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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Abstract Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan , respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Three rate-determining protein roles in photosynthetic O 2 -evolution addressed by time-resolved experiments on genetically modified photosystems

Light-driven water splitting by plants, algae and cyanobacteria is pivotal for global bioenergetics and biomass formation. A manganese cluster bound to the photosystem II proteins catalyzes the complex reaction at high rate, but the rate-determining factors are insufficiently understood. Here we trace the oxygen-evolution transition by time-resolved polarography and infrared spectroscopy for cyanobacterial photosystems genetically modified at two strategic sites, complemented by computational chemistry. Our results highlight three rate-determining roles of the protein environment of the metal cluster: acceleration of proton-coupled electron transfer, acceleration of substrate-water insertion after O 2 -formation, and balancing of rate-determining enthalpic and entropic contributions. Whereas in general the substrate-water insertion step may be unresolvable in time-resolved experiments, here it likely becomes traceable because of deceleration by genetic modification. Our results may stimulate new time-resolved experiments on substrate-water insertion in photosynthesis, clarification of enthalpy-entropy compensation in enzyme catalysis, and knowledge-guided development of inorganic catalyst materials.

Bioenergetics↗
DOE OSTI2025

Numerically exact configuration interaction at quadrillion-determinant scale

The combinatorial growth of configuration interaction (CI) has long limited this formally exact quantum chemistry method to only the smallest molecules. Here, we report a numerically exact CI calculation exceeding one quadrillion (10 15 ) determinants, made possible by a lossless categorical compression strategy within the small-tensor-product distributed active space (STP-DAS) framework. This approach overcomes the traditional memory bottlenecks of CI by a numerically exact compression of the wavefunction representation and reformulating the most computationally demanding matrix–vector operations. Using this method, we performed a fully relativistic CI calculation of the ground state of HBrTe with over 10 15 complex-valued determinants in just 34.5 h on 1000 computing nodes—the largest CI calculation ever reported. We further achieved fast computation for systems with hundreds of billions of determinants on only a few compute nodes. Extensive benchmarks confirm that the method retains full numerical exactness while cutting memory and computational cost by orders of magnitude. Compared to previous state-of-the-art CI calculations, this work achieves a 1000 times increase in CI space, a 10 6 -fold increase in floating-point operations performed, and a 10 6 -fold improvement in computational speed.

Computational chemistry↗
DOE OSTI2021

Determining the three-dimensional atomic structure of an amorphous solid

Amorphous solids such as glass, plastics and amorphous thin films are ubiquitous in our daily life and have broad applications ranging from telecommunications to electronics and solar cells 1-4 . However, owing to the lack of long-range order, the three-dimensional (3D) atomic structure of amorphous solids has so far eluded direct experimental determination 5-15 . Here we develop an atomic electron tomography reconstruction method to experimentally determine the 3D atomic positions of an amorphous solid. Using a multi-component glass-forming alloy as proof of principle, we quantitatively characterize the short- and medium-range order of the 3D atomic arrangement. We observe that, although the 3D atomic packing of the short-range order is geometrically disordered, some short-range-order structures connect with each other to form crystal-like superclusters and give rise to medium-range order. We identify four types of crystal-like medium-range order-face-centred cubic, hexagonal close-packed, body-centred cubic and simple cubic-coexisting in the amorphous sample, showing translational but not orientational order. These observations provide direct experimental evidence to support the general framework of the efficient cluster packing model for metallic glasses 10,12-14,16 . Finally, we expect that this work will pave the way for the determination of the 3D structure of a wide range of amorphous solids, which could transform our fundamental understanding of non-crystalline materials and related phenomena.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Determining the gluonic gravitational form factors of the proton

The proton is one of the main building blocks of all visible matter in the Universe. Among its intrinsic properties are its electric charge, mass and spin. These properties emerge from the complex dynamics of its fundamental constituents—quarks and gluons—described by the theory of quantum chromodynamics. The electric charge and spin of protons, which are shared among the quarks, have been investigated previously using electron scattering. An example is the highly precise measurement of the electric charge radius of the proton. By contrast, little is known about the inner mass density of the proton, which is dominated by the energy carried by gluons. Gluons are hard to access using electron scattering because they do not carry an electromagnetic charge. Here we investigated the gravitational density of gluons using a small colour dipole, through the threshold photoproduction of the J/ψ particle. We determined the gluonic gravitational form factors of the proton from our measurement. Here we used a variety of models and determined, in all cases, a mass radius that is notably smaller than the electric charge radius. In some, but not all cases, depending on the model, the determined radius agrees well with first-principle predictions from lattice quantum chromodynamics. This work paves the way for a deeper understanding of the salient role of gluons in providing gravitational mass to visible matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Determination of the Raman polarizability tensor in the optically anisotropic crystal potassium dihydrogen phosphate and its deuterated analog

