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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Exploring Structural Anisotropy in Amorphous Tb-Co via Changes in Medium-Range Ordering

Amorphous thin films grown by magnetron co-sputtering exhibit changes in atomic structure with varying growth and annealing temperatures. Structural variations influence the bulk properties of the films. Scanning nanodiffraction performed in a transmission electron microscope (TEM) is applied to amorphous Tb 17 Co 83 (a-Tb-Co) films deposited over a range of temperatures to measure relative changes in medium-range ordering (MRO). These measurements reveal an increase in MRO with higher growth temperatures and a decrease in MRO with higher annealing temperatures. The trend in MRO indicates a relationship between the growth conditions and local atomic ordering. By tilting select films, the TEM measures variations in the local atomic structure as a function of orientation within the films. The findings support claims that preferential ordering along the growth direction results from temperature-mediated adatom configurations during deposition, and that oriented MRO correlates with increased structural anisotropy, explaining the strong growth-induced perpendicular magnetic anisotropy found in rare earth–transition metal films. Beyond magnetic films, we propose the tilted FEM workflow as a method of extracting anisotropic structural information in a variety of amorphous materials with directionally dependent bulk properties, such as films with inherent bonding asymmetry grown by physical vapor deposition.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Scanning Transmission Electron Microscopy–Atom Probe Tomography Correlative Analysis for the Characterization of Solute-defect Interactions

Atom probe tomography (APT) and (scanning) transmission electron microscopy ((S)TEM) are complementary techniques that provide spatially resolved chemical and structural information at the atomic scale. Here, in this study, we employ two different STEM/APT correlative analysis methods to investigate Cr segregation at dislocation loops in ultra-high purity Fe–Cr alloys. APT needles for the correlative analysis were extracted either from bulk material or from thinned TEM lamellae. STEM analysis was used to determine the Burgers vectors of ion-irradiation-induced dislocation loops, while APT reconstruction of the same region revealed the Cr segregation to these loops. We extended the g•b = 0 invisibility criterion of dislocation loops from TEM mode in a lamella to STEM mode in a needle-shaped specimen. STEM and APT analysis on the same needle provide straightforward correlative analysis, although it is limited by a small observation volume. In contrast, iterative STEM analysis of TEM lamellae, followed by the selective extraction of specific regions of interest for APT analysis, expands the observation area by up to 100 times but requires additional time-consuming steps for APT needle extraction from the lamellae.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

The interaction between transport-segment DNA and topoisomerase IA—crystal structure of MtbTOP1 in complex with both G- and T-segments

Abstract Each catalytic cycle of type IA topoisomerases has been proposed to comprise multistep reactions. The capture of the transport-segment DNA (T-segment) into the central cavity of the N-terminal toroidal structure is an important action, which is preceded by transient gate-segment (G-segment) cleavage and succeeded by G-segment religation for the relaxation of negatively supercoiled DNA and decatenation of DNA. The T-segment passage in and out of the central cavity requires significant domain–domain rearrangements, including the movement of D3 relative to D1 and D4 for the opening and closing of the gate towards the central cavity. Here we report a direct observation of the interaction of a duplex DNA in the central cavity of a type IA topoisomerase and its associated domain–domain conformational changes in a crystal structure of a Mycobacterium tuberculosis topoisomerase I complex that also has a bound G-segment. The duplex DNA within the central cavity illustrates the non-sequence-specific interplay between the T-segment DNA and the enzyme. The rich structural information revealed from the novel topoisomerase–DNA complex, in combination with targeted mutagenesis studies, provides new insights into the mechanism of the topoisomerase IA catalytic cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural insights into RNA cleavage by a novel family of bacterial RNases

Abstract Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.

Biochemistry & Molecular Biology↗
DOE OSTI2024

VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers

Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Ab initio many-fermion structure calculations on a quantum computer

To overcome the limitations of existing algorithms for solving self-bound quantum many-body problems—such as those encountered in nuclear and particle physics—that access only a restricted subset of energy levels and provide limited structural information, we introduce and demonstrate a novel quantum-classical approach capable of resolving the complete bound-state spectrum. This method also provides the total angular momentum 𝐽 associated with each eigenstate. Here, our approach is based on expressing the Hamiltonian in second-quantized form within a novel input model combined with a scan scheme, enabling broad applicability to configuration-interaction calculations across diverse fields. We apply this hybrid method to compute, for the first time, the bound-state spectrum together with corresponding 𝐽 values of 20 O using a realistic strong-interaction Hamiltonian. Our approach applies to hadron spectra and 𝐽 values solved in the relativistic basis light-front quantization approach.

