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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase

All herpesviruses encode a conserved DNA polymerase that is required for viral genome replication and serves as an important therapeutic target. Currently available herpesvirus therapies include nucleoside and non-nucleoside inhibitors (NNI) that target the DNA-bound state of herpesvirus polymerase and block replication. Here we report the ternary complex crystal structure of Herpes Simplex Virus 1 DNA polymerase bound to DNA and a 4-oxo-dihydroquinoline NNI, PNU-183792 (PNU), at 3.5 Å resolution. PNU bound at the polymerase active site, displacing the template strand and inducing a conformational shift of the fingers domain into an open state. These results demonstrate that PNU inhibits replication by blocking association of dNTP and stalling the enzyme in a catalytically incompetent conformation, ultimately acting as a nucleotide competing inhibitor (NCI). Sequence conservation of the NCI binding pocket further explains broad-spectrum activity while a direct interaction between PNU and residue V823 rationalizes why mutations at this position result in loss of inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Observations of Disequilibrium CO Chemistry in the Coldest Brown Dwarfs

Cold brown dwarfs are excellent analogs of widely separated, gas giant exoplanets, and provide insight into the potential atmospheric chemistry and physics we may encounter in objects to be discovered by future direct imaging surveys. We present a low-resolution, R ∼ 300, M-band spectroscopic sequence of seven brown dwarfs with effective temperatures between 750 and 250 K along with Jupiter. These spectra reveal disequilibrium abundances of carbon monoxide (CO) produced by atmospheric quenching. We use the eddy diffusion coefficient (K {sub zz}) to estimate the strength of vertical mixing in each object. The K {sub zz} values of cooler gaseous objects are close to their theoretical maximum, and warmer objects show weaker mixing, likely due to less efficient convective mixing in primarily radiative layers. The CO-derived K {sub zz} values imply that disequilibrium phosphine (PH{sub 3}) should be easily observable in all of the brown dwarfs, but none as yet show any evidence for PH{sub 3} absorption. We find that ammonia is relatively insensitive to atmospheric quenching at these effective temperatures. We are able to improve the fit to WISE 0855's M-band spectrum by including both CO and water clouds in the atmospheric model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Nanocrystal Geometry Governs Phase Transformation Pathways in Palladium Hydride

Pathways and structural dynamics of phase transformations impact performance of materials in energy and information storage technologies. Palladium hydride (PdH x ) nanocrystals are an ideal model system for studying solute-induced phase transformations, where elastic energy from lattice mismatch between α-PdH x and β-PdH x phases is often considered a key to determining the transformation pathways. α/β-PdH x interfacial elastic energy is affected by the confined geometry of a nanocrystal. However, how nanocrystal geometry influences phase transformation pathways is largely unknown. Using in situ liquid phase transmission electron microscopy, we directly visualize hydrogenation in Pd nanocrystals with two geometries, a nanocube and a hexagonal nanoplate. Both follow similar sequences of an initially curved nucleus, interface flattening, and reverse-stage nucleation; however, their evolving α/β-PdH x interfaces exhibit geometry-dependent crystallographic alignments. In nanocubes, {100}-aligned configurations conform to static elastic energy ordering, representing a pathway that maintains a local mechanical equilibrium, whereas nanoplates display both {110}- and {211}-aligned interfaces. Theoretical simulations show that geometry determines the accessibility of alternative phase transformation pathways as the system is driven far from equilibrium during hydrogenation. In conclusion, these findings identify geometry as a fundamental parameter for directing phase transformation pathways, offering design principles for accessing atypical configurations and improving properties of intercalation-based devices.

Lee, Daewon [Lawrence Berkeley National Laboratory↗
DOE OSTI2025

Blocking C-terminal processing of KRAS4b via a direct covalent attack on the CaaX-box cysteine

