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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Double-Bilayer polar nanoregions and Mn antisites in (Ca, Sr)3Mn2O7

Abstract The layered perovskite Ca 3 Mn 2 O 7 (CMO) is a hybrid improper ferroelectric candidate proposed for room temperature multiferroicity, which also displays negative thermal expansion behavior due to a competition between coexisting polar and nonpolar phases. However, little is known about the atomic-scale structure of the polar/nonpolar phase coexistence or the underlying physics of its formation and transition. In this work, we report the direct observation of double bilayer polar nanoregions (db-PNRs) in Ca 2.9 Sr 0.1 Mn 2 O 7 using aberration-corrected scanning transmission electron microscopy (S/TEM). In-situ TEM heating experiments show that the db-PNRs can exist up to 650 °C. Electron energy loss spectroscopy (EELS) studies coupled with first-principles calculations demonstrate that the stabilization mechanism of the db-PNRs is directly related to an Mn oxidation state change (from 4+ to 2+), which is linked to the presence of Mn antisite defects. These findings open the door to manipulating phase coexistence and achieving exotic properties in hybrid improper ferroelectric.

36 MATERIALS SCIENCE↗
DOE OSTI2023

CryoET reveals organelle phenotypes in huntington disease patient iPSC-derived and mouse primary neurons

Huntington’s disease (HD) is caused by an expanded CAG repeat in the huntingtin gene, yielding a Huntingtin protein with an expanded polyglutamine tract. While experiments with patient-derived induced pluripotent stem cells (iPSCs) can help understand disease, defining pathological biomarkers remains challenging. Here, we used cryogenic electron tomography to visualize neurites in HD patient iPSC-derived neurons with varying CAG repeats, and primary cortical neurons from BACHD, deltaN17-BACHD, and wild-type mice. In HD models, we discovered sheet aggregates in double membrane-bound organelles, and mitochondria with distorted cristae and enlarged granules, likely mitochondrial RNA granules. We used artificial intelligence to quantify mitochondrial granules, and proteomics experiments reveal differential protein content in isolated HD mitochondria. Knockdown of Protein Inhibitor of Activated STAT1 ameliorated aberrant phenotypes in iPSC- and BACHD neurons. We show that integrated ultrastructural and proteomic approaches may uncover early HD phenotypes to accelerate diagnostics and the development of targeted therapeutics for HD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Atomic-scale origin of the low grain-boundary resistance in perovskite solid electrolyte Li 0.375 Sr 0.4375 Ta 0.75 Zr 0.25 O 3

Oxide solid electrolytes (OSEs) have the potential to achieve improved safety and energy density for lithium-ion batteries, but their high grain-boundary (GB) resistance generally is a bottleneck. In the well-studied perovskite oxide solid electrolyte, Li 3x La 2/3-x TiO 3 (LLTO), the ionic conductivity of grain boundaries is about three orders of magnitude lower than that of the bulk. In contrast, the related Li 0.375 Sr 0.4375 Ta 0.75 Zr 0.25 O 3 (LSTZ0.75) perovskite exhibits low grain boundary resistance for reasons yet unknown. Here, we use aberration-corrected scanning transmission electron microscopy and spectroscopy, along with an active learning moment tensor potential, to reveal the atomic scale structure and composition of LSTZ0.75 grain boundaries. Vibrational electron energy loss spectroscopy is applied for the first time to reveal atomically resolved vibrations at grain boundaries of LSTZ0.75 and to characterize the otherwise unmeasurable Li distribution therein. We find that Li depletion, which is a major reason for the low grain boundary ionic conductivity of LLTO, is absent for the grain boundaries of LSTZ0.75. Instead, the low grain boundary resistivity of LSTZ0.75 is attributed to the formation of a nanoscale defective cubic perovskite interfacial structure that contained abundant vacancies. Our study provides new insights into the atomic scale mechanisms of low grain boundary resistivity.

