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At least 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

When can we detect lianas from space? Toward a mechanistic understanding of liana‐infested forest optics

Abstract Lianas, woody vines acting as structural parasites of trees, have profound effects on the composition and structure of tropical forests, impacting tree growth, mortality, and forest succession. Remote sensing could offer a powerful tool for quantifying the scale of liana infestation, provided the availability of robust detection methods. We analyze the consistency and global geographic specificity of spectral signals—reflectance across wavelengths—from liana‐infested tree crowns and forest stands, examining the underlying mechanisms of these signals. We compiled a uniquely comprehensive database, including leaf reflectance spectra from 5424 leaves, fine‐scale airborne reflectance data from 999 liana‐infested canopies, and coarse‐scale satellite reflectance data covering 775 ha of liana‐infested forest stands. To unravel the mechanisms of the liana spectral signal, we applied mechanistic radiative transfer models across scales, establishing a synthesis of the relative importance of different mechanisms, which we corroborate with field data on liana leaf chemistry and canopy structure. We find a consistent liana spectral signal at canopy and stand scales across globally distributed sites. This signature mainly arises at the canopy level due to direct effects of more horizontal leaf angles, resulting in a larger projected leaf area, and indirect effects from increased light scattering in the near and short‐wave infrared regions, linked to lianas' less costly leaf construction compared with trees on average. The existence of a consistent global spectral signal for lianas suggests that large‐scale quantification of liana infestation is feasible. However, because the traits responsible for the liana canopy‐reflectance signal are not exclusive to lianas, accurate large‐scale detection requires rigorously validated remote sensing methods. Our models highlight challenges in automated detection, such as potential misidentification due to leaf phenology, tree life history, topography, and climate, especially where the scale of liana infestation is less than a single remote sensing pixel. The observed cross‐site patterns also prompt ecological questions about lianas' adaptive similarities in optical traits across environments, indicating possible convergent evolution due to shared constraints on leaf biochemical and structural traits.

Environmental Sciences & Ecology↗
DOE OSTI2025

Strain release through hydrogen bond–mediated layer twisting

Strain engineering, enabling the precise control over structure and functional properties, is a key strategy for the design of advanced materials. However, the mechanisms governing strain evolution and release at the nanoscale remain largely unexplored. In this study, we leverage in situ heating transmission electron microscopy and synchrotron x-ray spectroscopy to investigate the strain relaxation pathways of boehmite (γ-AlOOH) at 575 kelvin by revealing real-time structural dynamics. Through tracking the moiré pattern evolution, we identify distinct strain release mechanisms, including layer twisting, defect formation, and domain restructuring. Our neural network potential calculations reveal that energy fluctuations at small twist angles are dominated by an interference-like interaction modulation of hydrogen bonds between boehmite interlayers, with metastable twisted structures corresponding to local minima of the potential energy landscape. This work establishes a previously unidentified paradigm of two-dimensional layer twisting mediated by hydrogen bonding, offering insights into strain-driven transformation mechanisms, and thus may have broad implications for strain in material and earth sciences.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Unraveling the Crystallization Kinetics of 2D Perovskites with Sandwich-Type Structure for High-Performance Photovoltaics

2D perovskite solar cells with high stability and high efficiency have attracted significant attention. A systematical static and dynamic structure investigation is carried out to show the details of 2D morphology evolution. A dual additive approach is used, where the synergy between an alkali metal cation and a polar solvent leads to high-quality 2D perovskite films with sandwich-type structures and vertical phase segregation. Such novel structure can induce high-quality 2D slab growth and reduce internal and surface defects, resulting in a high device efficiency of 16.48% with enhanced continuous illumination stability and improved moisture (55-60%) and thermal (85°C) tolerances. Transient absorption spectra reveal the carrier migration from low n to high n species with different kinetics. An [PbI 6 ] 4- octagon coalescence transformation mechanism coupled with metal and organic cations wrapped is proposed. By solvent vapor annealing, a recrystallization and reorientation of the 2D perovskite slabs occurs to form an ideal structure with improved device performance and stability.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Evolution of the SARS-CoV -2 proteome in three dimensions (3D) during the first 6 months of the COVID -19 pandemic

Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein–protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Here detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein–protein and protein–nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Wintertime Arctic Oscillation and North Atlantic Oscillation and their impacts on the Northern Hemisphere climate in E3SM

