside antibiotics disrupt cell membrane integrity. Insights into the mechanism for this effect could be gained by further study of the ARF48 model system.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Atomistic Study of the Plastic Deformation of Transition Metals and High Entropy Alloys (Final Report)

The overarching goal of the research performed in the studies supported by the DOE Basic Energy Sciences has been investigation of mechanical properties of materials employed in technologies related to energy production and conversion using atomic level computer modeling. The materials studied are body-centered-cubic (BCC) transition metals, including α-iron, their alloys and most recently also compositionally complex, so called high entropy alloys (HEAs), which are believed to become future materials in high temperature applications. The goal of the research has been to achieve atomic level understanding of the deformation and fracture of these materials starting from the electronic structure, coarse grain the material energetics into potentials describing interaction between atoms and proceed via atomistic modeling and mesoscopic models to investigation of the glide of dislocations and thus advance the theory of plastic deformation of studied materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

2020 State of the Science Report, Chapter 2: Marine Renewable Energy: Environmental Effects and Monitoring Strategies

As we learn more about interactions between marine renewable energy (MRE) devices, the animals and habitats near them, and the oceanographic processes with which they interact, we need to clarify the language used to discuss those interactions. For example, if an MRE device or system negatively affected a number of animals, we could say that the device or the system of foundations, anchors, and mooring lines had an impact on the population, and take steps to avoid the impact or, in some cases, mitigate the impact. However, at this stage in MRE development, there are few, if any, cases in which a negative impact has been observed or measured. Instead, we are developing the building blocks that support investigations of interactions and potential impacts. https://tethys.pnnl.gov/publications/state-of-the-science-2020-chapter-2-environmental-effects

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

2020 State of the Science Report, Chapter 5: Risk to Animals from Electromagnetic Fields Emitted by Electric Cables and Marine Renewable Energy Devices

Interest in the potential effects of anthropogenic electromagnetic fields (EMFs) within the marine environment has increased in recent years, in part as a result of advanced knowledge gained from conducting dedicated research studies. To understand and interpret the potential environmental interactions of marine renewable energy (MRE)-related EMF emissions, it is necessary to consider the source of the EMFs and address the source within the context of the knowledge about the electro- and magneto-sensitivity of marine species. https://tethys.pnnl.gov/publications/state-of-the-science-2020-chapter-5-electromagnetic-fields

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

LDRD23-0184: Resilience and Hazard Risk Assessment to Prioritize Security Operations for Decisions and Impacts (RHAPSODI)

Recent examples provide a significant concern for the resilience of the U.S. electric grid and represent a need for enhanced decision-making to address an increasingly wide range of complex system interactions and potential consequences. In response, this LDRD project produced a proof-of-concept evaluation called the Resilience and Hazard Assessment to Prioritize Security Operations for Decisions and Impacts (RHAPSODI) methodology as an agile and flexible analytic framework capable of addressing multiple, diverse threats to desired electric grid performance. After empirically grounding needs for the future of U.S. electric grid resilience, this project employed the systems-theoretic process analysis (STPA) to develop a systems engineering risk model. The results of a completed feasibility study of a notional high voltage transmission system demonstrate an improved ability to incorporate both spatial (e.g., geographically distributed) and temporal (e.g., dynamic and time-dependent) elements of security risk to the gird. The success of this LDRD project provides the foundation for further evolution of the systems engineering risk model for the grid; derivation of quantitative approaches to evaluate risk and resilience performance; facilitation of agile experimenting and grid sensitivity to a range of vulnerabilities; and development of tools to assist decision-makers in enhancing U.S. electrical grid resilience.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Electric Vehicle Charging Data Falsification Attacks Utilizing Behavioral Models

A charging station (CS) and its associated electric vehicle supply equipment (EVSE) and charging electric vehicle (EV) interactions are potential targets for data falsification attacks since CSs are typically unmanned public facilities that are connected to the internet and EVs incorporate the vulnerable CAN bus network, which are both susceptible to remote attacks. The research question being addressed is how is the EV owner and CS negatively affected by CAN bus EV battery current sensor and battery temperature sensor data falsification attacks. Negative effects include economic losses from reduced life span of the battery, battery thermal runaway and fire (and potential loss of surrounding structure), and reduced utilization of the CS due to delayed departure time (longer charging times).

25 ENERGY STORAGE↗