Abstract The Raman tensor of the dominant A 1 modes of the nonlinear optical crystalline material potassium dihydrogen phosphate and its 70% deuterated analog have been ascertained. Challenges in determining the A 1 mode tensor element values based on previous reports have been resolved using a specially designed experimental setup that makes use of spherical crystal samples. This novel experimental design enabled the determination of measurement artifacts, including polarization rotation of the pump and/or scattered light propagating through the sample and the contribution of additional overlapping phonon modes, which have hindered previous efforts. Results confirmed that the polarization tensor is diagonal, and matrix elements were determined with high accuracy.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Determination of excited state molecular structures from time-resolved gas-phase X-ray scattering

We present a comprehensive investigation of a recently introduced method to determine transient structures of molecules in excited electronic states with sub-ångstrom resolution from time-resolved gas-phase scattering signals. The method, which is examined using time-resolved X-ray scattering data measured on the molecule N-methylmorpholine (NMM) at the Linac Coherent Light Source (LCLS), compares the experimentally measured scattering patterns against the simulated patterns corresponding to a large pool of molecular structures to determine the full set of structural parameters. In addition, we examine the influence of vibrational state distributions and find the effect negligible within the current experimental detection limits, despite that the molecules have a comparatively high internal vibrational energy. Here, the excited state structures determined using three structure pools generated using three different computational methods are in good agreement, demonstrating that the procedure is largely independent of the computational chemistry method employed as long as the pool is sufficiently expansive in the vicinity of the sought structure and dense enough to yield good matches to the experimental patterns.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Application of saturation absorption spectroscopy to study the hyperfine structure of 235U and accurate 235U/238U isotope ratio determinations at 861.031 nm

The uranium transition 5f 3 6d7s 2 ( 5 L 6 ) → 5f 3 7s 2 7p ( 5 K 5 ) at 861.031 nm was studied using saturation absorption spectroscopy. The hyperfine structure of the 235 U isotope was determined by measuring the Doppler-suppressed absorption spectrum, and the hyperfine structure constants were obtained by employing transition-specific line strength theory and spectral fitting. The magnetic-dipole and electric-quadrupole constants were determined to be A = -3.2887 ± 0.1957 mK and B = 31.8712 ± 8.0789 mK for the upper state 5f 3 7s 2 7p ( 5 K 5 ). A theoretical calculation for the hyperfine structure constants of the 235 U isotope was also carried out by the relativistic configuration-interaction (RCI) method, and the obtained values were found to be in agreement with the measured values. In addition, the line profile of 238 U was experimentally investigated for different excitation intensities and modeled using the RCI method for estimating the transition probability and oscillator strength, with various residual broadening mechanisms considered beyond the radiative decay. Finally, we show that these results allow us to make improvements on the precision of spectral measurements using our previously developed technique for isotope ratio determinations in atomic beams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Decoding substrate specificity determining factors in glycosyltransferase-B enzymes – insights from machine learning models

Substrate specificity is an essential characteristic of any enzyme's function and an understanding of the factors that determine this specificity is crucial for enzyme engineering. Unlike the structure of an enzyme which is directly impacted by its sequence, substrate specificity as an enzyme attribute involves a rather indirect relationship with sequence as it also depends on structural aspects that dictate substrate accessibility and active site dynamics. In this study, we explore the performance of classifier-based machine learning models trained on curated sequence and structural data for a class of glycosyltransferases (GTs), namely GT-Bs, to understand their substrate specificity determining factors. GTs enable the transfer of sugar moieties to other biomolecules such as oligosaccharides or proteins and are found in all kingdoms of life. In plants, GTs participate in the biosynthesis of plant cell wall biopolymers (e.g.: hemicelluloses and pectins) and are an integral part of the enzymatic machinery that enables the storage of carbon and energy as plant biomass. To elucidate the substrate specificity of uncharacterized GT-Bs, we constructed multi-label machine learning models (Support Vector Classifier, K-Nearest Neighbors, Gaussian Naïve-Bayes, Random Forest) that incorporate both sequence and structural features. These models achieve good predictive accuracies on test datasets. However, despite our use of structural information, we highlight that there is further scope for improvement in training these models to draw interpretable relationships between sequence, structure and substrate specificity determining motifs in GT-Bs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Sound speed determination in copper shock compressed to 190 GPa