The characteristics of the wintertime Arctic Oscillation (AO) and North Atlantic Oscillation (NAO) and their impacts on climate variability over the Northern Hemisphere are important metrics for evaluating a climate system model. Observational analyses reveal that the horizontal and vertical structures in the AO and NAO exhibit a meridional dipole and a large-scale barotropic pattern between the Arctic and mid-latitudes. Historical model simulations from the Energy Exascale Earth System Model (E3SM-HIST) are used to identify how well it captures these major climate modes. It is found that the simulated AO and NAO modes have spatial structures similar to the observed features. In addition, the observed frequency bands in the AO and NAO-related time variability are captured well in the E3SM-HIST simulation. Associated with the positive phase in wintertime AO and NAO, zonal flow and warm advection in mid-latitude continents are enhanced, along with stronger cold flow from enhanced northerly winds over high latitudes. These features are linked to the atmospheric circulation pattern reflected by lower SLP anomalies over the Arctic and higher SLP anomalies over the mid-latitudes. In E3SM-HIST, these spatial associations and main structural features are analogous to those in observations. In the time-height evolution related to winter AO and NAO modes, it can also be seen that the simulations reproduce the downward propagating patterns in observations. Nevertheless, the vertical structures associated with AO and NAO in E3SM-HIST exhibit substantial biases in the lower stratosphere. The cause of these stratospheric biases is investigated using the strength of climatological stratospheric polar vortex (SPV) and wave activity fluxes. The results herein suggest that E3SM-HIST has a reasonable skill in reproducing the observed characteristics related to the winter AO and NAO, although there exist systematic biases in the associated climate variability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Fullerene-like defects in high-temperature neutron-irradiated nuclear graphite

Irradiation-induced defect evolution in graphite is particularly important for its application in graphite-moderated nuclear reactors. The evolution of defects directly influences macroscopically observed property changes in irradiated nuclear graphite which, in turn, can govern the lifetime of graphite components. This article reports novel defect structures and the irradiation response of microstructural features occurring in high-temperature irradiated nuclear graphite IG-110. High resolution transmission electron microscopy (HRTEM) was used to characterize specimens neutron-irradiated at a high temperature (≥ 800°C) at doses of 1.73 and 3.56 atomic displacements per atom (dpa). Concentric shelled and fullerene-like defects were found to result in swelling along the c-axis and contraction along the a/b-axis of crystallites. Furthermore, such defects are shown to occur within, and partially fill, Mrozowski cracks prior to turnaround dose. In addition, in situ TEM under similar irradiation conditions was used to capture the real-time dynamic evolution of defects, providing unambiguous analysis of the evolution of the graphite structures during irradiation. Here, the results suggest the mainstream theory for radiation damage in nuclear graphite (which assumes additional basal plane formation as the sole reason) to be an incorrect interpretation of defect evolution contributing to irradiation-induced property changes at higher temperatures.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

How Accurate Can Crystal Structure Predictions Be for High-Energy Molecular Crystals?

Molecular crystals have shallow potential energy landscapes, with multiple local minima separated by very small differences in total energy. Predicting molecular packing and molecular conformation in the crystal generally requires ab initio methods of high accuracy, especially when polymorphs are involved. We used dispersion-corrected density functional theory (DFT-D) to assess the capabilities of an evolutionary algorithm (EA) for the crystal structure prediction (CSP) of well-known but challenging high-energy molecular crystals (HMX, RDX, CL-20, and FOX-7). While providing the EA with the experimental conformation of the molecule quickly re-discovers the experimental packing, it is more realistic to start instead from a naïve, flat, or neutral initial conformation, which reflects the limited experimental knowledge we generally have in the computational design of molecular crystals. By doing so, and using fully flexible molecules in fully variable unit cells, we show that the experimental structures can be predicted in fewer than 20 generations. Nonetheless, one must be aware that some molecular crystals have naturally hindered evolutions, requiring as many attempts as there are space groups of interest to predict their structures, and some may require the accuracy of all-electron calculations to discriminate between closely ranked structures. To save resources in this computationally demanding process, we showed that a hybrid xTB/DFT-D approach could be considered in a subsequent study to push the limits of CSP beyond 200+ atoms and for cocrystals.

