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At least 937 records · Page 52

A detailed phylogeny for the Methanomicrobiales

The small subunit rRNA sequence of twenty archaea, members of the Methanomicrobiales, permits a detailed phylogenetic tree to be inferred for the group. The tree confirms earlier studies, based on far fewer sequences, in showing the group to be divided into two major clusters, temporarily designated the "methanosarcina" group and the "methanogenium" group. The tree also defines phylogenetic relationships within these two groups, which in some cases do not agree with the phylogenetic relationships implied by current taxonomic names--a problem most acute for the genus Methanogenium and its relatives. The present phylogenetic characterization provides the basis for a consistent taxonomic restructuring of this major methanogenic taxon.

NASA Discipline Number 52-30↗

Rapid Identification of X-ray Diffraction Patterns Based on Very Limited Data by Interpretable Convolutional Neural Networks

Large volumes of data from material characterizations call for rapid and automatic data analysis to accelerate materials discovery. Herein, we report a convolutional neural network (CNN) that was trained based on theoretical data and very limited experimental data for fast identification of experimental X-ray diffraction (XRD) patterns of metal–organic frameworks (MOFs). To augment the data for training the model, noise was extracted from experimental data and shuffled; then it was merged with the main peaks that were extracted from theoretical spectra to synthesize new spectra. For the first time, one-to-one material identification was achieved. Theoretical MOFs patterns (1012) were augmented to a whole data set of 72 864 samples. It was then randomly shuffled and split into training (58 292 samples) and validation (14 572 samples) data sets at a ratio of 4:1. For the task of discriminating, the optimized model showed the highest identification accuracy of 96.7% for the top 5 ranking on a test data set of 30 hold-out samples. Neighborhood component analysis (NCA) on the experimental XRD samples shows that the samples from the same material are clustered in groups in the NCA map. Analysis on the class activation maps of the last CNN layer further discloses the mechanism by which the CNN model successfully identifies individual MOFs from the XRD patterns. Furthermore, this CNN model trained by the data augmentation technique would not only open numerous potential applications for identifying XRD patterns for different materials, but also pave avenues to autonomously analyze data by other characterization tools such as FTIR, Raman, and NMR spectroscopies.

36 MATERIALS SCIENCE↗

Amplified spontaneous emission in the extreme ultraviolet by expanding xenon clusters

Focused short-wavelength free-electron laser (FEL) pulses interacting with gas phase samples can induce by inner-shell ionization a short-lived population inversion, followed by coherent collective emission of directed, short, and strong radiation bursts. We extend our studies into the warm-dense matter (WDM) regime by investigating the nanoplasmas produced in an ensemble of nanometer-sized clusters by FEL irradiation. Here, additional pathways can also lead to strong, laserlike emission: Electron-ion collisions can yield a long-lived population inversion, and subsequent amplified spontaneous emission. We observe amplified spontaneous emission (ASE) in the extreme ultraviolet in xenon clusters excited by soft x-ray FEL pulses, we diagnose the generated nanoplasmas by fluorescence spectroscopy, and we study under various cluster and FEL parameters the directed ASE from the Xe 2+ 65 nm line. We show its exponential increase as a function of FEL irradiation power, and an accompanying collisional broadening of the emission spectra. These findings are corroborated by extensive numerical simulations based on theory, combining detailed hydrodynamic and kinetic simulations with time-dependent calculations of radiation transport, amplification, and collective emission in the WDM nanoplasma. Furthermore, our theoretical findings underline that population inversion is due to electron-ion collisions and that the observed decoherence processes can be empirically characterized by a phenomenological decoherence time in the range of 100–200 fs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗

Structural origin of disorder-induced ion conduction in NaFePO 4 cathode materials

Diffusion in NaFePO 4 can be enhanced through amorphization. Based on computations using DFT and machine learning potentials, we ascribe this phenomenon to the formation of less constrained Na-ion environments upon disordering. Most modern battery technologies depend on solid-state crystalline cathode materials. However, some of these materials are constrained by the low ionic conductivity of their most stable phases. An example of this is maricite (NaFePO 4 ). Interestingly, experiments have shown that maricite can improve its rate capability through disordering (amorphization). However, experimental characterization of amorphous cathode materials remains a major challenge, hindering a clear understanding of the structural origin of the disorder-induced improvement in sodium-ion mobility. To address this, we here employ molecular dynamics simulations by first training a machine learning potential for NaFePO 4 based on the atomic cluster expansion approach and a batch active learning potential parameterization scheme. This potential is then applied to explore the structural and dynamical properties of NaFePO 4 glasses as cathode materials. Specifically, we investigate the effect of glass structure on sodium-ion diffusion, revealing the relative influences of short-range and medium-range order features. We find significant heterogeneity in sodium-ion diffusivity in the glass, with fast-conducting ions residing in less constrained atomic environments with fewer P and Fe neighbors. These more mobile ions are also surrounded by larger ring-type structures. Overall, the results and developed approach present promising avenues for developing high-performance glassy cathodes for next-generation batteries.

