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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
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 OSTI2024

Structure–Function Insights into Thermoresponsive Copolymers as Lanthanide Precipitants

The synthetic toolbox for stimuli-responsive polymers has broadened to include many tunable variables, making these materials applicable in diverse technologies. However, unraveling the key composition–structure–function relationships to facilitate ground-up design remains a challenge due to the inherent dispersity in sequence and conformations for synthetic polymers. We here present a systematic study of these relationships using a model system of copolymers with a thermoresponsive (N-isopropylacrylamide) backbone in addition to metal-chelating (acrylic acid) and hydrophobic structural comonomers and evaluate their efficiency at isolating technologically critical lanthanide ions. The efficiency of lanthanide ion extraction by precipitation was quantitated with a metallochromic dye to reveal trends relating copolymer hydrophobicity to improved separations. Further, we examined the role of different hydrophobic comonomers in dictating the solution-phase conformation of the polymer in the presence and absence of lanthanide ions, and we correlated key features of the hydrophobic comonomer to extraction efficiency. Lastly, we identified how the local proximity of thermoresponsive, chelating, and hydrophobic subunits facilitates metal extraction by manipulating the copolymer sequence with multiblock polymerization. Through mechanistic analysis, we propose a binding-then-assembly process through which metal ions are coprecipitated with macromolecular chelators.

Copolymers↗
DOE OSTI2025

Unraveling trace anomaly of supradense matter via neutron star compactness scaling

The trace anomaly Δ ≡ 1/3 −𝑃/𝜖 =1/3 −𝜙 quantifies the possibly broken conformal symmetry in supradense matter under pressure 𝑃 at energy density 𝜖. Perturbative QCD (pQCD) predicts a vanishing Δ at extremely high energy or baryon densities when the conformal symmetry is realized but its behavior at intermediate densities reachable in neutron stars (NSs) is still very uncertain. The extraction of Δ from NS observations strongly depends on the employed model for nuclear equation of state (EOS). Using the IPAD-TOV method based on an intrinsic and perturbative analysis of the dimensionless (IPAD) Tolman-Oppenheimer-Volkoff (TOV) equations that are further verified numerically by using 10 5 EOSs generated randomly with a metamodel in a very broad EOS parameter space constrained by terrestrial nuclear experiments and astrophysical observations, here we first show that the compactness 𝜉 ≡ 𝐺⁡𝑀 NS /𝑅⁢𝑐 2 ≡ 𝑀 NS /𝑅 of a NS with mass 𝑀 NS and radius 𝑅 scales very accurately with $\bar{Π}$ c ≡ $Π$ c · (1 +18⁢X/25) ≡ X/(1 +3⁢X 2 +4⁢X) · (1 +18⁢X/25) where X ≡ 𝜙 c = 𝑃 c /𝜖 c is the ratio of pressure over energy density at NS centers. The scaling of NS compactness thus enables one to readily read off the central trace anomaly Δ c = 1/3 −X directly from the observational data of either the mass-radius or red-shift measurements. Finally, we then demonstrate indeed that the available NS data themselves from recent X-ray and gravitational wave observations can determine model insensitively the trace anomaly as a function of energy density in NS cores, providing a stringent test of existing NS models and a clear guidance in a new direction for further understanding the nature and EOS of supradense matter.

nuclear astrophysics↗
DOE OSTI2023

Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase

NADPH-dependent assimilatory sulfite reductase (SiR) from Escherichia coli performs a six-electron reduction of sulfite to the bioavailable sulfide. SiR is composed of a flavoprotein (SiRFP) reductase subunit and a hemoprotein (SiRHP) oxidase subunit. There is no known high-resolution structure of SiR or SiRFP, thus we do not yet fully understand how the subunits interact to perform their chemistry. Here, we used small-angle neutron scattering to understand the impact of conformationally restricting the highly mobile SiRFP octamer into an electron accepting (closed) or electron donating (open) conformation, showing that SiR remains active, flexible, and asymmetric even with these conformational restrictions. From these scattering data, we then model the first solution structure of SiRFP. Further, computational modeling of the N-terminal 52 amino acids that are responsible for SiRFP oligomerization suggests an eight-helical bundle tethers together the SiRFP subunits to form the SiR core. Finally, mass spectrometry analysis of the closed SiRFP variant show that SiRFP is capable of inter-molecular domain crossover, in which the electron donating domain from one polypeptide is able to interact directly with the electron accepting domain of another polypeptide. This structural characterization suggests that SiR performs its high-volume electron transfer through both inter- and intramolecular pathways between SiRFP domains and, thus, cis or trans transfer from reductase to oxidase subunits. Such highly redundant potential for electron transfer makes this system a potential target for designing synthetic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Stretchable electrochemical energy storage devices

