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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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

GPS-Based Gamma Survey for Characterizing and Decommissioning NORM Sites - 20389

Gamma survey techniques are an especially powerful decommissioning tool at naturally occurring radioactive material (NORM) sites due to both the low cost to obtain data over a large spatial scale and the abundance of gamma emitters in the uranium and thorium decay series. Gamma surveys are executed by coupling a detector - most often a sodium iodide crystal - to a global positioning system (GPS), then reporting a location and gross gamma reading coincidentally to a data logger. Systems may be carried by workers or mounted to a car, all-terrain vehicle, or unmanned aerial system (UAS). The resulting data set provides a high-resolution but low precision map of the gamma radiation field over the area surveyed. Frequently this map is also correlated to soil concentrations of NORM radionuclides (most often, Ra-226) and/or exposure rate. Gamma survey parameters such as movement speed, transect spacing, and data logging frequency define the spatial resolution of the resulting surface, and can be optimized depending on the desired survey sensitivity. This paper examines gamma survey as a tool for decommissioning NORM sites and provides an overview of current gamma survey technology designed to improve the efficiency and effectiveness of the decommissioning process. Topics to be discussed in the paper include: - An overview of gamma survey systems, and the utility of different delivery vehicles depending on desired cost, desired spatial resolution, and site topography. - The influence of physical detector characteristics on detection sensitivity and survey planning. - The tradeoff between high-resolution and large spatial extent, but inherently uncertain data, and low-resolution, low spatial extent, but highly certain data, as well as the specific utility of each of these types of data during NORM facility decommissioning. - Confounding variables that may limit the utility of gamma survey at some sites (e.g., radon gas and spatial heterogeneity / hot spots), and methods to plan for and control these conditions. Results show that the confounding variables, such as radon and data output can greatly influence the overall data quality associated with the decommissioning process. In addition, the use of real-time and aerial survey platforms provides a method for ensuring proper spatial extent of the data. When applied thoughtfully, gamma survey is a powerful tool for detecting NORM radionuclides in the environment and a cost-effective technique for identifying areas requiring remediation. However, entities performing or using gamma survey as a decommissioning tool must be aware of both its advantages and its limitations before basing remediation or regulatory action on gamma survey results. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Influence of electrical field on the susceptibility of gallium nitride transistors to proton irradiation

Radiation susceptibility of electronic devices is commonly studied as a function of radiation energetics and device physics. Often overlooked is the presence or magnitude of the electrical field, which we hypothesize to play an influential role in low energy radiation. Accordingly, we present a comprehensive study of low-energy proton irradiation on gallium nitride high electron mobility transistors (HEMTs), turning the transistor ON or OFF during irradiation. Commercially available GaN HEMTs were exposed to 300 keV proton irradiation at fluences varying from 3.76 × 10 12 to 3.76 × 10 14 cm 2 , and the electrical performance was evaluated in terms of forward saturation current, transconductance, and threshold voltage. The results demonstrate that the presence of an electrical field makes it more susceptible to proton irradiation. The decrease of 12.4% in forward saturation and 19% in transconductance at the lowest fluence in ON mode suggests that both carrier density and mobility are reduced after irradiation. Additionally, a positive shift in threshold voltage (0.32 V and 0.09 V in ON and OFF mode, respectively) indicates the generation of acceptor-like traps due to proton bombardment. high-resolution transmission electron microscopy and energy dispersive x-ray spectroscopy analysis reveal significant defects introduction and atom intermixing near AlGaN/GaN interfaces and within the GaN layer after the highest irradiation dose employed in this study. According to in-situ Raman spectroscopy, defects caused by irradiation can lead to a rise in self-heating and a considerable increase in (∼750 times) thermoelastic stress in the GaN layer during device operation. The findings indicate device engineering or electrical biasing protocol must be employed to compensate for radiation-induced defects formed during proton irradiation to improve device durability and reliability.