Christensen, Rasmus↗

Shallow cloud variability in Houston, Texas, during the ESCAPE and TRACER field experiments

Shallow convection plays an important role in Earth's climate system by regulating the vertical transport of heat, moisture, and momentum in the lower troposphere. Aerosols, large-scale meteorology, and low-level convergence influence the spatiotemporal variability in shallow convection, and the coastal urban area of Houston, Texas, is an ideal laboratory to investigate these complex interactions. Here, geostationary satellite and ground-based radar observations from June to September 2022 during the TRacking Aerosol Convection interactions ExpeRiment (TRACER) and Experiment of Sea Breeze Convection, Aerosols, Precipitation, and Environment (ESCAPE) field campaigns are used to characterize the spatial coverage, vertical extent, and precipitation fraction of shallow convective clouds. The fused operational remote sensing datasets over a 250 km × 250 km domain are evaluated against profiling observations. The domain-wide diurnal shallow cloud fractions are used to identify four distinct modes of shallow convection. In all clusters, the domain-wide cloud fractions are consistently higher than the domain-wide precipitation fractions, and shallow cloud fractions are higher over water than they are over land, while the shallow precipitation fractions show the opposite behavior. In the two modes with minimal deep cloud activity, shallow cloud frequency is highest over ocean in the early morning, and there is a transition to higher shallow cloud frequency over land by the afternoon in one cluster or to high shallow cloud frequencies everywhere by the afternoon in the other. Lastly, we find regions with higher shallow cloud top heights and a large region along the coastline where shallow clouds are more likely to precipitate.

54 ENVIRONMENTAL SCIENCES↗

Crystal Growth of ZnSe and Related Ternary Compound Semiconductors by Vapor Transport

The objective of the project is to determine the relative contributions of gravity-driven fluid flows to the compositional distribution, incorporation of impurities and defects, and deviation from stoichiometry observed in the crystals grown by vapor transport as results of buoyance-driven convection and growth interface fluctuations caused by irregular fluid-flows. ZnSe and related ternary compounds, such as ZnSeS and ZnSeTe, were grown by vapor transport technique with real time in-situ non-invasive monitoring techniques. The grown crystals were characterized extensively to correlate the grown crystal properties with the growth conditions. The following are the research progress in the past two years. In-situ monitoring of partial pressure by optical absorption technique and visual observation of the growing crystal were performed during vapor growth of ZnSe. Low-temperature photoluminescence (PL) spectra and glow discharge mass spectroscopy (GDMS) were measured on ZnSe starting materials provided by various vendors and on bulk crystals grown from these starting materials by physical vapor transport (PVT) to study the effects of purification and contamination during crystal growth process. Optical characterization was performed on wafers sliced from the grown crystals of ZnSe, ZnTe and ZnSe(1-x),Te(x), (0<x<0.4). Energy band gaps at room temperature were determined from optical transmission measurements and a best fit curve to the band gap vs. composition, x, data gives a bowing parameter of 1.45. Low-temperature photoluminescence (PL) spectra of ZnSe and ZnTe were dominated by near band edge emissions and no deep donor-acceptor pairs were observed. The PL spectrum exhibited a broad emission for the ZnSe(1-x),Te(x), samples, 0.09<x<0.39. The single broad PL emission spectra and the spectra measured as a function of temperature were interpreted as being associated with the exciton bound to Te clusters because of the high Te content in these samples. To validate numerical codes, in-situ monitoring during the PVT of HgI2 was designed. Optical absorption spectra of the vapor phase over HgI2 were measured for wavelengths between 200 and 600nm at sample temperatures between 349 and 610K. The Beer's Law constants for 15 wavelengths between 200 and 440 nm were determined. From these constants the vapor pressure of HgI2 was established as a function of temperature for the liquid and the solid Beta-phases To characterize the growth conditions during the PVT growth of In-doped ZnSe the optical absorbance of the vapor phase over the In-Se system were measured and were used to obtain the partial pressures of Se2(g) and In2Se(g).

