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At least 271 records · Page 15

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DOE OSTI2020

Moving beyond the Solvent-Tip Approximation to Determine Site-Specific Variations of Interfacial Water Structure through 3D Force Microscopy

Although interfacial solution structure impacts environmental, biological, and technological phenomena, including colloidal stability, protein assembly, heterogeneous nucleation, and water desalination, its molecular details remain poorly understood. Here, we visualize the three-dimensional (3D) hydration structure at the boehmite(010)-water interface using fast force mapping (FFM). Using a self-consistent scheme to decouple long-range tip-sample interactions from short-range solvation forces, we obtain the solution structure with lattice resolution. The results are benchmarked against molecular dynamics simulations that explicitly include the effects of the tip with different levels of approximation and systematically account for tip size, chemistry, and confinement effects. We find four laterally structured water layers within 1 nm of the surface, with the highest water densities at sites adjacent to hydroxyl groups. The key features beyond the first two layers can only be predicted using a full-scale simulation of the boehmite-water-silica system. Our findings further reveal a complex relationship between site-specific chemistry, water density, and long-range particle interactions; and present important advances toward quantitative data interpretation in 3D FFM.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Development of a Miniaturized Mobile Mapping System for In-Row, Under-Canopy Phenotyping

This paper focuses on the development of a miniaturized mobile mapping platform with advantages over current agricultural phenotyping systems in terms of acquiring data that facilitate under-canopy plant trait extraction. The system is based on an unmanned ground vehicle (UGV) for in-row, under-canopy data acquisition to deliver accurately georeferenced 2D and 3D products. The paper addresses three main aspects pertaining to the UGV development: (a) architecture of the UGV mobile mapping system (MMS), (b) quality assessment of acquired data in terms of georeferencing information as well as derived 3D point cloud, and (c) ability to derive phenotypic plant traits using data acquired by the UGV MMS. The experimental results from this study demonstrate the ability of the UGV MMS to acquire dense and accurate data over agricultural fields that would facilitate highly accurate plant phenotyping (better than above-canopy platforms such as unmanned aerial systems and high-clearance tractors). Plant centers and plant count with an accuracy in the 90% range have been achieved.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Steptoe Valley NV Data Compilation: Understanding a Stratigraphic Hydrothermal Resource through Geophysical Imaging

Sandia National Laboratories partnered with a multi-disciplinary group of subject matter experts to evaluate a stratigraphic geothermal resource in Steptoe Valley, Nevada using both established and novel geophysical imaging techniques. Provided here are a compilation of newly acquired data over the area and select modeling efforts. This encompasses a 3D geological model (inclusive of full Leapfrog files, Leapfrog viewer files, and XYZ data for faults and stratigraphy) with embedded geophysical modeling, controlled-source electromagnetic (CSEM) and magnetotelluric (MT) data packages, aqueous spring geochemistry data, seismic reflection interpretations, and a gravity data package. The stratigraphic reservoir in Steptoe Valley was previously discovered during oil and gas exploration. Subsequent studies, such as the Nevada Play Fairway Analysis, added data which further highlighted potential resource targets in the basin. Geophysical surveys, complimented with refined geologic mapping and geochemical sampling, were deployed to further characterize the resource. The resulting 3D geologic interpretation, conceptual model refinements, and reservoir simulations suggest that a power-capable reservoir is economically accessible in the Paleozoic carbonates of the deep/central basin. Additional geophysical characterization and exploration drilling efforts are recommended to calibrate interpretation and determine where/how to potentially develop the Steptoe resource. The geophysical tools, interpretations, lessons learned, and publicly available data generated by this study establish an exploration methodology to inform decisions for successful development of stratigraphic reservoirs.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

Increased enhancer–promoter interactions during developmental enhancer activation in mammals

Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here, in this study, we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A Comparative Study of the Perceptual Sensitivity of Topological Visualizations to Feature Variations