gallium nitride↗
DOE OSTI2025

Tuning the low-energy band structure in twisted bilayer WSe2

Tuning the electronic structures of two-dimensional (2D) material-based heterostructures is of crucial importance for their use in functional next-generation electronics. Here, through angle-resolved photoemission spectroscopy with nanoscale spatial resolution (nano-ARPES), we systematically track the evolution of the near-Fermi-level electronic structure of bilayer WSe2 over a large range of twist angle. While the momentum positioning of the valence-band maxima (VBM) is independent of twist angle, we find that the energetic separation between the hole bands at the K point of the Brillouin zone and the higher binding-energy hole band at Γ can be varied in excess of 100 meV. We explore the mechanisms underpinning this evolution and discuss the implications for tuning both the size of the band gaps, and the efficiency of the spin-dependent electron-phonon coupling channels in homobilayer transition-metal dichalcogenide devices.

Vu, T-H-Y↗
DOE OSTI2022

From ground to excited electronic state dynamics of electron and ion irradiated graphene nanomaterials

Microscopes utilizing convergent electron and ion beams are emerging as powerful tools for both imaging and manipulating two-dimensional materials with atomic resolution, allowing the ultimate limits of nanofabrication to be realized. In this chapter, we detail the use of time-dependent electronic structure theory to determine the excited state properties and reactivity of functionalized graphene nanostructures. A time-dependent density functional theory treatment of electronic excitations of materials is presented, with specific emphasis on predicting the position-dependent electronic response of two-dimensional nanomaterials to electron beams. The method is demonstrated in a study highlighting the important role that electronic excitation can play in opening reaction pathways relevant to atomically precise defect manipulation in graphene. Finally, we provide some perspective on future development directions for methods of simulating nonequilibrium electronic and vibrational dynamics induced by electron/ion beams.

Lingerfelt, David↗
DOE OSTI2021

Molecular imaging of plant-microbe interactions on the Brachypodium seed surface

Plant growth-promoting rhizobacteria (PGPR) play a crucial role in biological control and pathogenic defense on and with-in plant tissues, however the mechanism(s) by which plants associate with PGPR to elicit such beneficial effects needs further study. Here, we present high mass resolution time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging of Brachypodium distachyon (Brachypodium) seeds with and without exposure to two model PGPR, i.e., Gram-negative Pseudomonas fluorescens SBW25::GFP (P.) and Gram-positive Arthrobacter chlorophenolicus A6::GFP (A.). Delayed image extraction was used to image PGPB-treated seed sections to reveal morphological changes. ToF-SIMS spectral compari-son, principal component analysis (PCA), and two-dimensional (2D) imaging show that the selected PGPR have different effects on the host seed surface, resulting in changes in chemical composition and morphology. Metabolite prod-ucts and biomarkers, such as flavonoids, phenolic com-pounds, fatty acids, and indole-3-acetic acid (IAA), were ob-served on the PGPR-treated seed surfaces. These compounds had different distributions on the Brachypodium seed surface for the two PGPR, indicating that the different bacteria elicited distinct responses from the host. Our results illustrate that ToF-SIMS is an effective tool to study plant-microbe interac-tions and to provide insightful information with submicrome-ter lateral resolution of the chemical distributions associated with morphological features, potentially offering a new way to study the mechanisms underlying beneficial roles of PGPR.

PGPR, Brachypodium distachyon, ToF-SIMS, metabolit↗
DOE OSTI2020

High-speed volumetric imaging of formaldehyde in a lifted turbulent jet flame using an acousto-optic deflector

