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At least 1,243 records · Page 69

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DOE OSTI2024

Three-dimensional dispersion in the type-II Dirac semimetals PtTe 2 and PdTe 2 revealed through circular dichroism in angle-resolved photoemission spectroscopy

PtTe 2 and PdTe 2 are among the first transition metal dichalcogenides that were predicted to host type-II Dirac fermions, exotic particles prohibited in free space. These materials are layered and air stable, which makes them top candidates for technological applications that take advantage of their anisotropic magnetotransport properties. Here, in this work, we provide a detailed characterization of the electronic structure of PtTe 2 and PdTe 2 using angle-resolved photoemission spectroscopy (ARPES) and density functional theory calculations, offering an alternative interpretation for one of the Dirac-like dispersions in these materials. Through the use of circularly polarized light, we report a different behavior of such dispersion in PdTe 2 compared to PtTe 2 , that we relate to a symmetry analysis of the dipole matrix element. Such analysis reveals a link between the observed circular dichroism and the different momentum-dependent terms in the dispersion of these two compounds, despite their close similarity in crystal structure. Additionally, our data show a clear difference in the circular dichroic signal for the type-II Dirac cones characteristic of these materials, compared to their topologically protected surface states. Our paper provides a useful reference for the ARPES characterization of other transition metal dichalcogenides with topological properties and illustrates the use of circular dichroism as a guide to identify the topological character and attributes of two otherwise equivalent band dispersions.

angle-resolved photoemission spectroscopy↗

DOE OSTI2024

Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As

Abstract Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N 6 -methyladenosine (m 6 A) modifications near the 3′ end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m 6 As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m 6 A ensembles, and maintaining multiple of these m 6 As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Machine-Learning Functional Zonation Approach for Characterizing Terrestrial–Aquatic Interfaces: Application to Lake Erie

Ecosystems at coastal terrestrial–aquatic interfaces play a significant role in global biogeochemical cycles. In this study, we aimed to characterize coastal wetlands with particular focus on the co-variability between plant dynamics, topography, soil, and other environmental factors. We proposed a functional zonation approach based on machine learning clustering to identify the spatial regions, i.e., zones that capture these co-varied properties. This approach was applied to publicly available datasets along Lake Erie, in the Great Lakes Region. We investigated the heterogeneity of coastal ecosystem structures as a function of along-shore distance and transverse distance, based on the spatial data layers, including topography, wetland vegetation cover, and the time series of Landsat’s enhanced vegetation index (EVI) between 1990 and 2020. Results showed that the topographic metrics (elevation and slope), soil texture, and plant productivity influence the spatial distribution of wetland land-covers (emergent and phragmites). These results highlight a natural organization along the transverse axis, where the elevation and the EVI increase further away from the coastline. In addition, the clustering analysis allowed us to identify regions with distinct environmental characteristics, as well as the ones that are more sensitive to interannual lake-level variations.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Unveiling the nanoscale architectures and dynamics of protein assembly with in situ atomic force microscopy

Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter- and intra-molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter- and intra-molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high-speed AFM in near-native environments and recent AFM developments in the multimodal high-resolution imaging, bimodal imaging, live cell imaging, and machine-learning-enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.

36 MATERIALS SCIENCE↗

DOE OSTI2023

The Gross-Neveu-Yukawa archipelago

We perform a bootstrap analysis of a mixed system of four-point functions of bosonic and fermionic operators in parity-preserving 3d CFTs with O(N) global symmetry. Our results provide rigorous bounds on the scaling dimensions of the O(N)-symmetric Gross-Neveu-Yukawa (GNY) fixed points, constraining these theories to live in isolated islands in the space of CFT data. We focus on the cases N = 1, 2, 4, 8, which have applications to phase transitions in condensed matter systems, and compare our bounds to previous analytical and numerical results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Optimal sensor placement for reconstructing wind pressure field around buildings using compressed sensing

