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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors

Abstract Lung cancer is frequently caused by activating mutations in the epidermal growth factor receptor (EGFR). Allosteric EGFR inhibitors offer promise as the next generation of therapeutics, as they are unaffected by common ATP-site resistance mutations and synergize with the drug osimertinib. Here, we examine combinations of ATP-competitive and allosteric inhibitors to better understand the molecular basis for synergy. We identify a subset of irreversible EGFR inhibitors that display positive binding cooperativity and synergy with the allosteric inhibitor JBJ-04-125-02 in several EGFR variants. Structural analysis of these complexes reveals conformational changes occur mainly in the phosphate-binding loop (P-loop). Mutation of F723 in the P-loop reduces cooperative binding and synergy, supporting a mechanism in which F723-mediated contacts between the P-loop and the allosteric inhibitor are critical for synergy. These structural and mechanistic insights will aid in the identification and development of additional inhibitor combinations with potential clinical value.

Beyett, Tyler S. (ORCID:0000000155097004)↗
DOE OSTI2025

Revealing the evolution of order in materials microstructures using multi-modal computer vision

The development of high-performance materials for microelectronics, energy storage, and extreme environments depends on our ability to describe and direct property-defining microstructural order. Our present understanding is typically derived from laborious manual analysis of imaging and spectroscopy data, which is difficult to scale, challenging to reproduce, and lacks the ability to reveal latent associations needed for mechanistic models. Here, we demonstrate a multi-modal machine learning (ML) approach to describe order from electron microscopy analysis of the complex oxide La 1−x Sr x FeO 3 . We construct a hybrid pipeline based on fully and semi-supervised classification, allowing us to evaluate both the characteristics of each data modality and the value each modality adds to the ensemble. We observe distinct differences in the performance of uni- and multi-modal models, from which we draw general lessons in describing crystal order using computer vision.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-$α$-amino acids in vitro and in vivo

The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Naturally ornate RNA-only complexes revealed by cryo-EM

The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron microscopy (cryo-EM). GOLLD (Giant, Ornate, Lake- and Lactobacillales-Derived), ROOL (Rumen-Originating, Ornate, Large) and OLE (Ornate Large Extremophilic) RNAs form homo-oligomeric complexes whose stoichiometries are retained at lower concentrations than measured in cells. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome, each empty except for a disordered loop. Extensive intramolecular and intermolecular A-minor interactions, kissing loops, an unusual A–A helix and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Magnetic and dielectric property control in the multivalent nanoscale perovskite Eu 0.5 Ba 0.5 TiO 3

We report nanoscale Eu 0.5 Ba 0.5 TiO 3 , a multiferroic in the bulk and candidate in the search to quantify the electric dipole moment of the electron. Eu 0.5 Ba 0.5 TiO 3 , in the form of nanoparticles and other nanostructures is interesting for nanocomposite integration, biomedical imaging and fundamental research, based upon the prospect of polarizability, f-orbital magnetism and tunable optical/radio luminescence. We developed a [non-hydrolytic]sol–[H 2 O-activated]gel route, derived from in-house metallic Ba (s) /Eu (s) alkoxide precursors and Ti{(OCH(CH 3 ) 2 } 4 . Two distinct nanoscale compounds of Ba:Ti:Eu with the parent perovskite crystal structure were produced, with variable dielectric, magnetic and optical properties, based on altering the oxidizing/reducing conditions. Eu 0.5 Ba 0.5 TiO 3 prepared under air/O 2 atmospheres produced a spherical core–shell nanostructure (30–35 nm), with perovskite Eu 0.5 Ba 0.5 TiO 3 nanocrystal core-insulating oxide shell layer (~3 nm), presumed a pre-pyrochlore layer abundant with Eu 3+ . Fluorescence spectroscopy shows a high intensity 5 D 0 → 7 F 2 transition at 622 nm and strong red fluorescence. The core/shell structure demonstrated excellent capacitive properties: assembly into dielectric thin films gave low conductivity (2133 GΩ mm -1 ) and an extremely stable, low loss permittivity of ε eff ~25 over a wide frequency range (tan δ < 0.01, 100 kHz–2 MHz). Eu 0.5 Ba 0.5 TiO 3 prepared under H 2 /argon produced more irregular shaped nanocrystals (20–25) nm, with a thin film permittivity around 4 times greater ( ε eff 101, tan δ < 0.05, 10 kHz–2 MHz, σ ~59.54 kΩ mm -1 ). Field-cooled magnetization values of 0.025 emu g -1 for EBTO-Air and 0.84 emu g -1 for EBTO-Argon were observed. X-ray photoelectron spectroscopy analysis reveals a complex interplay of Eu II/III /Ti III/IV configurations which contribute to the observed ferroic and fluorescence behavior.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Simulation-guided analysis of resonant soft X-ray scattering for determining the microstructure of triblock copolymers