RAS is the most frequently mutated oncogene in cancer. RAS proteins show high sequence similarities in their G-domains but are significantly different in their C-terminal hypervariable regions (HVR). These regions interact with the cell membrane via lipid anchors that result from posttranslational modifications (PTM) of cysteine residues. KRAS4b is unique as it has only one cysteine that undergoes PTM, C185. Small molecule covalent modification of C185 would block any form of prenylation and subsequently inhibit attachment of KRAS4b to the cell membrane, blocking its biological activity. We translated this concept to the discovery and development of disulfide tethering screen hits into irreversible covalent modifiers of C185. These compounds inhibited proliferation of KRAS4b-driven mouse embryonic fibroblasts, but not cells driven by N-myristoylated KRAS4b that harbor a C185S mutation and are not dependent on C185 prenylation. Top–down proteomics was used to confirm target engagement in cells. These compounds bind in a pocket formed when the HVR folds back between helix 3 and 4 in the G-domain (HVR-α3-α4). This interaction can happen in the absence of small molecules as predicted by molecular dynamics simulations and is stabilized in the presence of C185 binders as confirmed by small-angle X-ray scattering and solution NMR. NOESY-HSQC, an NMR approach that measures internuclear distances of 6 Å or less, and structure analysis identified the critical residues and interactions that define the HVR-α3-α4 pocket. Further development of compounds that bind to this pocket could be the basis of a new approach to targeting KRAS cancers.

C185↗
DOE OSTI2023

Rock Valley Direct Comparison Relocation Working Group Location Results and Recommendations

Work accomplished: Collected and compared historic data for the 1993 Rock Valley earthquake sequence; Compared preliminary and prior location work from different location algorithms, phase pick sets, station constellations, and velocity models; Selected a common set of stations that could be used across all location methods for consistency; Reviewed 8 different sets of phase picks and converged on a single, reviewed set of picks for all common stations; Evaluated four pre-existing regional velocity models and incorporated new and preliminary results for five new velocity models that provide information on the very shallow (< 2km) structure near station RTPP; Compared location results from different methods while using the common sets of picks, stations, and velocity models

58 GEOSCIENCES↗
DOE OSTI2026

Methods for safely sharing dual-use genetic data

Background: Some genetic data has dual-use potential. Sharing pathogen data has shown tremendous value. For example therapeutic development and lineage tracking during the COVID pandemic. This data sharing is complicated by the fact that these data have the potential to be used for harm. The genome sequence of a pathogen can be used to enable malicious genetic engineering approaches or to recreate the pathogen from synthetic DNA. Standard data security methods can be applied to genetic data, but when data is shared between institutions, ensuring appropriate security can be difficult. Sensitive data that is shared internationally among a wide array of institutions can be especially difficult to control. Methods for securely storing and sharing genetic data with potential for dual-use are needed to mitigate this potential harm.Results: Here we propose new methods that allow genetic data to be shared in a data format that prevents a nefarious actor from accessing sensitive aspects of the data. Our methods obfuscate raw sequence data by pooling reads from different samples. This approach can ensure that data is secure while stored and during electronic transfer. We demonstrate that by pooling raw sequence data from multiple samples of the same organism, the ability to fully reconstruct any individual sample is prevented. In the pooled data, most genomic information remains, but reads or mutations cannot be directly attributed to any individual sample. To further restrict access to information, regions of a genome can be removed from the reads.Conclusion: Our methods obscure genomic information within raw sequence reads. This method can allow genetic data to be stored and shared while preventing a nefarious actor from being able to perfectly reconstruct an organism. Broad-scale sequence information remains, while fine scale details about specific samples are difficult or impossible to reconstruct. Our software is available at https://github.com/Geneinfosec-Inc/ReadMixer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Global overview and major challenges of host prediction methods for uncultivated phages

Bacterial communities play critical roles across all of Earth’s biomes, affecting human health and global ecosystem functioning. They do so under strong constraints exerted by viruses, i.e., bacteriophages or “phages”. Phages can reshape bacterial communities’ structure, influence long-term evolution of bacterial populations, and alter host cell metabolism during infection. Metagenomics approaches, i.e., shotgun sequencing of environmental DNA or RNA, recently enabled large-scale exploration of phage genomic diversity, yielding several millions of phage genomes now to be further analyzed and characterized. One major challenge however is the lack of direct host information for these phages. Several methods and tools have been proposed to bioinformatically predict the potential host(s) of uncultivated phages based only on genome sequence information. Here we review these different approaches and highlight their distinct strengths and limitations. We also outline complementary experimental assays which are being proposed to validate and refine these bioinformatic predictions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Epigenetic Footprints of CRISPR/Cas9-Mediated Genome Editing in Plants