Deciding how to optimally deploy sensors in a large, complex, and spatially extended structure is critical to ensure that the surface pressure field is accurately captured for subsequent analysis and design. In some cases, reconstruction of missing data is required in downstream tasks such as the development of digital twins. Here, this paper presents a data-driven sparse sensor selection algorithm, aiming to provide the most information contents for reconstructing aerodynamic characteristics of wind pressures over tall building structures parsimoniously. The algorithm first fits a set of basis functions to the training data, then applies a computationally efficient QR algorithm that ranks existing pressure sensors in order of importance based on the state reconstruction to this tailored basis. The findings of this study show that the proposed algorithm successfully re- constructs the aerodynamic characteristics of tall buildings from sparse measurement locations, generating stable and optimal solutions across a range of conditions. As a result, this study serves as a promising first step toward leveraging the success of data-driven and machine learning algorithms to supplement traditional genetic algorithms currently used in wind engineering.

42 ENGINEERING↗

DOE OSTI2023

Learning continuous models for continuous physics

Abstract Dynamical systems that evolve continuously over time are ubiquitous throughout science and engineering. Machine learning (ML) provides data-driven approaches to model and predict the dynamics of such systems. A core issue with this approach is that ML models are typically trained on discrete data, using ML methodologies that are not aware of underlying continuity properties. This results in models that often do not capture any underlying continuous dynamics—either of the system of interest, or indeed of any related system. To address this challenge, we develop a convergence test based on numerical analysis theory. Our test verifies whether a model has learned a function that accurately approximates an underlying continuous dynamics. Models that fail this test fail to capture relevant dynamics, rendering them of limited utility for many scientific prediction tasks; while models that pass this test enable both better interpolation and better extrapolation in multiple ways. Our results illustrate how principled numerical analysis methods can be coupled with existing ML training/testing methodologies to validate models for science and engineering applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

A Bayesian desmearing algorithm for Bonse–Hart USANS with anisotropic scattering

Ultra-small-angle neutron scattering (USANS) using Bonse–Hart optics provides micrometer-scale structural insights but suffers from severe slit-geometry smearing. While well-established for isotropic systems, quantitative desmearing of anisotropic data remains a challenge because conventional corrections break down for non-radial scattering. In this work, we address this by developing a resolution-aware Bayesian framework that explicitly incorporates anisotropy via an affine deformation to the scattering pattern, guided by the principle of parsimony. This results in orientation-resolved point-spread functions that enable a self-consistent determination of both the resolution and deformation parameters. Using Gaussian process regression with uncertainty quantification and a probabilistic correction for multiple scattering, we demonstrate the framework’s effectiveness through numerical benchmarks and experimental studies of a stretched polymer melt. Our approach enables the seamless integration of SANS and USANS data, facilitating quantitative structural analysis of deformed materials at nanometer to micrometer scales.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Galaxy Interactions in Filaments and Sheets: Effects of the Large-scale Structures Versus the Local Density

Abstract Major interactions are known to trigger star formation in galaxies and alter their color. We study the major interactions in filaments and sheets using SDSS data to understand the influence of large-scale environments on galaxy interactions. We identify the galaxies in filaments and sheets using the local dimension and also find the major pairs residing in these environments. The star formation rate (SFR) and color of the interacting galaxies as a function of pair separation are separately analyzed in filaments and sheets. The analysis is repeated for three volume limited samples covering different magnitude ranges. The major pairs residing in the filaments show a significantly higher SFR and bluer color than those residing in the sheets up to the projected pair separation of ∼50 kpc. We observe a complete reversal of this behavior for both the SFR and color of the galaxy pairs having a projected separation larger than 50 kpc. Some earlier studies report that the galaxy pairs align with the filament axis. Such alignment inside filaments indicates anisotropic accretion that may cause these differences. We do not observe these trends in the brighter galaxy samples. The pairs in filaments and sheets from the brighter galaxy samples trace relatively denser regions in these environments. The absence of these trends in the brighter samples may be explained by the dominant effect of the local density over the effects of the large-scale environment.