Color maps are a commonly used visualization technique in which data are mapped to optical properties, e.g., color or opacity. Color maps, however, do not explicitly convey structures (e.g., positions and scale of features) within data. Topology-based visualizations reveal and explicitly communicate structures underlying data. Although our understanding of what types of features are captured by topological visualizations is good, our understanding of people's perception of those features is not. Further, this paper evaluates the sensitivity of topology-based isocontour, Reeb graph, and persistence diagram visualizations compared to a reference color map visualization for synthetically generated scalar fields on 2-manifold triangular meshes embedded in 3D. In particular, we built and ran a human-subject study that evaluated the perception of data features characterized by Gaussian signals and measured how effectively each visualization technique portrays variations of data features arising from the position and amplitude variation of a mixture of Gaussians. For positional feature variations, the results showed that only the Reeb graph visualization had high sensitivity. For amplitude feature variations, persistence diagrams and color maps demonstrated the highest sensitivity, whereas isocontours showed only weak sensitivity. These results take an important step toward understanding which topology-based tools are best for various data and task scenarios and their effectiveness in conveying topological variations as compared to conventional color mapping.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Movement Models to Predict Low‐Altitude Flight of Soaring Birds Using Look‐Ahead Environmental Factors

Advances in fine-scale movement modeling of soaring birds can aid efforts to understand and resolve the impacts of anthropogenic activities on such birds. Soaring birds often rely on underlying terrain and low-altitude updrafts to govern their flights at rotor-swept altitudes (≤ 200 m above ground level), which puts them at risk of collision with wind turbines. We developed a data-driven Markov model at 1-s resolution that predicts the fine-scale flight behavior of golden eagles (Aquila chrysaetos) as a function of ecological covariates at the current location as well as those within an eagle's line of sight. We only considered ecological covariates that are readily available in real-time (ground elevation and wind conditions). Latent factors (age, sex, species, behavioral intent, migratory status) were intentionally left out of the model. We calibrated the model using golden eagle telemetry data collected in two different ecoregions of the United States. Given a starting location, the calibrated model simulates multiple stochastic 3D paths to produce a time-explicit and spatially explicit risk map of turbine collisions. We discovered an empirical relation between the rate of change of heading and the orographic updraft conditions within an eagle's line of sight. Our model performed most effectively when predicting predominantly-soaring flights at rotor-swept altitudes during wind conditions in which turbines are likely to be operational. The calibrated model could be used in concert with automated eagle detection and turbine curtailment technologies. Specifically, once an eagle is detected by those systems, our model could then provide accurate predictions of turbines the eagle is likely to interact with in the near term.

17 WIND ENERGY↗

DOE OSTI2021

3D radiation, density, and MHD structures following neon shattered pellet injection into stable DIII-D Super H-mode discharges

Six nominally repeat neon shattered pellet injection (SPI) shutdowns of stable DIII-D Super H-modes are studied to understand the 3D properties of the radiation and impurity transport. The radiation efficiency and radiation peaking determine whether first wall melting is expected following disruption mitigation in ITER. Previous studies make use of axisymmetric approximations to infer radiation efficiencies, but validating the high efficiency required by ITER necessitates improved accuracy, and this work contributes by exploring the 3D radiation and density structures that will inform forward modeling. When the neon shatter plume produced by the SPI reaches the plasma edge, m/n = 3/1 and 2/1 island O-points are observed to align with the injection trajectory in five out of six cases, suggesting that the injected material seeds the island O-points. Field aligned neon structures emitting Ne-I line radiation drift at 1 km/s in the ion diamagnetic drift direction during the pre-TQ, tracking the motion of the m/n = 2/1 island O-point. Neon fragments penetrate to the q = 2 surface by the time of the TQ. Techniques to constrain the 3D emissivity are explored, and one method constrains a 3D flux tube that is consistent with the radiation data, and when mapped to the interferometers, intersects the lasers that measure the highest density. The resulting structure derived from the radiation measurements exists near the 2/1 island X-point. In five repeatable discharges, the peak of the radiation in the toroidal direction exists in a 120° toroidal sector where the injection occurs, in contrast with the outlier discharge where the toroidal peak exists in the complementary 240° toroidal sector far from the injector, and where a 50% lower density rise is observed. In conclusion, the n = 1 phase behavior is markedly different in the outlier discharge, suggesting a possible dependence of the radiation structure and the assimilation efficiency on MHD.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

2D Reconstruction of Magnetotail Electron Diffusion Region Measured by MMS

Models for collisionless magnetic reconnection in near-Earth space are distinctly characterized as 2D or 3D. In 2D kinetic models, the frozen-in law for the electron fluid is usually broken by laminar dynamics involving structures set by the electron orbit size, while in 3D models the width of the electron diffusion region is broadened by turbulent effects. We present an analysis of in situ spacecraft observations from the Earth's magnetotail of a fortuitous encounter with an active reconnection region, mapping the observations onto a 2D spatial domain. While the event likely was perturbed by low-frequency 3D dynamics, the structure of the electron diffusion region remains consistent with results from a 2D kinetic simulation. As such, the event represents a unique validation of 2D kinetic, and laminar reconnection models.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Characterizing the magnetic fields of nearby molecular clouds using submillimeter polarization observations