The development of high-speed volumetric laser-induced fluorescence measurements of formaldehyde (CH 2 O-LIF) using a pulse-burst laser operated at a repetition rate of 100 kHz is presented here. A novel laser scanning system employing an acousto-optic deflector (AOD) enables quasi-4D CH 2 O-LIF imaging at a scan frequency of 10 kHz. The diagnostic capability of time-resolved volumetric imaging is demonstrated in a partially premixed DME/air lifted turbulent jet flame near the flame base. Simultaneous imaging of laser beam profiles is performed to account for the laser pulse energy fluctuation and laser sheet inhomogeneity. With the accurate registration of laser sheet positions, the volumetric reconstruction of CH 2 O-LIF signals is performed within a detection volume of 17.3 × 11.9 × 2.3 mm 3 with an average out-of-plane spatial resolution of 250μm. A surface detection algorithm with adaptive thresholding is used to determine the global maximum intensity gradient by calculating gradient percentiles. The flame topology characteristics are investigated by evaluating the 3D curvatures of CH 2 O surfaces. Curvatures calculated using 2D data systematically underestimate the full 3D curvature due to the lack of out-of-plane information. The inner surfaces near the turbulent fuel jet exhibit higher probabilities of large mean curvature than the outer surfaces. The saddle and cylindrical structures are dominant on both the inner and outer surfaces and the elliptic structures occur with lower probability. The results suggest that the damping of turbulent fluctuations by the temperature increase through the CH 2 O region reduces the curvature, but the local structure topology remains self-similar.

42 ENGINEERING↗
DOE OSTI2026

Activation dynamics of a water-soluble human mu-opioid receptor

The mu-opioid receptor (MOR), a class A G protein-coupled receptor mediates opioid analgesia and remains a central target for pain therapeutics. While crystal structures of MOR exist, they provide limited insight into the receptor’s dynamic conformational landscape underlying function. Here, we engineered a thermostable water-soluble MOR variant (wsMOR) that retains native-like ligand-binding and activation dynamics. This variant enables high-yield production and detailed solution-phase structural studies that are challenging with membrane-embedded MOR, providing a valuable tool for studying receptor activation and aqueous-phase drug screening. Using a combined computational and experimental approach, we performed long-timescale all-atom molecular dynamics simulations together with neutron scattering and single-molecule FRET, revealing a structurally stable receptor with a diverse ensemble of conformations at different temporal resolutions. In the ligand-free state, wsMOR displayed high conformational flexibility, which decreased upon agonist binding, particularly in transmembrane helix 6, a hallmark of G protein-coupled receptor activation. Positive allosteric modulation and G protein binding further stabilized active-like states. These findings highlight wsMOR’s conformational plasticity across picosecond to millisecond timescales and provide a foundation for structure-guided development of next-generation opioid ligands with improved efficacy and safety.

E, Agyemang [University of Tennessee Knoxville]↗
DOE OSTI2020

Evaluating the Utility of Permethylated Polysaccharide Solution NMR Data for Characterization of Insoluble Plant Cell Wall Polysaccharides

Plant cell wall polysaccharide analysis encompasses the utilization of a variety of analytical tools, including gas and liquid chromatography, mass spectrometry (MS), and nuclear magnetic resonance (NMR) spectroscopy. These methods provide complementary data, which enable confident structural proposals of the many complex polysaccharide structures that exist in the complex matrices of plant cell walls. However, cell walls contain fractions of varying solubilities, and a few techniques are available that can analyze all fractions simultaneously. We have discovered that permethylation affords the complete dissolution of both soluble and insoluble polysaccharide fractions of plant cell walls in organic solvents such as chloroform or acetonitrile, which can then be analyzed by a number of analytical techniques including MS and NMR. In this work, NMR structure analysis of 10 permethylated polysaccharide standards was undertaken to generate chemical shift data providing insights into spectral changes that result from permethylation of polysaccharide residues. This information is of especial relevance to the structure analysis of insoluble polysaccharide materials that otherwise are not easily investigated by solution-state NMR methodologies. The preassigned NMR chemical shift data is shown to be vital for NMR structure analysis of minor polysaccharide components of plant cell walls that are particularly difficult to assign by NMR correlation data alone. With the assigned chemical shift data, we analyzed the permethylated samples of destarched, alcohol-insoluble residues of switchgrass and poplar by two-dimensional NMR spectral profiling. Thus, we identified, in addition to the major polysaccharide components, two minor polysaccharides, namely, <5% 3-linked arabinoxylan (switchgrass) and <2% glucomannan (poplar). In particular, the position of the arabinose residue in the arabinoxylan of the switchgrass sample was confidently assigned based on chemical shift values, which are highly sensitive to local chemical environments. Furthermore, the high resolution afforded by the 1H NMR spectra of the permethylated switchgrass and poplar samples allowed facile relative quantitative analysis of their polysaccharide composition, utilizing only a few milligrams of the cell wall material. As a result, the concepts herein developed will thus facilitate NMR structure analysis of insoluble plant cell wall polysaccharides, more so of minor cell wall components that are especially challenging to analyze with current methods.