CRISPR/Cas9 has been widely applied to various plant species accelerating the pace of plant genome editing and precision breeding in crops. Unintended effects beyond off-target nucleotide mutations are still somewhat unexplored. We investigated the degree and patterns of epigenetic changes after gene editing. We examined changes in DNA methylation in genome-edited promoters of naturally hypermethylated genes (AT1G72350 and AT1G09970) and hypomethylated genes (AT3G17320 and AT5G28770) from Arabidopsis. Transgenic plants were developed via Agrobacterium-mediated floral dip transformation. Homozygous edited lines were selected from segregated T2 plants by an in vitro digestion assay using ribonucleoprotein complex. Bisulfite sequencing comparisons were made between paired groups of edited and non-edited plants to identify changes in DNA methylation of the targeted loci. We found that directed mutagenesis via CRISPR/Cas9 resulted in no unintended morphological or epigenetic alterations. Phenotypes of wild-type, transgenic empty vector, and transgenic edited plants were similar. Epigenetic profiles revealed that methylation patterns of promoter regions flanking target sequences were identical among wild-type, transgenic empty vector, and transgenic edited plants. There was no effect of mutation type on epigenetic status. We also evaluated off-target mutagenesis effects in the edited plants. Potential off-target sites containing up to 4-bp mismatch of each target were sequenced. No off-target mutations were detected in candidate sites. Our results showed that CRISPR/Cas9 did not leave an epigenetic footprint on either the immediate gene-edited DNA and flanking DNA or introduce off-target mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterization of microstructure and residual stress following the friction stir welding of dissimilar aluminum alloys

Friction-stir-welding (FSW) has gained importance as an effective way to join dissimilar materials due to its solid-state nature. However, FSW produces substantial residual stresses in aluminum welding, often deteriorating the component's structural performance and reliability. In the current study, the d-spacing (inter-atomic distance) of several locations on a battery tray and stress-free reference samples are measured with neutron diffraction to calculate the residual stresses in a lap 6061 to A365 dissimilar friction-stir-weld. Furthermore, the present study connects the measured residual stress to microstructure properties through electron backscatter diffraction (EBSD) and optical microscopy analyses. The EBSD results indicate that the FSW operation affects the grains’ orientation, thereby producing location-specific directionally varying elasticity across the weldment. Further, this varied elasticity creates unique d-spacing profiles even in the stress-free material. Additionally, the resulting stressed and stress-free d-spacing profiles show dependencies on the FSW tool geometry, traverse direction, and rotational direction. Lastly, this study suggests that the final component residual stress can be influenced by the sequence of multi-pass welds contributing to a rise in temperature in the presence of a completed weld relaxing its residual stress.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Out-of-time-order correlators bridge classical transport and quantum dynamics

The out-of-time-order correlator (OTOC) has emerged as a central tool for quantifying decoherence across wide-ranging physical platforms. Here, we demonstrate its direct measurement in a classical ensemble using nuclear magnetic resonance with a modulated gradient spin echo sequence and extend the method into a multidimensional correlation to track exchange phenomena. Position is encoded through magnetic field gradients and momentum through the velocity autocorrelation function, enabling experimental access to OTOCs for proton motion confined within the self-similar lattice of the metal–organic framework MOF-808. Here, water confined to specified geometries within the MOF pores gives rise to spatially distinct diffusive eigenmodes with characteristic relative entropies. We demonstrate that periodic radio frequency driving combined with gradient modulation yields entropy evolution through the selection of distinct diffusion modes. Frequency-resolved diffusion spectra connect these entropy dynamics to classical heat exchange laws, revealing how operational features of quantum systems are mirrored in confined, macroscopic spin ensembles.

Fricke, Sophia N. [University of California, Berke↗
DOE OSTI2022

High-precision inversion of dynamic radiography using hydrodynamic features

While radiography is routinely used to probe complex, evolving density fields in research areas ranging from materials science to shock physics to inertial confinement fusion and other national security applications, complications resulting from noise, scatter, complex beam dynamics, etc. prevent current methods of reconstructing density from being accurate enough to identify the underlying physics with sufficient confidence. In this work, we show that using only features that are robustly identifiable in radiographs and combining them with the underlying hydrodynamic equations of motion using a machine learning approach of a conditional generative adversarial network (cGAN) provides a new and effective approach to determine density fields from a dynamic sequence of radiographs. In particular, we demonstrate the ability of this method to outperform a traditional, direct radiograph to density reconstruction in the presence of scatter, even when relatively small amounts of scatter are present. Our experiments on synthetic data show that the approach can produce high quality, robust reconstructions. We also show that the distance (in feature space) between a testing radiograph and the training set can serve as a diagnostic of the accuracy of the reconstruction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

xSDK-batched Subcontract - Ginkgo Batched Iterative Solver Development (Final Report)