Of all the factors that influence star formation, magnetic fields are perhaps the least well understood. The goal of this paper is to characterize the 3D magnetic field properties of nearby molecular clouds through various methods of statistically analysing maps of polarized dust emission. Our study focuses on nine clouds, with data taken from the Planck Sky Survey as well as data from the Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry observations of Vela C. We compare the distributions of polarization fraction (p), dispersion in polarization angles ($\mathcal {S}$), and hydrogen column density (N H ) for each of our targeted clouds. To broaden the scope of our analysis, we compare the distributions of our clouds’ polarization observables with measurements from synthetic polarization maps generated from numerical simulations. We also use the distribution of polarization fraction measurements to estimate the inclination angle of each cloud’s cloud-scale magnetic field. We obtain a range of inclination angles associated with our clouds, varying from 16° to 69°. We establish inverse correlations between p and both $\mathcal {S}$ and NH in almost every cloud, but we are unable to establish a statistically robust $\mathcal {S}$ versus NH trend. By comparing the results of these different statistical analysis techniques, we are able to propose a more comprehensive view of each cloud’s 3D magnetic field properties. These detailed cloud analyses will be useful in the continued studies of cloud-scale magnetic fields and the ways in which they affect star formation within these molecular clouds.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

3D Seismic Anatomy of a Watershed Reveals Climate–Topography Coupling That Drives Water Flowpaths and Bedrock Weathering

To investigate how bedrock transforms to soil, we mapped the topography of the interface demarcating onset of weathering under an east-west trending shale watershed in the Valley and Ridge province in the U.S.A. Using wave-equation travel-time tomography from a seismic array of >4000 geophones, we obtained a 3D P-wave velocity (Vp) model that resolves structures ~20 m below land surface (mbls). The depth of mobile soil and the onset of dissolution of chlorite roughly match Vp = 600 m/s and Vp = 2700 m/s, respectively. Chlorite dissolution initiates porosity growth in the shale matrix. Depth to the 2700 m/s contour is greater under the N- as compared to S-facing hillslopes and under sub-planar as compared to concave-up land surfaces. Broadly, the geometries of the ‘soil’ and ‘chlorite’ Vp contours are consistent with the calculated potential for shear fracture opening under weak regional compression. However, this calculated fracture potential does not consistently explain observations related to N- vs. S-facing aspect nor fracture density observed by borehole televiewer. Apparently, regional compression is only a secondary influence on Vp: the primary driver of P-wave slowing in the upper layers of this catchment is topographic control of reactive water flowpaths and their integrated effects on weathering. Here, the Vp result is best explained as the long-term integrated effect of groundwater flow-induced geochemical weathering of shale in response to climate-driven patterns of micro- and macro-topography.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

4D Imaging of ZnO-Coated Nanoporous Al 2 O 3 Aerogels by Chemically Sensitive Ptychographic Tomography: Implications for Designer Catalysts

The 3D chemical structure (4D spectromicroscopy) of nanoporous Al 2 O 3 aerogels coated with ZnO by atomic layer deposition (ALD) was studied by multienergy scanning transmission X-ray microscopy. These materials are representative of a class of designer catalysts in which the nanoporous support is prepared separately from the active catalyst material, which is subsequently introduced by ALD, thereby allowing independent optimization of the morphology, chemistry, and spatial distribution of the support and catalyst. The samples studied were prepared by Ga ion and Xe plasma focused ion beam (FIB) milling as well as drop casting from water suspension. Zn L and Al K edge spectra of six samples with three different ZnO loadings were measured to investigate how loading and different sample preparation methods affect the 3D distribution of the ZnO and Al 2 O 3 . Scanning transmission X-ray microscopy (STXM) and ptychographic imaging at two energies each at the Zn L 3 and Al K edge were measured. The ptychography data were analyzed by using the SHARP reconstruction code to generate quantitative 2D chemical maps of the Al 2 O 3 and the ZnO. The STXM and ptychography maps were then measured at a sequence of tilt angles, covering up to 160° of rotation. The 3D structure of the ZnO and Al 2 O 3 was derived from the tilt series data by tomographic reconstruction using a compressed sensing algorithm. A twodimensional spatial resolution (half-period) of 6 nm, measured by Fourier ring correlation, and a 3D spatial resolution (half-period) of 9 nm, measured by Fourier shell correlation, were achieved when using the COSMIC beamline at the Advanced Light Source (ALS). The results show that for all of the ZnO loadings studied there is nonuniform coverage of the ZnO on the Al 2 O 3 aerogel framework. In addition, we found that both FIB methods create sample artifacts, although the distortion was less with Xe plasma than Ga ion FIB.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Probe the Localized Electrochemical Environment Effects and Electrode Reaction Dynamics for Metal Batteries using In Situ 3D Microscopy