Astronomy & Astrophysics↗

DOE OSTI2023

Parallel Algorithms for Computing the Tensor-Train Decomposition

The tensor-train (TT) decomposition expresses a tensor in a data-sparse format used in molecular simulations, high-order correlation functions, and optimization. In this paper, we propose four parallelizable algorithms that compute the TT format from various tensor inputs: (1) Parallel-TTSVD for traditional format, (2) PSTT and its variants for streaming data, (3) Tucker2TT for Tucker format, and (4) TT-fADI for solutions of Sylvester tensor equations. We provide theoretical guarantees of accuracy, parallelization methods, scaling analysis, and numerical results. For example, for a d-dimension tensor in $\mathbb{R}$ $n\times∙∙∙$$\times$$n$ a two-sided sketching algorithm PSTT2 is shown to have a memory complexity of $O(n^{[d/2]})$, improving upon $O(n^{d—1})$ from previous algorithms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Filtration Performance of Simulated 200 West Area Waste Feeds

This report describes the scaled experimental system and approach used to examine dead-end filtration performance of representative 200W waste feeds. The scaled system, which was originally designed and assembled to test Tank Side Cesium Removal (TSCR) system performance with higher-than-expected solid loadings in 2021 (Schonewill et al. 2021), was repurposed to conduct the current experiments at ~1/145 of full scale (based on throughput). Six experimental runs were conducted with five different 200W waste feed simulants: three using a DEF module scaled for TSCR and three using a DEF module scaled for the 200W process modules (based on the current design for the Advanced Modular Pretreatment System). Each experiment was run continuously for multiple days with an operating approach prototypic of the full-scale system. Staff performing the experimental runs monitored performance, obtained data from calibrated process instruments, and collected samples for observation and analysis. The measured data are presented with a focus on assessing DEF performance – specifically, the filters’ differential pressure response to the five waste simulants, frequency and efficacy of backwashing, and baseline recovery between experimental runs; data related to ion exchange column performance are also discussed in cases where the opportunity arose. The experimental campaign demonstrated that the DEFs satisfied their primary function of protecting the ion exchange column from solid intrusion for all the representative simulants used. The filters readily handled solids loadings of =500 ppm (and even greater), especially the modules scaled to the 200W process modules. Adjustments to the processing flow rate and reductions in feed temperature were observed to affect the rate of differential pressure increase on the filters, but neither adversely affected the ability of the DEFs to perform their primary function. Backflushing reliably recovered filter performance in all runs, although it did not prevent irreversible fouling for one simulant. The run that exhibited irreversible fouling established that both the quantity and the nature of the solids being filtered need to be considered when projecting filter performance.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Dark Energy Survey Year 3 results: Cosmology from cosmic shear and robustness to data calibration

This work, together with its companion paper, Secco, Samuroff et al., presents the Dark Energy Survey Year 3 cosmic shear measurements and cosmological constraints based on an analysis of over 100 million source galaxies. With the data spanning 4143 deg 2 on the sky, divided into four redshift bins, we produce the highest significance measurement of cosmic shear to date, with a signal-to-noise of 40. We conduct a blind analysis in the context of the ΛCDM model and find a 3% constraint of the clustering amplitude, S 8 ≡ σ 8 (Ω m /0.3) 0.5 = 0.759$^{+0.025}_{-0.023}$. A ΛCDM-Optimized analysis, which safely includes smaller scale information, yields a 2% precision measurement of S 8 = 0.772$^{+0.018}_{-0.017}$ that is consistent with the fiducial case. The two low-redshift measurements are statistically consistent with the Planck Cosmic Microwave Background result, however, both recovered S 8 values are lower than the high-redshift prediction by 2.3σ and 2.1σ (ρ-values of 0.02 and 0.05), respectively. The measurements are shown to be internally consistent across redshift bins, angular scales and correlation functions. The analysis is demonstrated to be robust to calibration systematics, with the S 8 posterior consistent when varying the choice of redshift calibration sample, the modeling of redshift uncertainty and methodology. Similarly, we find that the corrections included to account for the blending of galaxies shifts our best-fit S 8 by 0.5σ without incurring a substantial increase in uncertainty. We examine the limiting factors for the precision of the cosmological constraints and find observational systematics to be subdominant to the modeling of astrophysics. Specifically, we identify the uncertainties in modeling baryonic effects and intrinsic alignments as the limiting systematics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