Iterative solvers are fundamentally different from direct solvers in terms of execution as they generally do not execute a pre-defined sequence of operations or steps, but adapt the number of iterations to the specific problem and the preset solution quality. Generally, the adaptation of the iteration count to the problem is realized by monitoring the solver convergence and stopping the iteration process once the monitored metric, e.g., the residual norm, hits a pre-defined threshold. When addressing a set of problems with different properties, it is necessary to monitor the threshold for each problem individually and break up the SIMD execution style to avoid excess iterations for “easier” problems. Ginkgo integrates a simple but customizable stopping criterion for the residual norm and generally uses a pre-defined (relative or absolute) residual norm as the stopping criterion. In order to avoid the overhead of launching a kernel at every iteration, the iteration convergence and iteration control is part of the solver kernel. Each thread maintains its own copy of the iteration count.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A Comprehensive Study of the Impact of Inverter-Based Resource (IBR) Modeling and Control on Protection Relay Elements

Inverter-based resources (IBRs) exhibit fault responses that differ significantly from those of synchronous generators, which can challenge the reliable operation of many commonly used power system protection elements. The fault response of IBRs is primarily influenced by their control algorithms and configurations, but the impact of these controls on protection relays is not yet fully understood. This presentation provides a comprehensive study of how IBR modeling and controls affect transmission line protection. Key modeling and control aspects include the DC source, inverter model, power level control, current control, and current limiting. The study reveals that certain aspects - such as the type of DC source (battery, PV, or hybrid), inverter model (average vs. switching), and power level control methods (PQ dispatch vs. Vdc-Vac control for grid-following IBRs, and droop vs. VSM for grid-forming IBRs) - do not significantly affect relay response. However, faster control loops, such as current control and current limiting, do influence the relay behavior. Additionally, the study explores the effects of other factors, including momentary cessation, operating points, fast/slow current responses, and grid strength on relay performance. Finally, the study offers recommendations for both IBR and protection engineers to improve IBR fault response and enhance the reliability of protection systems.

14 SOLAR ENERGY↗
DOE OSTI2021

Stamping Nanoparticles onto the Electrode for Rapid Electrochemical Analysis in Microfluidics

Electrochemical analysis is an efficient way to study various materials. However, nanoparticles are challenging due to the difficulty in fabricating a uniform electrode containing nanoparticles. We developed novel approaches to incorporate nanoparticles as a working electrode (WE) in a three-electrode microfluidic electrochemical cell. Specifically, conductive epoxy was used as a medium for direct application of nanoparticles onto the electrode surface. Three approaches in this work were illustrated, including sequence stamping, mix stamping, and droplet stamping. Shadow masking was used to form the conductive structure in the WE surface on a thin silicon nitride (SiN) membrane. Two types of nanomaterials, namely cerium oxide (CeO2) and graphite, were chosen as representative nanoparticles. The as-fabricated electrodes with attached particles were characterized using atomic force microscopy (AFM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Electrochemical analysis was performed to verify the feasibility of these nanoparticles as electrodes. Nanomaterials can be quickly assessed for their electrochemical properties using these new electrode fabrication methods in a microfluidic cell, offering a passport for rapid nanomaterial electrochemical analysis in the future.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Extremely Metal-poor Galaxies in DESI DR1: Connections to Galaxies in the Early Universe

Extremely metal-poor galaxies (XMPGs), defined as having metallicities below 10% of the solar value, are considered possible local analogs to primordial systems and offer a unique window into early galaxy evolution. This study presents a large-scale search for XMPGs using data from the Dark Energy Spectroscopic Instrument Data Release 1, systematically evaluating their resemblance to high-redshift galaxies. From a parent sample of more than 14 million galaxies, we identify 662 (556 new) confirmed XMPGs and 763 (666 new) high-quality candidates via the direct T$_{e}$ method. Our results reveal that XMPGs follow a distinct star-forming main sequence (SFMS) that is elevated and shallower than that of the comparing star-forming galaxies. Notably, at higher stellar masses (M$_{⋆}$ > 10$^{7.5}$M$_{⊙}$), the XMPG SFMS converges with the sequence observed in high-redshift galaxies by the James Webb Space Telescope, indicating that mature XMPGs sustain star formation rates comparable to their primordial counterparts. Furthermore, XMPGs consistently deviate below the local fundamental metallicity relation, mirroring high-redshift galaxy behavior. These findings demonstrate that XMPGs not only exhibit low metallicities but also preserve scaling relations characteristic of the early Universe, confirming their potential value as local laboratories for studying early galaxy formation processes.