The increasingly intimate contact between electronics and the human body necessitates the development of stretchable energy storage devices that can conform and adapt to the skin. Therefore, the development of stretchable batteries and supercapacitors has received significant attention in recent years. This review provides an overview of the general operating principles of batteries and supercapacitors and the requirements to make these devices stretchable. The following sections provide an in-depth analysis of different strategies to convert the conventionally rigid electrochemical energy storage materials into stretchable form factors. Namely, the strategies of strain engineering, rigid island geometry, fiber-like geometry, and intrinsic stretchability are discussed. A wide range of materials are covered for each strategy, including polymers, metals, and ceramics. By comparing the achieved electrochemical performance and strain capability of these different materials strategies, we allow for a side-by-side comparison of the most promising strategies for enabling stretchable electrochemical energy storage. The final section consists of an outlook for future developments and challenges for stretchable supercapacitors and batteries.

25 ENERGY STORAGE↗
DOE OSTI2022

Structural organization of the spongy mesophyll

Summary Many plant leaves have two layers of photosynthetic tissue: the palisade and spongy mesophyll. Whereas palisade mesophyll consists of tightly packed columnar cells, the structure of spongy mesophyll is not well characterized and often treated as a random assemblage of irregularly shaped cells. Using micro‐computed tomography imaging, topological analysis, and a comparative physiological framework, we examined the structure of the spongy mesophyll in 40 species from 30 genera with laminar leaves and reticulate venation. A spectrum of spongy mesophyll diversity encompassed two dominant phenotypes: first, an ordered, honeycomblike tissue structure that emerged from the spatial coordination of multilobed cells, conforming to the physical principles of Euler’s law; and second, a less‐ordered, isotropic network of cells. Phenotypic variation was associated with transitions in cell size, cell packing density, mesophyll surface‐area‐to‐volume ratio, vein density, and maximum photosynthetic rate. These results show that simple principles may govern the organization and scaling of the spongy mesophyll in many plants and demonstrate the presence of structural patterns associated with leaf function. This improved understanding of mesophyll anatomy provides new opportunities for spatially explicit analyses of leaf development, physiology, and biomechanics.

3D↗
DOE OSTI2024

Multiple Functional Bonds Integrated Interphases for Long Cycle Sodium-Ion Batteries

Sodium-ion batteries (SIBs) have garnered significant interest as one of the most promising energy suppliers for power grid energy storage. However, the poor electrode/electrolyte interfacial stability leads to continual electrolyte decomposition and transition metal dissolution, resulting in rapid performance degradation of SIBs. In this work, we propose a strategy integrating multiple functional bonds to regulate electrode/electrolyte interphase by triple-coupling of succinonitrile (SN), sodium hexafluorophosphate (NaPF 6 ) and fluorinated ethylene carbonate (FEC). Theoretical calculation and experiment results show that the solvation structure of Na + and ClO 4 – is effectively reconfigured by the solvated FEC, SN and PF 6 – in PC-based carbonate electrolyte. The newly developed electrolyte demonstrates increased Na + -FEC coordination, weakened interaction of Na + -PC and participation of SN and PF 6 – anions in solvation, resulting in the formation of a conformal interfacial layer comprising of sodium oxynitrides (NaN x O y ), sodium fluoride (NaF) and phosphorus oxide compounds (NaP x O y ). Consequently, a 3 Ah pouch full cell of hard carbon//NaNi 1/3 Fe 1/3 Mn 1/3 O 2 exhibits an excellent capacity retention of 90.4 % after 1000 cycles. Detailed postmortem analysis of interface chemistry is further illustrated by multiple characterization methods. Finally, this study provides a new avenue for developing electrolyte formulations with multiple functional bonds integrated interphases to significantly improve the long-term cycling stability of SIBs.