Machine learning-based interatomic potential development and phase transition analysis of ferroelectric hafnium dioxide

The ferroelectric phase (𝑃⁢𝑐⁢𝑎⁢2 1 , which is in orthorhombic symmetry) of hafnium dioxide (HfO 2 ) has gained much attention due to its potential applications in nanoelectronics and advanced memory devices. However, its complex phase behavior under external stimuli, such as pressure and temperature, remains a subject of intense investigation. This study focuses on developing a machine learning-based interatomic potential (MLIP) that is trained with data from density-functional theory (DFT) calculations to simulate phase transitions and mechanical properties of HfO 2 . The developed MLIP predicts lattice parameters, equations of state, bulk and shear moduli, and elastic constants that closely align with DFT predictions for several phases and at various pressures. Once validated, the MLIP is used to investigate the phase transitions of ferroelectric HfO 2 (𝑃⁢𝑐⁢𝑎⁢2 1 ) under both isobaric and constant stress conditions at elevated temperatures ranging from 200 to 2500 K. We used several complementary methods, including local symmetry identification, radial distribution function, and x-ray diffraction characterization, to identify interesting phase transitions among several competitive hafnia phases predicted from our simulations. The suggested methods uniformly reveal that under pure deviatoric condition, the system favors a transition from the orthorhombic 𝑃⁢𝑐⁢𝑎⁢2 1 phase to a tetragonal (𝑃⁢4 2 /𝑛⁢𝑚⁢𝑐) phase, whereas a zero stress condition drives the system from the 𝑃⁢𝑐⁢𝑎⁢2 1 phase to another orthorhombic (𝑃⁢𝑏⁢𝑐⁢𝑛) phase. These findings provide crucial insights into stress and temperature-induced phase behavior of hafnia, guiding future experimental and theoretical studies for optimizing hafnia-based ferroelectric devices.

Ferroelectric HfO2↗

DOE OSTI2023

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Machine Intelligence-Centered System for Automated Characterization of Functional Materials and Interfaces

Classic design of experiment relies on a time-intensive workflow that requires planning, data interpretation, and hypothesis building by experienced researchers. Here, in this paper, we describe an integrated, machine-intelligent experimental system which enables simultaneous dynamic tests of electrical, optical, gravimetric, and viscoelastic properties of materials under a programmable dynamic environment. Specially designed software controls the experiment and performs on-the-fly extensive data analysis and dynamic modeling, real-time iterative feedback for dynamic control of experimental conditions, and rapid visualization of experimental results. The system operates with minimal human intervention and enables time-efficient characterization of complex dynamic multifunctional environmental responses of materials with simultaneous data processing and analytics. The system provides a viable platform for artificial intelligence (AI)-centered material characterization, which, when coupled with an AI-controlled synthesis system, could lead to accelerated discovery of multifunctional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Modeling Mycorrhizal Carbon Costs in Temperate Forests: The Impacts of Functional Diversity and Global Change Factors

Mycorrhizal fungi form symbiotic relationships with most plant species, facilitating nutrient acquisition while consuming a significant fraction of the plant's photosynthetic carbon (C), which we define as the mycorrhizal C cost. Drivers of the mycorrhizal C cost, which is crucial for predicting environmental impacts on plant productivity, remain under-explored and difficult to quantify. Ecosystem models that incorporate mycorrhizae can offer insights into mycorrhizal C cost dynamics, but their predictions have rarely been validated against empirical data. Here, in this study, we used the Myco-CORPSE model, which explicitly simulates mycorrhizal processes alongside soil carbon and nitrogen cycling, to investigate the drivers of mycorrhizal C cost in temperate forests. Applying this model to over 1,800 forest inventory plots across the eastern United States, we found that the simulations matched published data, showing higher C allocation to ectomycorrhizal (ECM) fungi (16.0% of net primary production (NPP)) compared to arbuscular mycorrhizal (AM) fungi (5.8% of NPP). Further analysis showed that mixed forests, co-dominated by both AM and ECM trees, allocated less C to mycorrhizal fungi compared to forests dominated by either AM or ECM fungi alone, due to complementary nutrient acquisition strategies. Elevated Nitrogen (N) deposition and higher temperatures reduce mycorrhizal C costs, favoring AM strategies. Conversely, elevated CO 2 (eCO 2 ) increased plant N demand and mycorrhizal C costs, favoring ECM strategies that access organic N sources. These findings underscore the critical role of mycorrhizal functional diversity in plant nutrient acquisition and C dynamics, providing new insights into how mycorrhizal symbioses respond to global change.