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

The co-located arrangement of ECEI and MIR microwave imaging diagnostics on EAST tokamak

The co-located configuration of Passive Electron Cyclotron Emission Imaging (ECEI) and active Microwave Imaging Reflectometry (MIR) diagnostics systems has been successfully implemented on the EAST fusion reactor. These advanced 2D microwave diagnostic tools offer 10–20 mm poloidal spatial resolution through large aperture quasi optics. This arrangement not only optimizes the utilization of limited observation windows but also facilitates concurrent measurements of plasma density and electron temperature at specific toroidal positions. Furthermore, this co-located setup holds great promise for enhancing research into electron heat transport and other pivotal plasma phenomena.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Subtropical Jet Regulates Arabian Winter Precipitation: A Viable Mechanism

The present study explores the mechanism governing wintertime (November–April) precipitation over the Arabian Peninsula (AP) using a 17-yr-long (2002–18) high-resolution WRF simulation. The composite analysis of strong precipitation events suggests that the equatorward extension of the upper-level jet together with the embedded upper-level trough creates a positive (cyclonic) midlevel vorticity and subsequently generates an anomalous lower-level convergence through Ekman pumping. This leads to the development of an anomalous surface low, which is further enhanced in the presence of the existing Red Sea trough over the AP. This surface low weakens the persistent anticyclone over the AP, shifting it further eastward to the Arabian Sea. The eastward shift in the lower-level anticyclone contributes to the transport of warm, moist air from the Arabian Sea and the Red Sea toward the AP. This warm, moist air converges with the cold and dry air advected by the midlatitude jet and creates a moisture convergence zone, leading to the initiation of convection. We test the proposed mechanism through numerical experiments with modified upper-level wind and demonstrate that a strong, southward intrusion of the jet can indeed lead to precipitation over the AP. The above mechanism also explains the interannual variability of precipitation over the AP. During wet years, we notice approximately 3 m s -1 stronger jet core magnitude and about a 2° equatorward shift of the jet compared to dry years. While the equatorward extension of the jet explains about 21% of the interannual variability, the jet magnitude explains around 7% of the variability during wet years.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Intermittent Frontogenesis in the Alboran Sea

Abstract We present a phenomenological description and dynamical analysis of the Alboran fronts using a realistic simulation at submesoscale resolution. The study is focused on east Alboran fronts emerging within relatively strong flows that separate from the Spanish coast into the basin interior. Despite modest lateral shifting associated with the position of the Alboran anticyclonic gyres and variations in intensity, these fronts present a similar structure and dynamical configuration as the climatological Almeria–Oran front. The statistical analysis of our solution shows that strained-induced frontogenesis is a recurrent submesoscale mechanism associated with these fronts, and the process is assessed in terms of the advective Lagrangian frontogenetic tendencies associated with buoyancy and velocity horizontal gradients. Intermittency in their strength and patterns is indicative of high variability in the occurrence of active frontogenesis in association with the secondary (overturning) circulation across the frontal gradient. As a result, we find many episodes with strong surface fronts that do not have much associated downwelling. Frontogenesis and the associated secondary circulation are further explored during two particular frontal events, both showing strong downwelling of (1) cm s −1 extending down into the pycnocline. A frontogenetic contribution of turbulent vertical momentum mixing to the secondary circulation is identified in the easternmost region during the cold season, when the dynamics are strongly influenced by the intrusion of the salty Northern Current. The background vertical velocity fields observed during the analyzed events indicate other currents in the submesoscale range, including tidal and topographic internal waves.