25 ENERGY STORAGE↗
DOE OSTI2023

The little skate genome and the evolutionary emergence of wing-like fins

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins—including gene expression, chromatin occupancy and three-dimensional conformation—we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Psychomedical Interventions with Transgender People in Portugal and Brazil: A Critical Approach

This study aims to analyze biopsychomedical interventions with transgender people. For this purpose, we carried out 35 semi-structured interviews with people who self-identify as transsexuals and transvestites in Brazil and Portugal. The responses of the study participants were systematized according to a thematic analysis, which led to the emergence of the following three main themes: “institutional power”, “expectations of trans-bodies”, and “experiences in health services”. This study demonstrates how some trans people perform bodily modifications to fight the transphobia they experience throughout their lives. In addition, they believe that, by making their bodies conform to each other, they may become more attractive and desirable. The process of cisnormativity is, furthermore, conveyed by the idea present in the answers of some respondents: that having “integrated” bodies means facing less discrimination and that they will, therefore, obtain more satisfactory ways of personally and socially experiencing their identities. This study contributes to a deepening critical reflection on the experiences/exclusions of trans people, especially in the psychomedical context of “normalization” devices. Hence, just as social structures produce and sustain transphobia, the same structures are responsible for combating it.

Rodrigues, Liliana↗
DOE OSTI2020

Conducting Industrial Hygiene Exposure Assessments at Scale Using Non-Parametric Upper Tolerance Limits at the Hanford Site - 20439

Chemical vapors are generated in the radioactive waste storage tanks at the Hanford Site due to ongoing chemical and radiological activity. Hanford's Tank Operations Contractor conducts exposure assessments for individual tank farms to identify, evaluate, and recommend controls or other worker protection measures for chemical, physical, and biological hazards present within each tank farm. These exposure assessments conform to the American Industrial Hygiene Association assessment strategy and recommended statistical procedures. The exposure assessment process involved manually processing tens of thousands of records that were collected over several years and entered into a central database. Working with Pacific Northwest National Laboratory, this process has been largely automated, providing a scalable analysis process that reduced processing time by over 90%, while providing defensible results and improved data quality. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Efficient BiVO 4 /CoFeO x H y photoanodes using controlled annealing and conformal linear-sweep electrocatalyst photodeposition

Although monoclinic bismuth vanadate (BiVO 4 ) is a promising photoanode for solar water splitting, its practical use is hindered by imperfect photocurrent generation/collection, low photovoltage compared to the bandgap, and corrosion side reactions that limit durability. Here, we introduce a controlled-annealing sol–gel process for BiVO 4 thin-film photoanodes along with an optimized linear-sweep-voltammetry photodeposition of CoFeO x H y cocatalysts. The resulting BiVO 4 films annealed at 550 °C exhibited a photocurrent density of 4.1 mA/cm 2 at 1.23 V RHE under 1 sun AM 1.5G solar simulation and a low onset potential of 0.26 V RHE due to high majority carrier conductivity, a crystalline bulk with reduced defects as evidenced by x-ray photoelectron spectroscopy and photoluminescence lifetime analysis, and thus enhanced photocarrier collection. However, significant degradation in performance was found due to interfacial photocorrosion. To protect the surface and speed the oxygen-evolution reaction CoFeO x H y cocatalyst layers were deposited. By varying the number of consecutive sweeps and adjusting the applied bias range, an ultra-thin (~15 nm) CoFeO x H y cocatalyst layer was uniformly grown deposited over 30 cycles on the BiVO 4 surface. The resulting BiVO 4 /CoFeO x H y yielded 4.03 mA/cm 2 at 1.23 V RHE and onset potential of 0.24 V RHE , with stable operation (~15 % loss in photocurrent at 1.23 V RHE relative to ~60 % loss in the uncatalyzed control sample). These conformal CoFeO x H y catalytic layers function simultaneously to selectively collect photoexcited holes from the BiVO 4 , catalyze the water-oxidation reaction, and protect the BiVO 4 from photodegradation.