42 ENGINEERING↗
DOE OSTI2020

Modeling the role of local crystallographic correlations in microstructures of Ti-6Al-4V using a correlated structure visco-plastic self-consistent polycrystal plasticity formulation

This paper presents a multi-level crystal plasticity-based simulation framework for modeling mechanical response and microstructure evolution of Ti-6Al-4V with α-lath/lamellar microstructures. Here, the model is a correlated structure visco-plastic self-consistent (CS-VPSC) formulation linking three scales: a single crystals micro-scale, a lath/lamellar colony meso-scale, and a lath/lamellar aggregate macro-scale. A selected hardening law for the evolution of critical resolved shear stress per slip system used in CS-VPSC is phenomenological. However, it adjusts the resistances of basal and prismatic slip systems based on the geometry of slip transfer between adjacent lamellae. Consistent with experimental evidences, the resolved shear stress on the pyramidal slip planes is dependent not only on the stress in the direction of slip but also on the two orthogonal shear stress components and the three normal stress components (non-Schmid effects). Electron backscatter diffraction (EBSD) data in conjunction with a procedure relying on α→β phase transformation is used to construct paired variants of α-laths/lamellae satisfying their local crystallographic correlations. The procedure fits volume fractions of individual laths/lamellae with the experimental EBSD data and selects a distribution of habit planes between adjacent variants with respect to the loading direction. The simulation framework is applied to interpret the deformation behavior in tension and compression along two sample directions of Ti-6Al-4V fabricated via laser powder bed fusion. Moreover, the model is used to simulate texture evolution during rolling of the material to large strains. It is demonstrated that the model is capable of predicting plastic anisotropy/asymmetry and the concomitant texture evolution. While the model reveals a significant effect of habit plane inclination with respect to the loading direction on yield stress, the comparison of the data and model predictions shows that a random distribution of habit planes fits the flow response. It is further inferred that the tension-compression asymmetry arises from the non-Schmid effects.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A Machine Learning–Based Approach to Time-series Wave Identification in the Solar Wind

The Wind spacecraft has yielded several decades of high-resolution magnetic field data, a large fraction of which displays small-scale structures. In particular, the solar wind is full of wavelike fluctuations that appear in both the field magnitude and its components. The nature of these fluctuations can be tied to the properties of other structures in the solar wind, such as shocks, that have implications for the time evolution of the solar wind. As such, having a large collection of wave events would facilitate further study of the effects that these fluctuations have on solar wind evolution. Given the large volume of magnetic field data available, machine learning is the most practical approach to classifying the myriad small-scale structures observed. To this end, a subset of Wind data is labeled and used as a training set for a multibranch 1D convolutional neural network aimed at classifying circularly polarized wave modes. Using this algorithm, a preliminary statistical study of 1 yr of data is performed, yielding about 300,000 wave intervals out of about 5,000,000 solar wind intervals. The wave intervals come about more often in the fast solar wind and at higher temperatures, and the number of waves per day is highly periodic. This machine learning–based approach to wave detection has the potential to be a powerful, inexpensive way to catalog waves throughout decades of spacecraft data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Crystal structure of a guanine nucleotide exchange factor encoded by the scrub typhus pathogen Orientia tsutsugamushi

Rho family GTPases regulate an array of cellular processes and are often modulated by pathogens to promote infection. In this work, we identify a cryptic guanine nucleotide exchange factor (GEF) domain in the OtDUB protein encoded by the pathogenic bacterium Orientia tsutsugamushi. A proteomics-based OtDUB interaction screen identified numerous potential host interactors, including the Rho GTPases Rac1 and Cdc42. We discovered a domain in OtDUB with Rac1/Cdc42 GEF activity (OtDUB GEF ), with higher activity toward Rac1 in vitro. While this GEF bears no obvious sequence similarity to known GEFs, crystal structures of OtDUB GEF alone (3.0 Å) and complexed with Rac1 (1.7 Å) reveal striking convergent evolution, with a unique topology, on a V-shaped bacterial GEF fold shared with other bacterial GEF domains. Structure-guided mutational analyses identified residues critical for activity and a mechanism for nucleotide displacement. Ectopic expression of OtDUB activates Rac1 preferentially in cells, and expression of the OtDUBGEF alone alters cell morphology. Cumulatively, this work reveals a bacterial GEF within the multifunctional OtDUB that co-opts host Rac1 signaling to induce changes in cytoskeletal structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Shell structure of 43 S and collapse of the N = 28 shell closure

The single-particle structure of the N = 27 isotones provides insights into the shell evolution of neutron-rich nuclei from the doubly-magic 48 Ca toward the drip line. 43 S was studied employing the one-neutron knockout reaction from a radioactive 44 S beam. Using a combination of prompt and delayed γ-ray spectroscopy the level structure of 43 S was clarified. Momentum distributions were analyzed and allowed for spin and parity assignments. The deduced spectroscopic factors show that the 44 S ground-state configuration has a strong intruder component. Here, the results were confronted with shell model calculations using two effective interactions. General agreement was found between the calculations, but strong population of states originating from the removal of neutrons from the 2p 3/2 orbital in the experiment indicates that the breakdown of the N = 28 magic number is more rapid than the theoretical calculations suggest.