Sui, Jipeng [Beijing Observ.; Beijing, GUCAS] (ORC↗
DOE OSTI2025

Automated Direct Perturbation Calculations with SCALE TSUNAMI [Abstract]

In nuclear criticality safety analysis, the sensitivity of the eigenvalue keff to uncertainties in nuclear data and its evaluation are crucial. The TSUNAMI sequences within the SCALE code system offer users various options with both multigroup (MG) and continuous-energy (CE) 3D Monte Carlo (MC) transport capabilities for calculating keff sensitivity coefficients and storing them in a sensitivity data file (SDF). Each methodology available in TSUNAMI offers distinct advantages and limitations, and its effectiveness can vary based on the specific problem being solved. As a best practice, practitioners typically use the direct perturbation (DP) method as a confirmatory step alongside their sensitivity calculations to verify the accuracy of the sensitivity data generated. In this process, DP calculations are usually performed on select nuclides, those considered most important for validating their total sensitivities. However, because of code limitations, analysts use a workaround method when conducting DP calculations for a single nuclide: rather than perturbing the nuclide's microscopic cross section, an equivalent number density for this nuclide is calculated to reflect the effect of a change in the macroscopic cross section due to a perturbation in the microscopic cross section. The current approach requires rerunning the CSAS criticality calculation several times with model changes. Although this method can yield results with acceptable accuracy, it is labor-intensive and prone to errors.

AZURE: SAMMY↗
DOE OSTI2024

Observational evidence for Criegee intermediate oligomerization reactions relevant to aerosol formation in the troposphere

Criegee intermediates are reactive intermediates that are implicated in transforming the composition of Earth’s troposphere and in the formation of secondary organic aerosol, impacting Earth’s radiation balance, air quality and human health. Yet, direct identification of their signatures in the field remains elusive. Here, from particulate and gas-phase mass-spectrometric measurements in the Amazon rainforest, we identify sequences of masses consistent with the expected signatures of oligomerization of the CH 2 OO Criegee intermediate, a process implicated in ozonolysis-driven aerosol formation. In this study, we assess the potential contributions of oligomerization through laboratory ozonolysis experiments, direct kinetic studies of Criegee intermediate reactions, and high-level theoretical calculations. Global atmospheric models built on these kinetics results indicate that Criegee intermediate chemistry may play a larger role in altering the composition of Earth’s troposphere than is captured in current atmospheric models, especially in areas of high humidity. However, the models still capture only a relatively small fraction of the observed signatures, suggesting considerable underestimates of Criegee intermediate concentrations and reactivity and/or the dominance of other, presently uncharacterized, oxidation mechanisms. Resolving the remaining uncertainties in emission inventories and the effects of atmospheric water vapour on key chemical reactions will be required to definitively assess the role of Criegee intermediate oligomerization reactions.

58 GEOSCIENCES↗
DOE OSTI2022

Janus Monolayers for Ultrafast and Directional Charge Transfer in Transition Metal Dichalcogenide Heterostructures

Charge transfer properties of van der Waals heterostructures formed by Janus and regular transition metal dichalcogenide monolayers are studied by time-resolved pump–probe measurements and photoluminescence spectroscopy. Measurements of electron and hole transfer in three heterostructures with atomic layer sequences of S–W–Se/S–W–S, Se–W–S/S–W–S, and S–W–Se/Se–W–Se reveal that charge transfer from regular to Janus monolayers is ultrafast regardless of the direction of the built-in electric field of the Janus monolayer (Janus field). However, the charge transfer from Janus to regular layers is directional and controlled by the Janus field. When the current direction is along the field, the charge transfer is ultrafast and efficient, while the field blocks the charge transfer with an opposite charge current direction. The transferred carriers form interlayer excitons with extended lifetimes compared to the intralayer excitons. The demonstrated ultrafast and directional charge transfer between Janus and regular TMD layers shows that the Janus structures can be used to make 2D heterostructures with efficient and directional charge transfer properties.

36 MATERIALS SCIENCE↗