Uncontrollable dendrite growth is closely related to non-uniform reaction environments. However, there is a lack of understanding and analysis methods to probe the localized electrochemical environment (LEE). Here the effects of the LEE are investigated, including localized ion concentrations, current density, and electric potential, on metal plating/stripping dynamics and dendrite minimization. A novel in situ 3D microscopy technique is developed to image the morphology dynamics and deposition rate of Zn plating/stripping processes on 3D Zn–Mn anodes. Using the in situ 3D microscope, the electrode morphology changes during the reactions are directly imaged and Zn deposition rate maps at different time points are obtained. It is found that reaction kinetics are highly correlated to LEE and electrode morphology. To further quantify the LEE effects, the digital twin technique is employed that allows the accurate calculation of the electrochemical environments, such as localized ion concentrations, current density, and electric potential, which cannot be directly measured from experiments. We found that the curvature of the 3D electrode surface determines the LEE and significantly influences reaction kinetics. This provides a new strategy to minimize the dendrite formation by designing and optimizing the 3D geometry of the electrode to control the LEE.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Accelerating Quantum Materials Development with Advances in Transmission Electron Microscopy

Quantum materials are driving a technology revolution in sensing, communication, and computing, while simultaneously testing many core theories of the past century. Materials such as topological insulators, complex oxides, superconductors, quantum dots, color center-hosting semiconductors, and other types of strongly correlated materials can exhibit exotic properties such as edge conductivity, multiferroicity, magnetoresistance, superconductivity, single photon emission, and optical-spin locking. These emergent properties arise and depend strongly on the material’s detailed atomic-scale structure, including atomic defects, dopants, and lattice stacking. In this review, we describe how progress in the field of electron microscopy (EM), including in situ and in operando EM, can accelerate advances in quantum materials and quantum excitations. We begin by describing fundamental EM principles and operation modes. We then discuss various EM methods such as (i) EM spectroscopies, including electron energy loss spectroscopy (EELS), cathodoluminescence (CL), and electron energy gain spectroscopy (EEGS); (ii) four-dimensional scanning transmission electron microscopy (4D-STEM); (iii) dynamic and ultrafast EM (UEM); (iv) complementary ultrafast spectroscopies (UED, XFEL); and (v) atomic electron tomography (AET). We describe how these methods could inform structure–function relations in quantum materials down to the picometer scale and femtosecond time resolution, and how they enable precision positioning of atomic defects and high-resolution manipulation of quantum materials. For each method, we also describe existing limitations to solve open quantum mechanical questions, and how they might be addressed to accelerate progress. Among numerous notable results, our review highlights how EM is enabling identification of the 3D structure of quantum defects; measuring reversible and metastable dynamics of quantum excitations; mapping exciton states and single photon emission; measuring nanoscale thermal transport and coupled excitation dynamics; and measuring the internal electric field and charge density distribution of quantum heterointerfaces- all at the quantum materials’ intrinsic atomic and near atomic-length scale. Finally, we conclude by describing open challenges for the future, including achieving stable sample holders for ultralow temperature (below 10K) atomic-scale spatial resolution, stable spectrometers that enable meV energy resolution, and high-resolution, dynamic mapping of magnetic and spin fields. With atomic manipulation and ultrafast characterization enabled by EM, quantum materials will be poised to integrate into many of the sustainable and energy-efficient technologies needed for the 21st century.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies

Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level. We present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Understanding a Stratigraphic Hydrothermal Resource – Geophysical Imaging at Steptoe Valley, Nevada