Capó, Esther↗
DOE OSTI2022

Classification of Wetland Vegetation Based on NDVI Time Series from the HLS Dataset

Natural wetlands are intrinsically heterogeneous and typically composed of a mosaic of ecosystem patches with different vegetation types. Hydrological and biogeochemical processes in wetlands vary strongly among these ecosystem patches. To date, most remote sensing classification approaches for wetland vegetation either rely on coarse images that cannot capture the spatial variability of wetland vegetation or rely on very-high-resolution multi-spectral images that are detailed but very sporadic in time (less than once per year). This study aimed to use NDVI time series, generated from NASA’s HLS dataset, to classify vegetation patches. We demonstrate our approach at a temperate, coastal lake, estuarine marsh. To classify vegetation patches, a standard time series library of the four land-cover patch types was built from referencing specific locations that were identified as “pure” pixels. These were identified using a single-time high-resolution image. We calculated the distance between the HLS-NDVI time series at each pixel and the “pure”-pixel standards for each land-cover type. The resulting true-positive classified rate was >73% for all patch types other than water lily. The classification accuracy was higher in pixels of a more uniform composition. A set of vegetation maps was created for the years 2016 to 2020 at our research site to identify the vegetation changes at the site as it is affected by rapid water elevation increases in Lake Erie. Our results reveal how changes in water elevation have changed the patch distribution in significant ways, leading to the local extinction of cattail by 2019 and a continuous increase in the area cover of water lily patches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Spatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development

Most legumes can establish a symbiotic association with soil rhizobia that trigger the development of root nodules. These nodules host the rhizobia and allow them to fix nitrogen efficiently. The perception of bacterial lipo-chitooligosaccharides (LCOs) in the epidermis initiates a signaling cascade that allows rhizobial intracellular infection in the root and de-differentiation and activation of cell division that gives rise to the nodule. Thus, nodule organogenesis and rhizobial infection need to be coupled in space and time for successful nodulation. The plant hormone cytokinin (CK) contributes to the coordination of this process, acting as an essential positive regulator of nodule organogenesis. However, the temporal regulation of tissue-specific CK signaling and biosynthesis in response to LCOs or Sinorhizobium meliloti inoculation in Medicago truncatula remains poorly understood. In this study, using a fluorescence-based CK sensor (pTCSn::nls:tGFP), we performed a high-resolution tissue-specific temporal characterization of the sequential activation of CK response during root infection and nodule development in M. truncatula after inoculation with S. meliloti. Loss-of-function mutants of the CK-biosynthetic gene ISOPENTENYLTRANSFERASE 3 (IPT3) showed impairment of nodulation, suggesting that IPT3 is required for nodule development in M. truncatula. Simultaneous live imaging of pIPT3::nls:tdTOMATO and the CK sensor showed that IPT3 induction in the pericycle at the base of nodule primordium contributes to CK biosynthesis, which in turn promotes expression of positive regulators of nodule organogenesis in M. truncatula.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantifying the impact of operating temperature on cracking in battery electrodes, using super-resolution of microscopy images and stereology

There are numerous factors that can have an impact on the degradation behavior of batteries, such as the number of recharge cycles or the charge rate. Here, we investigate the influence of operating temperature on the structural degradation of the microstructure in lithium-ion positive electrodes. For that purpose, the microstructure is characterized for cathodes which have been cycled for 200 cycles under 6C (10-minute) charging at different operating temperatures, namely, 20°C, 30°C, 40°C, and 50°C. For each operating condition scanning electron microscopy (SEM) images of cross-sectioned Li x Ni 0.5 Mn 0.3 Co 0.2 O 2 (NMC532) electrodes have been analyzed, to determine structural descriptors such as global particle porosity, crack size/length/width distribution, and porosity and specific surface area distribution of individual particles. Additionally, a stereological method has been deployed to investigate the local particle porosity as a function of distance to the particle center. Results show that particle porosity increases with increasing cycling temperature. Particle porosity is greatest at the particle center and decreases along the particle radius to the exterior. Particle surface area is similar across the four cycling-temperature aging conditions.