Su, Ching-Hua↗

Accurate Modeling of Bromide and Iodide Hydration with Data-Driven Many-Body Potentials

Ion–water interactions play a central role in determining the properties of aqueous systems in a wide range of environments. However, a quantitative understanding of how the hydration properties of ions evolve from small aqueous clusters to bulk solutions and interfaces remains elusive. Here, we introduce the second generation of data-driven many-body energy (MBnrg) potential energy functions (PEFs) representing bromide–water and iodide–water interactions. The MB-nrg PEFs use permutationally invariant polynomials to reproduce two-body and three-body energies calculated at the coupled cluster level of theory, and implicitly represent all higher-body energies using classical many-body polarization. Further, a systematic analysis of the hydration structure of small Br - (H 2 O) n and I - (H 2 O) n clusters demonstrates that the MBnrg PEFs predict interaction energies in quantitative agreement with “gold standard” coupled cluster reference values. Importantly, when used in molecular dynamics simulations carried out in the isothermal-isobaric ensemble for single bromide and iodide ions in liquid water, the MB-nrg PEFs predict extended X-ray absorption fine structure (EXAFS) spectra that accurately reproduce the experimental spectra, which thus allows for characterizing the hydration structure of the two ions with high level of confidence.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Two- and three-nucleon contact interactions and ground-state energies of light- and medium-mass nuclei

Classes of two-nucleon (2N) contact interactions are developed in configuration space at leading order (LO), next-to-leading order (NLO), and next-to-next-to-next-to-leading order (N3LO) by fitting the experimental singlet np scattering length and deuteron binding energy at LO, and np and pp scattering data in the laboratory-energy ranges 0–15 MeV at NLO and 0–25 MeV at N3LO. These interactions are regularized by including two Gaussian cutoffs, one for T = 0 and the other for T = 1 channels. The cutoffs are taken to vary in the ranges R 0 = (1.5 –2.3) fm and R 1 = (1.5 –3.0) fm. The 780 (1100) data points up to 15 (25) MeV energy, primarily differential cross sections, are fitted by the NLO (N3LO) models with a χ 2 / datum about 1.7 or less (well below 1.5), when harder cutoff values are adopted. As a first application, we report results for the binding energies of nuclei with mass numbers A = 3 –6 and 16 obtained with selected LO and NLO 2N models both by themselves as well as in combination with a LO three-nucleon (3N) contact interaction. The latter is characterized by a single low-energy constant that is fixed to reproduce the experimental 3 H binding energy. The inclusion of the 3N interaction largely removes the sensitivity to cutoff variations in the few-nucleon systems and leads to predictions for the 3 He and 4 He binding energies that cluster around 7.8 and 30 MeV, respectively. However, in 16 O this cutoff sensitivity remains rather strong. Finally, predictions at LO only are also reported for medium-mass nuclei with A = 40 , 48, and 90.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Remote Sensing-Informed Zonation for Understanding Snow, Plant and Soil Moisture Dynamics within a Mountain Ecosystem

In the headwater catchments of the Rocky Mountains, plant productivity and its dynamics are largely dependent upon water availability, which is influenced by changing snowmelt dynamics associated with climate change. Understanding and quantifying the interactions between snow, plants and soil moisture is challenging, since these interactions are highly heterogeneous in mountainous terrain, particularly as they are influenced by microtopography within a hillslope. Recent advances in satellite remote sensing have created an opportunity for monitoring snow and plant dynamics at high spatiotemporal resolutions that can capture microtopographic effects. In this study, we investigate the relationships among topography, snowmelt, soil moisture and plant dynamics in the East River watershed, Crested Butte, Colorado, based on a time series of 3-meter resolution PlanetScope normalized difference vegetation index (NDVI) images. To make use of a large volume of high-resolution time-lapse images (17 images total), we use unsupervised machine learning methods to reduce the dimensionality of the time lapse images by identifying spatial zones that have characteristic NDVI time series. We hypothesize that each zone represents a set of similar snowmelt and plant dynamics that differ from other identified zones and that these zones are associated with key topographic features, plant species and soil moisture. We compare different distance measures (Ward and complete linkage) to understand the effects of their influence on the zonation map. Results show that the identified zones are associated with particular microtopographic features; highly productive zones are associated with low slopes and high topographic wetness index, in contrast with zones of low productivity, which are associated with high slopes and low topographic wetness index. The zones also correspond to particular plant species distributions; higher forb coverage is associated with zones characterized by higher peak productivity combined with rapid senescence in low moisture conditions, while higher sagebrush coverage is associated with low productivity and similar senescence patterns between high and low moisture conditions. In addition, soil moisture probe and sensor data confirm that each zone has a unique soil moisture distribution. This cluster-based analysis can tractably analyze high-resolution time-lapse images to examine plant-soil-snow interactions, guide sampling and sensor placements and identify areas likely vulnerable to ecological change in the future.