Du, Weijie [Chinese Academy of Sciences (CAS), Lan↗
DOE OSTI2022

X-ray diffraction measurements and pressure determination in nanosecond compression of solids up to 600 GPa

X-ray diffraction measurements under laser-driven dynamic compression now allow us to investigate the atomic structure of matter at TPa pressures and thousands of degree temperatures with broad implications for condensed matter physics, planetary science and astronomy. Furthermore, pressure determination in these experiments often relies on velocimetry measurements coupled with modeling that requires accurate knowledge of the optical and thermo-mechanical properties of a window material, resulting in significant systematic uncertainty. Here we demonstrate different approach applicable to X-ray diffraction experiments under quasi-isentropic ramp-compression based on the use of in-situ pressure calibrants, similar to the methods often adopted in static-compression experiments with diamond anvil cells. Focusing on experiments using a diamond window, we discuss challenges and mitigation strategies for the novel approach. Our study, in addition to providing new structural information of 5 metals up to hundreds of GPa, provides validation to the currently used methods based on time-resolved measurement of the diamond free-surface velocity, and reveals that the use of in-situ calibrants enables a factor of four reduction in the pressure uncertainty in these experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Extracting free-space observables from trapped interacting clusters

The energy spectrum of two short-range interacting particles in a harmonic potential trap has previously been related to free-space scattering phase shifts. But the existing formula for systems with a nonzero interaction range is exact only in the limit of an infinitely shallow trap. Here I provide a systematically improved formula—describing the low-energy dynamics—that enables the use of finite traps. This paves the way for extracting nuclear scattering phase shifts from ab initio nuclear many-body structure calculations, a long-sought goal in nuclear physics. In this work, the derivation establishes effective field theory as a powerful framework for studying the connection between structure information of a trapped system (with two or more subclusters) and continuum physics in the fields of both nuclear and condensed-matter physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Measurement of the 2 ν β β Decay Rate and Spectral Shape of Mo 100 from the CUPID-Mo Experiment

Neutrinoless double beta decay (0νββ) is a yet unobserved nuclear process that would demonstrate Lepton number violation, a clear evidence of beyond standard model physics. The process two neutrino double beta decay (2νββ) is allowed by the standard model and has been measured in numerous experiments. In this Letter, we report a measurement of 2νββ decay half-life of 100 Mo to the ground state of 100 Ru of [7.07±0.02(stat)±0.11(syst)]×10 18 yr by the CUPID-Mo experiment. With a relative precision of ±1.6% this is the most precise measurement to date of a 2νββ decay rate in 100 Mo. In addition, we constrain higher-order corrections to the spectral shape, which provides complementary nuclear structure information. We report a novel measurement of the shape factor ξ 3,1 =0.45±0.03(stat)±0.05(syst) based on a constraint on the ratio of higher-order terms from theory, which can be reliably calculated. This is compared to theoretical predictions for different nuclear models. Finally, we also extract the first value for the effective axial vector coupling constant obtained from a spectral shape study of 2νββ decay.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

The AXEAP2 program for K β X-ray emission spectra analysis using artificial intelligence

The processing and analysis of synchrotron data can be a complex task, requiring specialized expertise and knowledge. Our previous work addressed the challenge of X-ray emission spectrum (XES) data processing by developing a standalone application using unsupervised machine learning. However, the task of analyzing the processed spectra remains another challenge. Although the non-resonant K β XES of 3 d transition metals are known to provide electronic structure information such as oxidation and spin state, finding appropriate parameters to match experimental data is a time-consuming and labor-intensive process. Here, a new XES data analysis method based on the genetic algorithm is demonstrated, applying it to Mn, Co and Ni oxides. This approach is also implemented as a standalone application, Argonne X-ray Emission Analysis 2 ( AXEAP2 ), which finds a set of parameters that result in a high-quality fit of the experimental spectrum with minimal intervention. AXEAP2 is able to find a set of parameters that reproduce the experimental spectrum, and provide insights into the 3 d electron spin state, 3 d –3 p electron exchange force and K β emission core-hole lifetime.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Development of a versatile electrochemical cell for in situ grazing-incidence X-ray diffraction during non-aqueous electrochemical nitrogen reduction

In situ techniques are essential to understanding the behavior of electrocatalysts under operating conditions. When employed, in situ synchrotron grazing-incidence X-ray diffraction (GI-XRD) can provide time-resolved structural information of materials formed at the electrode surface. In situ cells, however, often require epoxy resins to secure electrodes, do not enable electrolyte flow, or exhibit limited chemical compatibility, hindering the study of non-aqueous electrochemical systems. Here, a versatile electrochemical cell for air-free in situ synchrotron GI-XRD during non-aqueous Li-mediated electrochemical N 2 reduction (Li-N 2 R) has been designed. This cell not only fulfills the stringent material requirements necessary to study this system but is also readily extendable to other electrochemical systems. Under conditions relevant to non-aqueous Li-N 2 R, the formation of Li metal, LiOH and Li 2 O as well as a peak consistent with the α-phase of Li 3 N was observed, thus demonstrating the functionality of this cell toward developing a mechanistic understanding of complicated electrochemical systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Comparing Mapper Graphs of Artificial Neuron Activations

The mapper graph is a popular tool from topological data analysis that provides a graphical summary of point cloud data. It has been used to study data from cancer research, sports analytics, neurosciences, and machine learning. In particular, mapper graphs have been used recently to visualize the topology of high-dimensional artificial neural activations from convolutional neural networks and large language models. However, a key question that arises from using mapper graphs across applications is how to compare mapper graphs to study their structural differences. In this paper, we introduce a distance between mapper graphs using tools from optimal transport. We demonstrate the utility of such a distance by studying the topological changes of neural activations across convolutional layers in deep learning, as well as by capturing the loss of structural information for multiscale mapper.