25 ENERGY STORAGE↗
DOE OSTI2023

Atomic-scale probing of short-range order and its impact on electrochemical properties in cation-disordered oxide cathodes

Abstract Chemical short-range-order has been widely noticed to dictate the electrochemical properties of Li-excess cation-disordered rocksalt oxides, a class of cathode based on earth abundant elements for next-generation high-energy-density batteries. Existence of short-range-order is normally evidenced by a diffused intensity pattern in reciprocal space, however, derivation of local atomic arrangements of short-range-order in real space is hardly possible. Here, by a combination of aberration-corrected scanning transmission electron microscopy, electron diffraction, and cluster-expansion Monte Carlo simulations, we reveal the short-range-order is a convolution of three basic types: tetrahedron, octahedron, and cube. We discover that short-range-order directly correlates with Li percolation channels, which correspondingly affects Li transport behavior. We further demonstrate that short-range-order can be effectively manipulated by anion doping or post-synthesis thermal treatment, creating new avenues for tailoring the electrochemical properties. Our results provide fundamental insights for decoding the complex relationship between local chemical ordering and properties of crystalline compounds.

25 ENERGY STORAGE↗
DOE OSTI2025

PhaseT3M: 3D imaging at 1.6 Å resolution via electron cryo-tomography with nonlinear phase retrieval

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple scattering further complicates interpretation. These effects degrade resolution, particularly in conventional reconstruction algorithms, which assume linearity. Particle averaging can reduce such issues but is unsuitable for heterogeneous or dynamic samples ubiquitous in biology, chemistry, and materials sciences. Here, we develop a phase retrieval-based cryo-ET method, PhaseT3M. We experimentally demonstrate its application to an approximately 7 nm Co3O4 nanoparticle on an approximately 30 nm carbon substrate, achieving a maximum resolution of 1.6 Å, surpassing conventional limits using standard cryo-TEM equipment. PhaseT3M uses a multislice model for multiple scattering and Bayesian optimization for alignment and computational aberration correction, with a positivity constraint to recover ‘missing wedge’ information. Applied directly to biological particles, it enhances reconstruction quality and reduces artifacts, establishing a standard for routine 3D imaging with phase contrast.

Biophysics↗
DOE OSTI2026

Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment

The FOXG1 transcription factor is a crucial regulator of embryonic brain development. Pathogenic FOXG1 variants cause FOXG1 syndrome. Although structural variants in the non-coding region downstream of FOXG1 have been reported in 38 individuals with similar characteristics, the regulatory pathomechanisms remain unknown. Here, we identify two non-coding structural variants in individuals with FOXG1 syndrome-like features, allowing us to delineate a ~ 124 kb commonly affected regulatory region. Using epigenomic profiling and in vivo enhancer assays, we characterize and validate regulatory elements within the commonly affected regulatory region and wider FOXG1 TAD. We see strong activation of previously validated forebrain enhancers, and identify an enhancer cluster and progenitor-specific enhancer region that are strongly activated during forebrain-directed neural progenitor cell differentiation, a process in which FOXG1 is an important regulator. Perturbation of these elements results in varying degrees of reduced FOXG1 transcription in forebrain neural progenitor cells and in population shifts within these cells, while removal of the TAD boundary leads to aberrant expression of the neighbouring PRKD1 gene. Our findings characterize enhancer and architectural elements essential for proper FOXG1 transcription during neurodevelopment, therefore improving variant interpretation in this region.

Hamerlinck, Lisa↗
DOE OSTI2021

Defect detection in atomic-resolution images via unsupervised learning with translational invariance

Abstract Crystallographic defects can now be routinely imaged at atomic resolution with aberration-corrected scanning transmission electron microscopy (STEM) at high speed, with the potential for vast volumes of data to be acquired in relatively short times or through autonomous experiments that can continue over very long periods. Automatic detection and classification of defects in the STEM images are needed in order to handle the data in an efficient way. However, like many other tasks related to object detection and identification in artificial intelligence, it is challenging to detect and identify defects from STEM images. Furthermore, it is difficult to deal with crystal structures that have many atoms and low symmetries. Previous methods used for defect detection and classification were based on supervised learning, which requires human-labeled data. In this work, we develop an approach for defect detection with unsupervised machine learning based on a one-class support vector machine (OCSVM). We introduce two schemes of image segmentation and data preprocessing, both of which involve taking the Patterson function of each segment as inputs. We demonstrate that this method can be applied to various defects, such as point and line defects in 2D materials and twin boundaries in 3D nanocrystals.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Leveraging generative adversarial networks to create realistic scanning transmission electron microscopy images