25 ENERGY STORAGE↗
DOE OSTI2024

Synthesis, Processing, and Use of Isotopically Enriched Epitaxial Oxide Thin Films

Isotopic engineering has emerged as a key approach to study the nucleation, diffusion, phase transitions, and reactions of materials at an atomic level. It aims to uncover mass transport pathways, kinetics, and operational and failure mechanisms of functional materials and devices. Understanding these phenomena leads to deeper insights into important physical processes, such as the transport of ions in energy conversion and storage devices and the role of active sites and supports during heterogeneous catalytic reactions. Likewise, isotopic engineering is being pursued as a means of modifying functionality to enable future technological applications. In this Account, we summarize our recent work employing isotope labeling (e.g., 18 O 2 and 57 Fe) during thin film synthesis and postgrowth processing to reveal growth mechanisms, defect chemistry, and elemental diffusion under working and extreme conditions. Isotope-resolved analysis techniques with nanometer-scale spatial resolution, such as time-of-flight secondary ion mass spectrometry and atom probe tomography, facilitate the accurate quantification of isotopic placement and concentration in our well-defined heterostructures with precisely positioned, isotope-enriched layers. By measuring the nanometer-scale redistribution between natural abundance and isotopically enriched oxygen layers during the deposition of Fe 2 O 3 and Cr 2 O 3 by molecular beam epitaxy, we identified intermixing processes driven by surface adatoms occurring both at the film growth surface and within the first few layers below the surface. Further insights into synthesis mechanisms were gained by studying the tungsten oxide thin films grown by evaporating WO 3 powder in the presence of background 18 O 2 , revealing minimal incorporation of background oxygen during the film formation process. Thermal and radiation-enhanced diffusion in epitaxial Fe and Cr oxides were precisely tracked using 18 O and 57 Fe tracer layers incorporated into model epitaxial oxide thin films. This approach has allowed us to access thermal diffusion behavior at lower temperatures than previously measured, revealing a potential changeover in diffusion mechanism. Understanding radiation-enhanced diffusion in model oxides that represent the surface layers on the structural components of nuclear reactors informs our understanding of their corrosion behavior under irradiation. Isotopic labeling can also provide unique insights into the surface exchange reactions and defect chemistry of electrocatalysts. For instance, tracking the change in 18 O concentration at the surface of an epitaxial LaNiO 3 thin film after the electrocatalytic oxygen evolution reaction revealed the participation of lattice oxygen, confirming a hypothesis that had been proposed previously. Lastly, we highlight a new direction wherein we perform in situ processing studies utilizing isotopic tracers in conjunction with model epitaxial thin films within the atom probe tomography instrument. Additionally, this Account illustrates the great potential of isotopic engineering to enable fundamental mechanistic insights into physical processes and engineer functional properties in epitaxial films, heterostructures, and superlattices.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Riboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. Such RNAs regulate expression of downstream genes by recognizing a specific cellular effector. Although nearly 50 riboswitch classes are known, only a handful recognize multiple effectors. Here, we report the 2.60-Å resolution co-crystal structure of a class I type I preQ 1 -sensing riboswitch that reveals two effectors stacked atop one another in a single binding pocket. These effectors bind with positive cooperativity in vitro and both molecules are necessary for gene regulation in bacterial cells. Stacked effector recognition appears to be a hallmark of the largest subgroup of preQ 1 riboswitches, including those from pathogens such as Neisseria gonorrhoeae. We postulate that binding to stacked effectors arose in the RNA World to closely position two substrates for RNA-mediated catalysis. These findings expand known effector recognition capabilities of riboswitches and have implications for antimicrobial development.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2020

A robust benchmark for detection of germline large deletions and insertions

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.

59 BASIC BIOLOGICAL SCIENCES↗