Resonant soft X-ray scattering (RSoXS) probes structure with chemical sensitivity that is useful for determining the morphology of multiblock copolymers. However, the hyperspectral scattering data produced by this technique can be challenging to interpret. Here, in this study, we use computational scattering simulations to extract the microstructure of a model triblock copolymer from the energy-dependent scattering from RSoXS. An ABC triblock terpolymer formed from poly(4-methylcaprolactone) (P4MCL), poly(2,2,2-trifluoroethylacrylate) (PTFEA), and poly (dodecylacrylate) (PDDA), P4MCL-block-PTFEA-block-PDDA, was synthesized as the model triblock system. Through quantitative evaluation of simulated scattering data from a physics-informed set of candidate structure models against experimental RSoXS data, we find the best agreement with hexagonally packed core–shell cylinders. This result is also consistent with electron-density reconstruction from hard X-ray scattering data evaluated against electron-density maps generated with the same model set. These results demonstrate the utility of simulation-guided scattering analysis to study complex microstructures that are challenging to image by microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass

Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33–9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032–0.131 (g/g) and lipid contents were 13.5–53.7% (g/g). Four strains had significantly higher lipid yields and contents. Finally, one of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

MaNGA galaxy properties – II. A detailed comparison of observed and simulated spiral galaxy scaling relations

ABSTRACT We present a catalogue of dynamical properties for 2368 late-type galaxies from the MaNGA survey. The latter complements the catalogue of photometric properties for the same sample based on deep optical dark energy sky instrument legacy imaging survey (DESI) photometry processed with autoprof . Rotation curves (RCs), extracted by model-fitting H α velocity maps from the MaNGA Data Analysis Pipeline, extend out to 1.4 (1.9) Re for the primary (secondary) MaNGA samples, respectively. The RCs and ancillary MaNGA Pipe3D data products were used to construct various fundamental galaxy scaling relations that are also compared uniformly with similar relations from numerical investigation of a hundred astrophysical object (NIHAO) zoom-in simulations. Simulated NIHAO galaxies were found to broadly reproduce the observed MaNGA galaxy population for $\log (M_*/{\rm {\rm M}_{\odot })\, \gt\, 8.5}$. Some discrepancies remain, such as those pertaining to central stellar densities and the diversity of RCs due to strong feedback schemes. Also presented are spatially resolved scatters for the velocity-size-stellar mass (VRM*) structural relations using MaNGA and NIHAO samples. The scatter for these relations in the galaxian interiors is a consequence of the diversity of inner RC shapes, while scatter in the outskirts is dictated by the large range of stellar surface densities, which is itself driven by sporadic star formation. The detailed, spatially resolved scatter analysis highlights the complex interplay between local and global astrophysical processes and provides a strong constraint to numerical simulations.