Shao, Siya [Dartmouth College, Hanover, NH (United↗

DOE OSTI2024

Top-down proteomics

Proteoforms arising from posttranslational modifications, genetic polymorphisms, and RNA splice variants, play a pivotal role as the key drivers in biology. Thus, a comprehensive understanding of proteoforms is essential for unraveling the intricacies of biological systems and bridging the gap between genotype and phenotype. By analyzing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and presents a next-generation approach for deciphering protein function, uncovering disease mechanisms, and advancing precision medicine. This Primer embarks on a journey into the world of TDP by encapsulating its historical context, underlying principles, recent advances, and an outlook on the future of TDP. The experimental section navigates instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques, and data collection. Results decipher raw data, visualize intact protein spectra, unravel data analysis, and explain proteoform identification, characterization, and quantitation, as well as statistical analysis. Various applications of TDP spanning the human proteoform project, biomedical, biopharmaceutical, and clinical applications are described. These are complemented by discussions on measurement reproducibility, limitations, and a forward-looking perspective outlining uncharted waters where the field can advance, and potential exciting future applications of TDP.

Roberts, David S.↗

DOE OSTI2023

Prevalence of Self-Reported Bothersome Tinnitus in U.S. Army Soldiers From January 1, 2015, Through September 30, 2019

Purpose: Tinnitus is a symptom of auditory dysfunction or injury and can be a precursor to permanent hearing loss. Tinnitus can interfere with communication, sleep, concentration, and mood; when this occurs, it is referred to as bothersome tinnitus. Annual hearing surveillance in the U.S. Army includes screening for bothersome tinnitus. Estimating the prevalence of self-reported bothersome tinnitus can facilitate prioritization of prevention and education efforts. The objective of this study was to examine Army hearing conservation data to estimate the prevalence of self-reported bothersome tinnitus as a function of age, hearing, sex, service component, and pay grade. Method: The study employed a cross-sectional, retrospective design. Records from 1,485,059 U.S. Army Soldiers retrieved from the Defense Occupational and Environmental Health Readiness System–Hearing Conservation were analyzed. Descriptive statistics and multinomial logistic regression analysis were used to estimate the prevalence of bothersome tinnitus and its associations with Soldiers' demographic characteristics. Results: The estimated prevalence of self-reported bothersome tinnitus was 17.1% between January 1, 2015, and September 30, 2019; 13.6% of the Soldiers reported “bothered a little” and 3.5% reported “bothered a lot.” Proportionally, the prevalence of self-reported bothersome tinnitus was higher for males, older Soldiers, and Reserve Component Soldiers. For every 1-year increase in age, the odds of self-reporting “bothered a little” tinnitus relative to “bothered not at all tinnitus” would be expected to increase by 2.2% (2.1%, 2.3%), and the odds of self-reporting “bothered a lot” tinnitus relative to “bothered not at all” tinnitus would be expected to increase by 3.6% (3.5%, 3.7%). Conclusions: The self-reported prevalence of bothersome tinnitus in the U.S. Army (17.1%) is substantially higher than that of the general population, where prevalence of bothersome tinnitus is estimated at 6.6%. Examination of bothersome tinnitus among Soldiers is an important step toward optimizing prevention, education, and intervention efforts.

Audiology & Speech-Language Pathology↗