39 ≤ A ≤ 58↗
DOE OSTI2021

Experimental Verification of Ir 5d Orbital States and Atomic Structures in Highly Active Amorphous Iridium Oxide Catalysts

In iridium oxide catalysts, the electronic states whose energies are in the range of energetics and charge transfer kinetics of the oxygen evolution reaction (OER) originate from the Ir 5d orbital states. However, the understanding of the atomic structures and orbital states underlying catalytic reactivity in amorphous iridium oxide oxygen evolving catalysts (Ir-OECs) is incomplete compared to that of crystalline oxides, owing to a lack of direct experimental verification. Here, we present experimental approaches using resonant inelastic X-ray scattering (RIXS) to directly access Ir 5d orbital excitations at the Ir L 3 edge and atomic pair distribution function (PDF) measurements to characterize electronic and coordination structures at the atomic scale. The so-called iridium blue layer (IrBL) and IrO x were formed from the organometallic precursor complex [Cp*Ir(H 2 O) 3 ]SO 4 and the inorganic precursor IrCl 3 , respectively. Ex situ IrBL and IrO x films for RIXS and PDF measurements were prepared by conditioning electrodeposited films at a low voltage. The incident energy RIXS profile of IrO x exhibited extra weak resonantly enhanced excitation below 2 eV energy loss. The feature was clearly different from a single high-energy excitation above 3 eV of IrBL related to the interband transition between π- and σ-antibonding states. The atomic structure refinement based on PDF measurements revealed the atomic structure domains to have edge- and corner-shared IrO 6 octahedra with trigonal-type distortion. Furthermore, density functional theory calculations guided by the refined atomic structures shed light on the electronic structure corresponding to experimental results, including insulating and metallic phases in ex situ IrBL and IrO x films, respectively. Our study establishes different Ir 5d orbital states and atomic structures in two amorphous Ir oxide OER catalysts in their reduction states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Real-time damage characterization for GFRCs using high-speed synchrotron X-ray phase contrast imaging

Here, we report the application of high-speed synchrotron X-ray phase contrast imaging (PCI) in real-time damage characterization for glass fiber reinforced composites (GFRCs) subjected to dynamic loading. Dynamic single-edge notched bending (DSENB) experiments on pre-notched S-2 GFRCs were performed on a modified Kolsky compression bar. During loading, the synchrotron X-ray beam penetrated through the composite specimen from the side to detect damage evolution inside the material. Entire dynamic events were recorded by a high-speed camera as image sequences.0° and 90° unidirectional and cross-ply composites were investigated. An optical imaging technique was also employed to capture similar dynamic events in comparison with the radiographic imaging. It is demonstrated that high-speed X-ray PCI had sufficient phase contrast to characterize a crack initiation at a 20-μm spatial resolution within 920 ns and track the crack geometry during propagation, thereby providing reliable data to quantify the dynamic damage resistance of GFRCs. Furthermore, being capable of recognizing microscopic damage-related features at a sub-10-μm resolution, high-speed X-ray PCI provided fundamental material failure mechanisms to reveal the essential of macroscale structural failure of composites. It can also track the damage evolution inside and between individual plies of laminated composites. However, current high-speed X-ray PCI technique only supports in-situ observation and the high timing and spatial resolutions are limited within a field of view of ~2.5 mm in square, preventing its application in the three-dimensional and larger-area damage detection for GFRC structures.

42 ENGINEERING↗
DOE OSTI2025

Designing Peptide Fossils That Model the Evolution of the Bacterial Ferredoxin Fold