Astronomy & Astrophysics↗
DOE OSTI2025

Spin-flop-like transition as quantum critical point in Cs2⁢RuO4

We report thermodynamic, neutron diffraction, and inelastic neutron scattering measurements on Cs2⁢RuO4, a member of the celebrated family of frustrated magnets Cs2⁢𝑀⁢𝑋4 (𝑀 = Cu, Co, 𝑋 = Br, Cl). Unlike the previously studied members, it is based on 4⁢𝑑 transition metal ions with 𝑆=1. Mapping out the 𝐻−𝑇 magnetic phase diagram reveals an unusual continuous spin-flop-like phase transition associated with a quantum critical point within the antiferromagnetically ordered phase. A quantitative analysis of the complex magnetic excitation spectrum measured in zero field allows us to derive a model magnetic Hamiltonian for this compound. Its main feature is a frustration of magnetic anisotropy on a level that is much higher than in any of the previously studied species. This frustration naturally explains the peculiar phase transition observed.

Nabi, S [Laboratory for Solid State Physics, ETH Z↗
DOE OSTI2022

Efficient Clustering of Software Vulnerabilities using Self Organizing Map (SOM)

The common vulnerabilities and exposures (CVE) database was created with a mission to ``identify, define, and catalog publicly disclosed cybersecurity vulnerabilities''. This rich body of information can be used to enable rapid and efficient response to secure and defend cyber operations and protect critical cyber infrastructure. The main goal of this paper is to develop a visual analytics tool to enable deep analysis of CVEs using unsupervised clustering techniques. We enhance our analysis by first mapping CVEs to hierarchical-classes in Common Weakness Enumeration (CWE) using information in the National Vulnerability Database (NVD). Both the mapping and the numerical representation of CVEs are enabled by V2W-BERT, which uses natural language processing of the extensive information in NVD to generate a large tabular database of 137,226 CVE entries from 1999 to 2020, where each CVE is represented by a vector of 768 numerical features. The vectorized data is processed by Self-Organizing Maps (SOM), which is an unsupervised machine learning technique for dimensionality reduction, visual representation and clustering. Using a Torus map of 6417 units, we achieve ~10-fold data compression of ~140k CVEs using SOM. The trained map is further clustered using standard K-means clustering into 138 clusters of CVEs. We conducted a brief investigation of the rich mapping of CVEs to best-matching-units to K-means clusters, as well as CVEs to CWEs. For example, this novel mapping provided insight into the role of CWE-59 and CWE-264 in several CVEs that is otherwise hard to explore in the original data. We conclude that our this novel approach will not only enable deep analysis of the complex relationships between CVEs and CWEs, but also a mechanism to quickly respond to and design mitigation actions for rapidly evolving vulnerabilities that have not been mapped to existing CWEs.

Panchal, Khyati↗
DOE OSTI2021

Homogenous Voltage-Matched Strings Using Three-Terminal Tandem Solar Cells: Fundamentals and End Losses

Strings constructed from three-terminal tandem (3TT) solar cells offer the performance benefits of voltage-matching (which reduces sensitivity to spectral variation), but without the subcell voltage isolation required by four-terminal cells. However, the circuitry for a 3TT string can become complex, making circuit analysis more challenging. Here, we illustrate the essential features of “homogenous” voltage-matched (VM) 3TT strings, for which all 3TT cells in the string are nominally identical (with the same design/doping sequence, such that they can be fabricated on the same manufacturing line). Several representative VM string configurations are explicitly considered, and used to describe the general construction of string I(V) curves. End losses intrinsic to these strings are discussed in detail, along with mitigation strategies to minimize their impact. Our analysis agrees with experimental results for eight-cell strings constructed from GaInP/GaAs 3TT devices.