mapper graphs, computational topology, machine lea↗
DOE OSTI2023

Unraveling Li growth kinetics in solid electrolytes due to electron beam charging

Revealing the local structure of solid electrolytes (SEs) with electron microscopy is critical for the fundamental understanding of the performance of solid-state batteries (SSBs). However, the intrinsic structural information in the SSB can be misleading if the sample’s interactions with the electron beams are not fully understood. In this work, we systematically investigate the effect of electron beams on Al-doped lithium lanthanum zirconium oxide (LLZO) under different imaging conditions. Li metal is observed to grow directly on the clean surface of LLZO. The Li metal growth kinetics and the morphology obtained are found to be heavily influenced by the temperature, accelerating voltage, and electron beam intensity. We prove that the lithium growth is due to the LLZO delithiation activated by a positive charging effect under electron beam emission. Our results deepen the understanding of the electron beam impact on SEs and provide guidance for battery material characterization using electron microscopy.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Visualizing the strong field–induced molecular breakup of C 60 via x-ray diffraction

Laser-driven dynamics in polyatomic molecules poses a complex many-body problem. Understanding intense light-matter interaction is crucial for steering intramolecular quantum dynamical processes. Here, we record time-resolved x-ray diffraction images of C 60 molecules during and after their interaction with intense near-infrared fields, giving direct access to structural changes of the molecules and their fragmentation in real time. Tuning the intensity of the excitation pulses, we uncover a transition from a weak-field regime of excited but stable molecules to a high-field regime dominated by Coulomb explosion. In the transition region, the molecules expand by up to 50% of their initial size within just 140 fs, with major fragmentation only setting in afterward. This work demonstrates that x-ray diffractive imaging is capable of retrieving time-resolved structural information of large molecules reshaped by intense laser fields. Laser-driven fragmentation is a first step toward observing molecular processes modified by laser fields of increasing intensity.

Schnorr, Kirsten [Paul Scherrer Inst. (PSI), Villi↗
DOE OSTI2023

Statistical (n,$$\gamma $$) cross section model comparison for short-lived nuclei

Abstract Neutron-capture cross sections of neutron-rich nuclei are calculated using a Hauser–Feshbach model when direct experimental cross sections cannot be obtained. A number of codes to perform these calculations exist, and each makes different assumptions about the underlying nuclear physics. We investigated the systematic uncertainty associated with the choice of Hauser-Feshbach code used to calculate the neutron-capture cross section of a short-lived nucleus. The neutron-capture cross section for $$^{73}\hbox {Zn}$$ 73 Zn (n, $$\gamma $$ γ ) $$^{74}\hbox {Zn}$$ 74 Zn was calculated using three Hauser-Feshbach statistical model codes: TALYS, CoH, and EMPIRE. The calculation was first performed without any changes to the default settings in each code. Then an experimentally obtained nuclear level density (NLD) and $$\gamma $$ γ -ray strength function ( $$\gamma \hbox {SF}$$ γ SF ) were included. Finally, the nuclear structure information was made consistent across the codes. The neutron-capture cross sections obtained from the three codes are in good agreement after including the experimentally obtained NLD and $$\gamma \hbox {SF}$$ γ SF , accounting for differences in the underlying nuclear reaction models, and enforcing consistent approximations for unknown nuclear data. It is possible to use consistent inputs and nuclear physics to reduce the differences in the calculated neutron-capture cross section from different Hauser-Feshbach codes. However, ensuring the treatment of the input of experimental data and other nuclear physics are similar across multiple codes requires a careful investigation. For this reason, more complete documentation of the inputs and physics chosen is important.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

NuclPred v1

This tool takes a genome assembly as input and predicts per-site nucleosome occupancy as output. Trained on physical maps of nucleosome binding preferences across the fungal kingdom, NuclPred can be applied broadly across fungi (and other eukaryotes). This breadth, combined with its accuracy, means it could have both basic and applied biological implications, for example in understanding eukaryotic gene regulation and genetic engineering. Almost universally across eukaryotes, nucleosomes - each wrapping ~150 base pairs of DNA - serve to package DNA inside the nucleus, with major consequences on DNA access, gene activity and DNA integration. NuclPred was generated using a supervised deep learning approach combining convolutional and recurrent neural networks to take DNA features (nucleotides, GC content and structural information) as input, then use that information to predict the physical attractiveness DNA sequences might have for forming nucleosomes. With this information at hand, researchers can design more efficient CRISPR constructs, explore the interplay between DNA signatures and other regulators impact nucleosome locations, predict expression patterns, etc. This tool will be published as part of a manuscript currently under revision at iScience (draft attached).

Mondo, Stephen↗
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↗
DOE OSTI2025

TaTi_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys tantalum-titanium (Ta-Ti). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Hf and Nb. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions. The calculations have been collected on Air Force HPC11 cluster using the VASP 6.5.1. Additional methodology and file structure information is available in the dataset README.txt file.

36 MATERIALS SCIENCE↗