54 ENVIRONMENTAL SCIENCES↗

Reduction of solar cell efficiency by edge defects across the back-surface-field junction - A developed perimeter model

Material imperfections, impurity clusters and fabrication defects across the back-surface-field junction can degrade the performance of high-efficiency solar cells. The degradation from defects appearing on the circumference of a solar cell is analyzed using a two-region developed perimeter device model. The width of the defective perimeter region is characterized by the range or the distance-of-influence of the defective edge and this width is about two diffusion lengths. The defective edge is characterized by a surface recombination velocity. Family of theoretical curves and numerical examples are presented to show that significant reduction of open-circuit voltage can occur in high-efficiency cells which are thin compared with the diffusion length. In one example, the degradation is decreased from 135 mV to 75 mV when the cell size is increased from 10 to 100 times the diffusion length in a thin cell whose thickness is 1% of the diffusion length.

Sah, C. T.↗

Demonstration of a Segment Alignment Maintenance System on a Seven-Segment Sub-Array of the Hobby-Eberly Telescope

NASA's Marshall Space Flight Center, in collaboration with Blue Line Engineering of Colorado Springs, Colorado, is developing a Segment Alignment Maintenance System (SAMS) for McDonald Observatory's Hobby-Eberly Telescope (HET). The SAMS shall sense motions of the 91 primary mirror segments and send corrections to HET's primary mirror controller as the mirror segments misalign due to thermo-elastic deformations of the mirror support structure. The SAMS consists of inductive edge sensors supplemented by inclinometers for global radius of curvature sensing. All measurements are sent to the SAMS computer where mirror motion corrections are calculated. In October 2000, a prototype SAMS was installed on a seven-segment cluster of the HET. Subsequent testing has shown that the SAMS concept and architecture are a viable practical approach to maintaining HET's primary mirror figure, or the figure of any large segmented telescope. This paper gives a functional description of the SAMS sub-array components and presents test data to characterize the performance of the sub-array SAMS.

Rakoczy, John↗

Segment Alignment Maintenance System for the Hobby-Eberly Telescope

NASA's Marshall Space Flight Center, in collaboration with Blue Line Engineering of Colorado Springs, Colorado, is developing a Segment Alignment Maintenance System (SAMS) for McDonald Observatory's Hobby-Eberly Telescope (HET). The SAMS shall sense motions of the 91 primary mirror segments and send corrections to HET's primary mirror controller as the mirror segments misalign due to thermo -elastic deformations of the mirror support structure. The SAMS consists of inductive edge sensors. All measurements are sent to the SAMS computer where mirror motion corrections are calculated. In October 2000, a prototype SAMS was installed on a seven-segment cluster of the HET. Subsequent testing has shown that the SAMS concept and architecture are a viable practical approach to maintaining HET's primary mirror figure, or the figure of any large segmented telescope. This paper gives a functional description of the SAMS sub-array components and presents test data to characterize the performance of the subarray SAMS.

Rakoczy, John↗

Electronic Spin Relaxation and Clustering in High-Pressure High-Temperature Synthesized Microcrystalline Diamond Particles with Reduced Nitrogen Content

The negatively charged nitrogen-vacancy (NV – ) color center in diamonds is widely studied because of numerous applications of this unique quantum system in sensing and quantum information sciences. While substitutional nitrogen is required to form the NV – centers in diamond, it also yields other paramagnetic defects─primarily the neutrally charged substitutional nitrogen centers (P1)─that decrease NV – spin coherence, which in turn degrades performance in applications. Herein, we investigate high-pressure high-temperature synthesized diamond microparticles (ca. 140–185 μm) having lower─ranging from 3 to 38 ppm─than the typical nitrogen content of type 1b diamond ( ca. 100 ppm and higher) typically used for the production of fluorescent diamond particles with NV – centers. A suite of electron paramagnetic resonance, optically detected magnetic resonance, and nuclear magnetic resonance methods are used to characterize spin properties of P1 and NV – centers in the particles. Upon decreasing the nitrogen content from 29 to 3 ppm, the ensemble NV – T 2 relaxation time increased by about 3-fold as measured directly in the Hahn Echo experiment at magnetic field of 1.2 T. Analysis of electronic relaxation of P1 centers revealed the existence of at least two distinct populations of P1 centers, consisting of fast and slower relaxing spins and allowed for an estimation of local concentrations. Even with <10 ppm nitrogen contents, the analysis indicated a highly heterogeneous distribution of P1 centers, suggesting the possibility of P1 spin clustering even at low nitrogen concentrations. The combined data demonstrate that the particles prepared from HPHT diamond with a low nitrogen content offer improved spin properties that are beneficial for NV – sensing applications.