14 SOLAR ENERGY↗
DOE OSTI2025

Spectral Clustering-Based Partitioning of Large-Scale Power Electronics-Based Power Systems for Small-Signal Stability Analysis

The nodal admittance matrix (NAM)-based approach is well-suited for small-signal stability analysis of large-scale power electronics-based power systems (PEPSs), as it preserves the system structure through its admittance matrix. Previous studies have explored partitioning such systems into subareas and interconnections to reduce computational burden; however, they lacked a formal algorithmic procedure for determining feasible partitions. While several grid partitioning methods, such as those based on graph theory or machine learning, exist in the literature, they cannot be directly applied to NAM-based analysis due to differing objectives and constraints. Here, this paper addresses this gap by presenting a systematic, step-by-step procedure for applying a spectral partitioning algorithm that yields a division of the system into subareas suitable for NAM-based analysis. The computational complexity of the proposed method is also derived to demonstrate its efficiency and justify the practicality of the resulting subarea decomposition. The performance of the partitioning method is evaluated by applying the spectral clustering-derived subareas and interconnections to the NAM-based partitioning approach on a 140-bus system. Computational times for the full-system and partitioned NAM analyses are compared using MATLAB. Additionally, PSCAD simulations of the complete system and partitioned subareas are carried out to verify the effectiveness of the proposed method.

Nupur [Univ. of Tennessee, Knoxville, TN (United S↗
DOE OSTI2021

Voltage-Matched Strings using 3-Terminal Tandems: Fundamentals and End Losses

Strings constructed from 3-terminal tandem (3TT) cells can provide some of the performance benefits of voltage-matching with less cell complexity than strings based on 4-terminal tandem cells. However, the circuitry for a 3TT string can become more complex, making circuit analysis more challenging. Here we illustrate the essential features of single-polarity voltage-matched (VM) 3TT strings using representative examples. End losses are intrinsic to this type of string, but can be reduced by minimizing m and n in the Vtop/Vbot VM ratio m/n, and further mitigated by increasing the string length. This analysis agrees with preliminary experimental results.

3TT↗
DOE OSTI2025

S AP F LOWER : an automated tool for sap flow data preprocessing, gap-filling, and analysis using deep learning

Sap flow, a critical process in plant water use and ecosystem water cycles, is often measured using thermal dissipation probes (TDP) due to their ease of installation and continuous data collection. However, sap flow data frequently include noise, outliers, and gaps, creating challenges for analysis and requiring substantial manual processing. We developed S AP F LOWER , a tool that automates data preprocessing, model training, gap-filling, sapwood area scaling and modeling, and water use analysis. It integrates autocleaning, machine learning and deep learning models (e.g. random forest, Gaussian process regression, long short-term memory (LSTM), bidirectional LSTM (BiLSTM)), and efficient workflows to process sap flow data. S AP F LOWER can remove over 90% of noisy data while preserving legitimate variations and achieve high accuracy in gap-filling based on user-determined parameters. Random forest, LSTM, and BiLSTM models reduced root mean square error to 10% or less for long-term gaps. Model training and prediction can be performed efficiently within seconds. S AP F LOWER significantly enhances the efficiency and accessibility of TDP data analysis by automating complex tasks, enabling researchers without programming expertise to employ advanced techniques. Future improvements will focus on species-specific corrections for TDP and support for additional measurement methods. S AP F LOWER is openly available on GitHub (https://github.com/JiaxinWang123/SapFlower) and Zenodo (doi: 10.5281/zenodo.13665919).

ecosystem water balance↗
DOE OSTI2021

Turbo FRMAC 2021 v.11.0.0

The Turbo FRMAC analysis tool performs complex calculations to quickly evaluate radiological hazards during an emergency response by assessing impacts to the public, workers, and the food supply. Turbo FRMAC can be used to evaluate the hazard from a wide variety of radiological incidents. Turbo FRMAC calculations are based on methods established by the Federal Radiological Monitoring and Assessment (FRMAC). Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-10713 O

Whitener, Dustin↗
DOE OSTI2024

Systemic immunological responses are dependent on sex and ovarian hormone presence following acute inhaled woodsmoke exposure