Sandia National Laboratories partnered with a multi-disciplinary group of subject matter experts to evaluate a stratigraphic geothermal resource in Steptoe Valley, Nevada using both established and novel geophysical imaging techniques. The stratigraphic reservoir in northern Steptoe Valley was previously discovered during oil and gas exploration. Subsequent studies, such as the Nevada Play Fairway Analysis, included data which further highlighted potential resource targets in the basin. Geophysical surveys, complemented with refined geologic mapping and geochemical sampling, were deployed to further characterize the resource. The resulting 3D geologic interpretation, conceptual model refinements, and reservoir simulations suggest that a >100MWe power-capable reservoir is likely economically accessible using conventional well placement and stimulation techniques in the Paleozoic carbonates of the deep/central basin of northern Steptoe Valley. Additional geophysical characterization and exploration drilling efforts are recommended to calibrate interpretation and determine where/how to potentially develop the northern Steptoe resource. The geophysical tools, interpretations, lessons learned, and public data generated by this study establish an exploration methodology to inform decisions for characterization and development of northern Steptoe Valley and other stratigraphic geothermal reservoirs in the western U.S.

15 GEOTHERMAL ENERGY↗

DOE OSTI2025

Machine Learning for Predicting Multipactor Susceptibility in Planar RF Structures

Multipactor discharge is a persistent challenge in high-power microwave (HPM) and accelerator systems, where secondary electron avalanches can cause heating, vacuum degradation, and failure. This work presents the first supervised machine learning (ML) framework for multipactor prediction, trained on high-fidelity 3D Particle-in-Cell (PIC) simulation data in planar geometries. The model maps operational, geometric, and material-dependent secondary electron yield (SEY) parameters to the time-averaged electron growth rate, enabling rapid reconstruction of susceptibility charts. Among the models evaluated, tree-based ensemble methods such as Random Forest and Extra Trees demonstrate superior generalization to unseen materials compared to neural networks such as multilayer perceptron (MLP). Performance metrics, including Intersection over Union (IoU), Structural Similarity Index Measure (SSIM), and Pearson correlation, show close agreement with simulation benchmarks. Principal Component Analysis attributes generalization limits to material feature-space disjointedness.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Classification of electronic nematicity in three-dimensional crystals and quasicrystals

Electronic nematic order has been reported in a rich landscape of materials, encompassing not only a range of intertwined correlated and topological phenomena but also different underlying lattice symmetries. Motivated by these findings, we investigate the behavior of electronic nematicity as the spherical symmetry of three-dimensional (3D) space is systematically lowered by the lattice environment. Here, we consider all 32 crystallographic point groups as well as four major classes of quasicrystalline point groups, given the recent observations of electronic phases of interest in quasicrystalline materials and artificial twisted quasicrystals. Valuable insights are gained by establishing a mapping between the five-component charge-quadrupolar nematic order parameter of the electronic fluid and the 3D tensorial order parameter of nematic liquid crystals. We find that a uniaxial nematic state is only generically realized in polyhedral point groups (icosahedral and cubic), with the nematic director pointing along different sets of rotational symmetry axes. Interestingly, icosahedral point groups are the only ones in which the five nematic order parameter components transform as the same irreducible representation, making them the closest analog of 3D isotropic nematics. In axial point groups, one of the nematic components is always condensed, whereas the other four components decompose into an in-plane and an out-of-plane nematic doublet, resulting in biaxial nematic ground states. Because these two nematic doublets behave as Z q clock order parameters, this allows us to identify the types of crystals and quasicrystals that can host interesting electronic nematic phenomena enabled by the critical properties of the q ≥ 4 clock model, such as emergent continuous nematic fluctuations in 3D, critical phases with quasi-long-range nematic order in two dimensions (2D), and Ashkin-Teller nematicity in 2D.

3-dimensional systems↗

DOE OSTI2023

Biomimetic tissue phantoms for neurosurgical near-infrared fluorescence imaging

Neurosurgical fluorescence imaging is a well-established clinical approach with a growing range of indications for use. However, this technology lacks effective phantom-based tools for development, performance testing, and clinician training. Our primary aim was to develop and evaluate 3D-printed phantoms capable of optically and morphologically simulating neurovasculature under fluorescence angiography. Volumetric digital maps of the circle of Willis with basilar and posterior communicator artery aneurysms, along with surrounding cerebral tissue, were generated. Phantoms were fabricated with a stereolithography printer using custom photopolymer composites, then visualized under white light and near-infrared fluorescence imaging. Feature sizes of printed components were found to be within 13% of digital models. Phantoms exhibited realistic optical properties and convincingly recapitulated fluorescence angiography scenes. Methods identified in this study can facilitate the development of realistic phantoms as powerful new tools for fluorescence imaging.

3D modeling↗