Abstract The rise of automation and machine learning (ML) in electron microscopy has the potential to revolutionize materials research through autonomous data collection and processing. A significant challenge lies in developing ML models that rapidly generalize to large data sets under varying experimental conditions. We address this by employing a cycle generative adversarial network (CycleGAN) with a reciprocal space discriminator, which augments simulated data with realistic spatial frequency information. This allows the CycleGAN to generate images nearly indistinguishable from real data and provide labels for ML applications. We showcase our approach by training a fully convolutional network (FCN) to identify single atom defects in a 4.5 million atom data set, collected using automated acquisition in an aberration-corrected scanning transmission electron microscope (STEM). Our method produces adaptable FCNs that can adjust to dynamically changing experimental variables with minimal intervention, marking a crucial step towards fully autonomous harnessing of microscopy big data.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Exploring electron-beam induced modifications of materials with machine-learning assisted high temporal resolution electron microscopy

Directed atomic fabrication using an aberration-corrected scanning transmission electron microscope (STEM) opens new pathways for atomic engineering of functional materials. In this approach, the electron beam is used to actively alter the atomic structure through electron beam induced irradiation processes. One of the impediments that has limited widespread use thus far has been the ability to understand the fundamental mechanisms of atomic transformation pathways at high spatiotemporal resolution. Here, we develop a workflow for obtaining and analyzing high-speed spiral scan STEM data, up to 100 fps, to track the atomic fabrication process during nanopore milling in monolayer MoS 2 . An automated feedback-controlled electron beam positioning system combined with deep convolution neural network (DCNN) was used to decipher fast but low signal-to-noise datasets and classify time-resolved atom positions and nature of their evolving atomic defect configurations. Through this automated decoding, the initial atomic disordering and reordering processes leading to nanopore formation was able to be studied across various timescales. Using these experimental workflows a greater degree of speed and information can be extracted from small datasets without compromising spatial resolution. This approach can be adapted to other 2D materials systems to gain further insights into the defect formation necessary to inform future automated fabrication techniques utilizing the STEM electron beam.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A new resolution quest in electron microscopy

Since its development over 20 years ago, aberration correction has revolutionized the way we study materials at the atomic scale. In this paper, I outline a set of technical developments for electron microscopes that, when implemented and combined, will enable us to better understand how matter behaves.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Extreme dimensions — how big (or small) can tailed phages be?

Bacteriophages (phages), that is, viruses that infect bacteria, represent an extremely diverse, yet under-characterized, group of viruses. Although most known phages harbour genomes that are shorter than 200 kb packaged into capsids with a diameter under 100 Å, more and more ‘extremely large’ phages are being discovered. Early reports of phages with genomes larger than 200 kb defined them as ‘jumbo phages’1. Phylogenetic analysis of these jumbo phages revealed that they form distinct and cohesive groups with multiple independent origins. This suggested that jumbo phages are not merely mistakes or aberrations of smaller phages that got too big, but that large genome size is generally a stable trait. In fact, a larger genome can be advantageous; almost all jumbo phages encode their own specific transcription factors, at least some parts of the replication machinery, and many also have their own tRNA genes, which enables increased independence from their host. Here, large genomes also provide more flexibility in terms of transcription strategy; smaller phage genomes tend to have a strict modular genome structure to increase efficiency, whereas jumbo phage genomes may be much less organized in the absence of a strong selection pressure to maintain a compact genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome expansion by a CRISPR trimmer-integrase

CRISPR–Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1–Cas2 integrase is necessary but not sufficient. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation, but many CRISPR–Cas systems lack Cas4. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1–Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ion irradiation induced phase transformation in gold nanocrystalline films

Gold is a noble metal typically stable as a solid in a face-centered cubic (FCC) structure under ambient conditions; however, under particular circumstances aberrant allotropes have been synthesized. In this work, we document the phase transformation of 25 nm thick nanocrystalline (NC) free-standing gold thin-film via in situ ion irradiation studied using atomic-resolution transmission electron microscopy (TEM). Utilizing precession electron diffraction (PED) techniques, crystallographic orientation and the radiation-induced relative strains were measured and furthermore used to determine that a combination of surface and radiation-induced strains lead to an FCC to hexagonal close packed (HCP) crystallographic phase transformation upon a 10 dpa radiation dose of Au 4+ ions. Contrary to previous studies, HCP phase in nanostructures of gold was stabilized and did not transform back to FCC due to a combination of size effects and defects imparted by damage cascades.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Genome-wide discovery of G-quadruplexes in barley

G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5' untranslated region (5' UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Phase evolution and structural modulation during in situ lithiation of MoS 2 , WS 2 and graphite in TEM