Background: Rural regions of the western United States have experienced a noticeable surge in both the frequency and severity of acute wildfire events, which brings significant challenges to both public safety and environmental conservation efforts, with impacts felt globally. Identifying factors contributing to immune dysfunction, including endocrinological phenotypes, is essential to understanding how hormones may influence toxicological susceptibility. Methods: This exploratory study utilized male and female C57BL/6 mice as in vivo models to investigate distinct responses to acute woodsmoke (WS) exposure with a focus on sex-based differences. In a second set of investigations, two groups were established within the female mouse cohort. In one group, mice experienced ovariectomy (OVX) to simulate an ovarian hormone-deficient state similar to surgical menopause, while the other group received Sham surgery as controls, to investigate the mechanistic role of ovarian hormone presence in driving immune dysregulation following acute WS exposure. Each experimental cohort followed a consecutive 2-day protocol with daily 4-h exposure intervals under two conditions: control HEPA-filtered air (FA) and acute WS to simulate an acute wildfire episode. Results: Metals analysis of WS particulate matter (PM) revealed significantly increased levels of 63 Cu, 182 W, 208 Pb, and 238 U, compared to filtered air (FA) controls, providing insights into the specific metal components most impacted by the changing dynamics of wildfire occurrences in the region. Male and female mice exhibited diverse patterns in lung mRNA cytokine expression following WS exposure, with males showing downregulation and females displaying upregulation, notably for IL-1β, TNF-α, CXCL-1, CCL-5, TGF-β, and IL-6. After acute WS exposure, there were notable differences in the responses of macrophages, neutrophils, and bronchoalveolar lavage (BAL) cytokines IL-10, IL-6, IL-1β, and TNF-α. Significant diverse alterations were observed in BAL cytokines, specifically IL-1β, IL-10, IL-6, and TNF-α, as well as in the populations of immune cells, such as macrophages and polymorphonuclear leukocytes, in both Sham and OVX mice, following acute WS exposure. These findings elucidated the profound influence of hormonal changes on inflammatory outcomes, delineating substantial sex-related differences in immune activation and revealing altered immune responses in OVX mice due to ovarian hormone deficiency. In addition, the flow cytometry analysis highlighted the complex interaction between OVX surgery, acute WS exposure, and their collective impact on immune cell populations within the hematopoietic bone marrow niche. Conclusions: In summary, both male and female mice, alongside females subjected to OVX and those who had sham surgery, exhibit significant variations in the expression of proinflammatory cytokines, chemokines, lung mRNA gene expression, and related functional networks linked to signaling pathways. These differences potentially act as mediators of sex-specific and hormonal influences in the systemic inflammatory response to acute WS exposure during a wildfire event. Understanding the regulatory roles of genes expressed differentially under environmental stressors holds considerable implications, aiding in identifying sex-specific therapeutic targets for addressing acute lung inflammation and injury.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An automated workflow to screen alkene reductases using high-throughput thin layer chromatography

Background: Synthetic biology efforts often require high-throughput screening tools for enzyme engineering campaigns. While innovations in chromatographic and mass spectrometry-based techniques provide relevant structural information associated with enzyme activity, these approaches can require cost-intensive instrumentation and technical expertise not broadly available. Moreover, complex workflows and analysis time can significantly impact throughput. To this end, we develop an automated, 96-well screening platform based on thin layer chromatography (TLC) and use it to monitor in vitro activity of a geranylgeranyl reductase isolated from Sulfolobus acidocaldarius (SaGGR). Results: Unreduced SaGGR products are oxidized to their corresponding epoxide and applied to thin layer silica plates by acoustic printing. These derivatives are chromatographically separated based on the extent of epoxidation and are covalently ligated to a chromophore, allowing detection of enzyme variants with unique product distributions or enhanced reductase activity. Herein, we employ this workflow to examine farnesol reduction using a codon-saturation mutagenesis library at the Leu377 site of SaGGR. We show this TLC-based screen can distinguish between fourfold differences in enzyme activity for select mutants and validated those results by GC–MS. Conclusions: With appropriate quantitation methods, this workflow can be used to screen polyprenyl reductase activity and can be readily adapted to analyze broader catalyst libraries whose products are amenable to TLC analysis.

09 BIOMASS FUELS↗