Carbon↗

Fourier transform infrared and Raman spectroscopic characterization of homogeneous solution concentration gradients near a container wall at different temperatures

Fourier transform infrared (FTIR) and Raman spectroscopic techniques were used to study the solution concentration gradient in succino nitrile-rich and water-rich homogeneous solutions. The spectroscopic data shows significant concentration dependency. Although FTIR-attenuated total reflectance could not yield surface spectra since the evanescent infrared wave penetrated deep into the bulk solution, it showed that water-rich clusters were decreased at higher temperatures. This result is consistent with the calorimetric results reported earlier.

Loo, B. H.↗

Irradiation damage reduces alloy corrosion rate via oxide space charge compensation effects

Radiation effects in materials often compound and accelerate other detrimental phenomena such as embrittlement, oxidation and creep. However, irradiation can also decrease the oxidation rate, for instance with ZrNb alloys nuclear fuel cladding. In this study, we rationalize this observation on Zr-0.5Nb alloy by introducing a mechanism based on oxide space charge modification, resulting from irradiation enhanced Nb clustering. Here, this mechanism is investigated using a multiscale approach: from the macroscale, to determine post-irradiation oxidation kinetics, to the atomic scale, using in-situ atom probe tomography sample oxidation, to observe elemental solute redistribution across the oxide/metal interface. The mechanism is further supported by high resolution transmission electron microscopy characterization and density functional theory calculations. A point defect model is proposed to account for oxide space charge effects and their changes under irradiation. This integrated, multiscale experimental and modeling approach challenges the current paradigm on irradiation effects and how they can potentially improve materials performance in extreme environments.

36 MATERIALS SCIENCE↗

Unexpected Conformational Behavior of Poly(poly(ethylene glycol) methacrylate)-Poly(propylene carbonate)-Poly(poly(ethylene glycol) methacrylate) (PPEGMA-PPC-PPEGMA) Amphiphilic Block Copolymers in Micellar Solution and at the Air-Water Interface

Self-assemblies (bulk micelles and Langmuir monolayers) of a new amphiphilic block copolymer, poly(poly(ethylene glycol) methacrylate)-poly(propylene carbonate)-poly(poly(ethylene glycol) methacrylate) (PPEGMA-PPC-PPEGMA), were investigated in dilute aqueous solution and at the air-water interface. An important feature that distinguishes PPEGMA-PPC-PPEGMA from conventional linear PEG-based polymer surfactants is that in the hydrophilic PPEGMA block the PEG moieties exist as side chains attached to the poly(methacrylate) (PMA) backbone. This study was performed using three PPEGMA-PPC-PPEGMA samples having an identical PPC molecular weight (5.6 kDa) and different PPEGMA molecular weights (7.3, 2.8 and 2.1 kDa on either side) (named as “G7C6G7”, “G3C5G3”, and “G2C6G2”, respectively). Cryo-TEM images revealed that G2C6G2 micelles form large clusters, whereas G7C6G7 micelles exist as unimers; the behavior of G3C6G3 is intermediate. The average core surface distance between two adjacent G2C6G2 micelles in a cluster was estimated to be only about 3.7 nm, which suggests that in the micelle corona layer only the PEG side chains (but not the PMA backbone) exist as hydrated brush chains. A calculation showed that at the small micelle separation distance observed, the van der Waals attractive forces become significant, and are thus likely responsible for the cluster formation. Steady shear rheometry measurements confirmed that G2C6G2 micelles are indeed only weakly bound in clusters, and these micelle clusters are thus prone to breakup even under mild steady shear. The micelle breakup force estimated from the shear viscosity data is in reasonable agreement with an estimate obtained from the theoretical van der Waals interaction potential. Langmuir monolayers formed at the air-water interface by PPEGMA-PPC-PPEGMA were also characterized; surface pressure-area measurements were performed. Detailed features of the surface pressure-area isotherms further supported that only the PEG side chains are hydrated in the subphase, while the PMA backbone remains unhydrated and situated on the water surface.

Lee, Jaewon↗