Electron transfer coupled to redox chemistry is at the heart of metabolism. The proteins responsible for moving electrons (protein electron carriers) must have emerged at the origin of life. The small iron–sulfur-binding bacterial ferredoxins were likely among these first proteins. Embedded within the ferredoxin sequence and structure is a symmetry that points to an ancient gene duplication event. Little is understood about the nature of ferredoxins prior to this duplication event or what environmental factors may have driven the selection for more complex forms. The deep-time molecular history of ferredoxins goes back billions of years and cannot be reconstructed by phylogenetic analyses based on amino acid sequences. Here, we use structure-guided protein design to model a fossil half-ferredoxin stage in the evolution of this fold, the semidoxins, and their symmetric full-length counterparts, the symdoxins. Semidoxin designs homodimerize, exhibiting structural, thermodynamic, and electrochemical behaviors in most cases identical to cognate symdoxins. However, the semi- and symdoxin fossil stages behave differently when incorporated into an in vivo electron transfer complementation assay. Both can support bacterial growth dependent on protein expression. Growth rates of bacteria expressing the semidoxins are much more sensitive to oxygen than those of bacteria expressing symdoxins. Motivated by the in vivo functionality of designed semidoxins, we identified putative naturally occurring semidoxins in extant anaerobic microorganisms. This is consistent with the observed in vivo oxygen sensitivity of the semidoxin designs. One natural semidoxin is shown to be folded and redox active. However, it exists as a mixture of monomers and dimers, suggesting a potential connection between semidoxins and even simpler single iron–sulfur cluster-binding peptides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Geometric transformation and three-dimensional hopping of Hopf solitons

Arising in many branches of physics, Hopf solitons are three-dimensional particle-like field distortions with nontrivial topology described by the Hopf map. Despite their recent discovery in colloids and liquid crystals, the requirement of applied fields or confinement for stability impedes their utility in technological applications. Here we demonstrate stable Hopf solitons in a liquid crystal material without these requirements as a result of enhanced stability by tuning anisotropy of parameters that describe energetic costs of different gradient components in the molecular alignment field. Nevertheless, electric fields allow for inter-transformation of Hopf solitons between different geometric embodiments, as well as for their three-dimensional hopping-like dynamics in response to electric pulses. Numerical modelling reproduces both the equilibrium structure and topology-preserving out-of-equilibrium evolution of the soliton during switching and motions. Our findings may enable myriads of solitonic condensed matter phases and active matter systems, as well as their technological applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

MHD-induced beta limits in the Large Helical Device

Using the extended-magnetohydrodynamics code, M3D-C1, we perform a systematic numerical study of the effect of externally applied heating on the achievable plasma beta in a ten field-period heliotron. Heat sources of varying intensity are applied to a vacuum magnetic field that is representative of the standard configuration of the Large Helical Device, with R 0 = 3.66 m, where R 0 is the radial position of the magnetic axis in vacuum. As the system is driven to a state that is unstable to low-n magnetohydrodynamic (MHD) modes, nonlinear mode interactions lead to the formation of chaotic magnetic fields. With sufficiently strong heating, a collapse of the electron temperature profile is observed. This demonstrates the necessity of simulating the self-consistent evolution of plasma profiles, without imposing assumptions on the structure of the magnetic field, to accurately determine transport properties in stellarator plasmas. It also highlights the value of these advanced simulation capabilities for accelerating the development of high-performance stellarator operating scenarios.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Effects of external magnetic fields on the multi-mode Rayleigh–Taylor instability

The magneto-Rayleigh–Taylor instability (mRTI) is a key process in inertial confinement fusion and is thought to be widespread in the interstellar medium, where it can concentrate plasma into discrete structures. We present resistive MHD simulations of the nonlinear evolution of multi-mode mRTI in both two and three dimensions, examining the effects of uniform external magnetic fields oriented either parallel or perpendicular to the initial interface. In both 2D and 3D, weak parallel fields enhance mixing-zone growth, whereas stronger fields suppress it. For perpendicular fields, growth is initially inhibited but becomes enhanced at later times. These behaviors arise from magnetic tension, which modifies flow anisotropy, buoyancy, drag, and vortex dynamics. The interplay of these mechanisms governs the distinct ways in which magnetic fields influence mRTI evolution.

Flow instabilities↗
DOE OSTI2024

Structural and functional dynamics of human cone cGMP-phosphodiesterase important for photopic vision

Cone cGMP-phosphodiesterase (PDE6) is the key effector enzyme for daylight vision, and its properties are critical for shaping distinct physiology of cone photoreceptors. We determined the structures of human cone PDE6C in various liganded states by single-particle cryo-EM that reveal essential functional dynamics and adaptations of the enzyme. Our analysis exposed the dynamic nature of PDE6C association with its regulatory γ-subunit (Pγ) which allows openings of the catalytic pocket in the absence of phototransduction signaling, thereby controlling photoreceptor noise and sensitivity. We demonstrate evolutionarily recent adaptations of PDE6C stemming from residue substitutions in the Pγ subunit and the noncatalytic cGMP binding site and influencing the Pγ dynamics in holoPDE6C. Thus, our structural analysis sheds light on the previously unrecognized molecular evolution of the effector enzyme in cones that advances adaptation for photopic vision.

Science & Technology - Other Topics↗