42 ENGINEERING↗
DOE OSTI2022

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Preliminary benchmarks and analysis of boundary conditions in a trenched microstructured silicon radiation detector

Microstructured neutron detectors have the benefit of enhanced neutron detection efficiency as compared to planar devices, achieved by etching 6 LiF-filled trenches on the top surface of a silicon PIN diode. This sensor geometry results in a complex electric field distribution and depletion characteristics within the diode under reverse bias. For the first time on record, the effects of a fixed oxide charge on the microstructured device depletion characteristics and mobile carrier transport is investigated. Prototype detectors were fabricated with non-conformal surface doping. Capacitance voltage and current voltage measurements were performed for these prototypes and compared with COMSOL Multiphysics simulations. A spectral response from an 241Am alpha particle source was acquired and analyzed. It was found that monoenergetic alpha particles produce three prominent peaks in the pulse height spectrum output by the device. The peaks were confirmed by simulations to correlate with dead layers and incident trajectories into the microstructure. It was also found that significant differences in pulse rise time result, corresponding with events arriving in a low-field region in the fins and a high-field region in the bulk. Geant4 was utilized for radiation transport, interaction modeling, and benchmarking the spectral data. The results of this simulation work provide confidence in the ability to attain and benchmark electrical characteristics and spectral data for semiconductor radiation detectors employing complex microstructures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Consideration of Initial Cloud Droplet Size Distribution Shapes in Quantifying Different Entrainment-Mixing Mechanisms

Entrainment-mixing process significantly affects cloud micro/macrophysics and the evaluation of aerosol indirect effects. However, it remains an open question as to how to quantify entrainment-mixing mechanism for broad cloud droplet size distributions (CDSDs). Here, CDSDs with different spectral widths are used to initialize the Explicit Mixing Parcel Model to address this problem, and microphysical properties are compared for different CDSD widths. For relatively broad CDSDs, as the number concentration and liquid water content decrease, the volume-mean radius and mean radius increase, which is opposite to the scenario for relatively narrow CDSDs and the homogeneous/inhomogeneous conceptual model. For the relatively broad CDSDs, such relationships could be mistaken as inhomogeneous mixing with subsequent ascent in analysis of the conventional microphysical mixing diagram. This then causes traditional homogenous mixing degrees to be unrealistically negative and not applicable for relatively broad CDSDs. New measures are introduced to explicitly account for the effect of CDSD spectral shapes on quantifying entrainment-mixing mechanism. The new measures yield reasonable ranges of values that conform to the dynamical measures such as the Damköhler and transitional scale numbers, and their temporal variation can be explained physically. This study extends the measures of homogeneous mixing degrees from narrow to broad CDSDs, and sheds new light on the consideration of CDSD shapes in parameterizations of entrainment-mixing mechanism.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Active conformation of the p97-p47 unfoldase complex

The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a “hand-over-hand” mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Self-consistent analysis for the η c → γ γ process

The next-to-next-to-leading-order (NNLO) perturbative QCD (pQCD) predictions for both the decay width and the transition form factor in the η c → γ γ process, based on nonrelativistic QCD (NRQCD), deviate from precise experimental measurements. These significant discrepancies have cast doubt on the applicability of NRQCD to charmonium processes. In this paper, we analyze the η c → γ γ process by applying the principle of maximum conformality (PMC), a systematic method for eliminating renormalization scheme-and-scale ambiguities. The PMC renormalization scales are determined by absorbing the nonconformal β -terms that govern the behavior of the QCD running coupling via the renormalization group equation. We obtain the PMC scale Q ⋆ = 4.49 m c for the η c → γ γ decay width. Even after using the PMC method, the convergence of the pQCD series is still poor, which indicates the importance of uncalculated next-to-next-to-next-to-leading-order and higher-order terms. The resulting value for Γ η c → γ γ is in agreement with the Particle Data Group’s reported value of Γ η c → γ γ = 5.1 ± 0.4 keV within the bounds of uncertainties. Moreover, the transition form factor obtained using the PMC is also in good agreement with precise experimental measurements. The application of the PMC suggests a potential resolution to η c → γ γ puzzle and supports the applicability of NRQCD to charmonium processes. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Nramp: Deprive and conquer?

Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.

59 BASIC BIOLOGICAL SCIENCES↗