Li-ion batteries function by Li intercalating into and through the layered electrode materials. Intercalation is a solid-state interaction resulting in the formation of new phases. The new observations presented here reveal that at the nanoscale the intercalation mechanism is fundamentally different from the existing models and is actually driven by nonuniform phase distributions rather than the localized Li concentration: the lithiation process is a ‘distribution-dependent’ phenomena. Direct structure imaging of 2H and 1T dual-phase microstructures in lithiated MoS 2 and WS 2 along with the localized chemical segregation has been demonstrated in the current study. Li, a perennial challenge for the TEM, is detected and imaged using a low-dose, direct-electron detection camera on an aberration-corrected TEM and confirmed by image simulation. This study shows the presence of fully lithiated nanoscale domains of 2D host matrix in the vicinity of Li-lean regions. This confirms the nanoscale phase formation followed by Oswald ripening, where the less-stable smaller domains dissolves at the expense of the larger and more stable phases.

25 ENERGY STORAGE↗
DOE OSTI2021

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy

Animal models have expanded our understanding of temporal lobe epilepsy (TLE). However, translating these to cell-specific druggable hypotheses is not explored. Herein, we conducted an integrative insilico-analysis of an available transcriptomics dataset obtained from animals with pilocarpine-induced-TLE. A set of 119 genes with subtle-to-moderate impact predicted most forms of epilepsy with ~ 97% accuracy and characteristically mapped to upregulated homeostatic and downregulated synaptic pathways. The deconvolution of cellular proportions revealed opposing changes in diverse cell types. The proportion of nonneuronal cells increased whereas that of interneurons, except for those expressing vasoactive intestinal peptide (Vip), decreased, and pyramidal neurons of the cornu-ammonis (CA) subfields showed the highest variation in proportion. A probabilistic Bayesian-network demonstrated an aberrant and oscillating physiological interaction between nonneuronal cells involved in the blood–brain-barrier and Vip interneurons in driving seizures, and their role was evaluated insilico using transcriptomic changes induced by valproic-acid, which showed opposing effects in the two cell-types. Additionally, we revealed novel epileptic and antiepileptic mechanisms and predicted drugs using causal inference, outperforming the present drug repurposing approaches. These well-powered findings not only expand the understanding of TLE and seizure oscillation, but also provide predictive biomarkers of epilepsy, cellular and causal micro-circuitry changes associated with it, and a drug-discovery method focusing on these events.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Five-second STEM dislocation tomography for 300 nm thick specimen assisted by deep-learning-based noise filtering

Scanning transmission electron microscopy (STEM) is suitable for visualizing the inside of a relatively thick specimen than the conventional transmission electron microscopy, whose resolution is limited by the chromatic aberration of image forming lenses, and thus, the STEM mode has been employed frequently for computed electron tomography based three-dimensional (3D) structural characterization and combined with analytical methods such as annular dark field imaging or spectroscopies. However, the image quality of STEM is severely suffered by noise or artifacts especially when rapid imaging, in the order of millisecond per frame or faster, is pursued. Here we demonstrate a deep-learning-assisted rapid STEM tomography, which visualizes 3D dislocation arrangement only within five-second acquisition of all the tilt-series images even in a 300 nm thick steel specimen. The developed method offers a new platform for various in situ or operando 3D microanalyses in which dealing with relatively thick specimens or covering media like liquid cells are required.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Cdk5 mediates rotational force-induced brain injury

Abstract Millions of traumatic brain injuries (TBIs) occur annually. TBIs commonly result from falls, traffic accidents, and sports-related injuries, all of which involve rotational acceleration/deceleration of the brain. During these injuries, the brain endures a multitude of primary insults including compression of brain tissue, damaged vasculature, and diffuse axonal injury. All of these deleterious effects can contribute to secondary brain ischemia, cellular death, and neuroinflammation that progress for weeks, months, and lifetime after injury. While the linear effects of head trauma have been extensively modeled, less is known about how rotational injuries mediate neuronal damage following injury. Here, we developed a new model of repetitive rotational head trauma in rodents and demonstrated acute and prolonged pathological, behavioral, and electrophysiological effects of rotational TBI (rTBI). We identify aberrant Cyclin-dependent kinase 5 (Cdk5) activity as a principal mediator of rTBI. We utilized Cdk5-enriched phosphoproteomics to uncover potential downstream mediators of rTBI and show pharmacological inhibition of Cdk5 reduces the cognitive and pathological consequences of injury. These studies contribute meaningfully to our understanding of the mechanisms of rTBI and how they may be effectively treated.

60 APPLIED LIFE SCIENCES↗