Sound speed measurements in shock compressed solids have long been valuable for the development of equations of state at extreme conditions, shock-induced phase transformations, and a comprehensive characterization of the thermophysical response of high-pressure standards. We present results from plate impact experiments to 190 GPa to determine the longitudinal sound speed in copper—an important high-pressure standard. Surprisingly, the sound speeds determined using the two most common experimental techniques—the front surface impact (FSI) approach and the release wave overtake (RWO) approach—diverge significantly for stresses greater than ~100 GPa. Further analyses, including numerical simulations, show that the FSI experiments provide the correct sound speeds and that fundamental assumptions underlying the RWO method are likely violated due to the complex release response of shock compressed copper. The sound speeds determined using the FSI approach provide for a more accurate high-pressure description of copper in dynamic compression experiments. The present findings are in contrast to the results for shock compressed silver [Wallace et al., Phys. Rev. B 104, 214106 (2021)], where both methods provided consistent sound speed results. Thus, the findings presented here demonstrate the need to experimentally verify the validity of the RWO method on a case-by-case basis. Finally, we note that even at the high stresses in the present work, the copper unloading response shows a time-dependent, quasielastic response often observed in metals at lower stresses.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Systematic Source Determination and X-Ray Radiography Detection of Nonuniformities on High-Density Carbon Ablators

Recent deuterium-tritium (D-T)–layered implosion experiments at the National Ignition Facility have achieved a burning plasma and >1-MJ neutron yield. A series of repeat experiments have shown that the degree of performance is very likely dependent on capsule quality, including the quantity of what are collectively termed “high- Z particles.” These particles are detected on a custom-built radiography system, known as the Sagometer, during the final target qualification process. The term particles is misleading, as the source of these nonuniformities in the capsule images is uncertain; the term detection will be used instead. An increased number of D-T targets have been rejected at the final stages of production due to Sagometer detections. Late detections are deleterious in terms of loss of production parts, effort, and overall operating efficiency. In response, we undertook an effort to determine the origin of these detections and to ultimately mitigate target losses caused by them. Through careful testing and analysis, we have determined neither insufficient production cleanliness nor hohlraum shedding is responsible for the detections on the capsule. Here, we determined that the detections are inherent to the capsule and have made efforts to use the Zeiss Xradia to identify them earlier in the production process. While testing revealed the Xradia is not currently sufficient for identifying such particles using radiography images, we continue to look to other forms of metrology to down select the capsules early in the process.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Experimental determination of the valence band offsets of ZnGeN 2 and (ZnGe) 0.94 Ga 0.12 N 2 with GaN

A predicted type-II staggered band alignment with an approximately 1.4 eV valence band offset at the ZnGeN 2 /GaN heterointerface has inspired novel band-engineered III-N/ZnGeN 2 heterostructure-based device designs for applications in high performance optoelectronics. We report on the determination of the valence band offset between metalorganic chemical vapor deposition grown (ZnGe) 1- x Ga 2 x N 2 , for x = 0 and 0.06, and GaN using x-ray photoemission spectroscopy. The valence band of ZnGeN 2 was found to lie 1.45–1.65 eV above that of GaN. This result agrees well with the value predicted by first-principles density functional theory calculations using the local density approximation for the potential profile and quasiparticle self-consistent GW calculations of the band edge states relative to the potential. For (ZnGe) 0.94 Ga 0.12 N 2 the value was determined to be 1.29 eV, ~10%–20% lower than that of ZnGeN 2 . The experimental determination of the large band offset between ZnGeN 2 and GaN provides promising alternative solutions to address challenges faced with pure III-nitride-based structures and devices.

Physics↗
DOE OSTI2020

Determination of latent dimensionality in international trade flow

Currently, high-dimensional data is ubiquitous in data science, which necessitates the development of techniques to decompose and interpret such multidimensional (aka tensor) datasets. Finding a low dimensional representation of the data, that is, its inherent structure, is one of the approaches that can serve to understand the dynamics of low dimensional latent features hidden in the data. Moreover, decomposition methods with non-negative constraints are shown to extract more insightful factors. Nonnegative RESCAL is one such technique, particularly well suited to analyze self-relational data, such as dynamic networks found in international trade flows. Particularly, non-negative RESCAL computes a low dimensional tensor representation by finding the latent space containing multiple modalities. Furthermore, estimating the dimensionality of this latent space is crucial for extracting meaningful latent features. Here, to determine the dimensionality of the latent space with non-negative RESCAL, we propose a latent dimension determination method which is based on clustering of the solutions of multiple realizations of non-negative RESCAL decompositions. We demonstrate the performance of our model selection method on synthetic data. We then apply our method to decompose a network of international trade flows data from International Monetary Fund and shows that with a correct latent dimension determination, the resulting features are able to capture relevant empirical facts from economic literature.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Determination of fluorine distribution in shark teeth by laser-induced breakdown spectroscopy

Quantifying the chemical composition of fast-growing hard tissues in the environment can shed valuable information in terms of understanding ecosystems both prehistoric and current. Changes in chemical composition can be correlated with environmental conditions and can provide information about the organism's life. Sharks can lose 0.1 to 1.1 teeth/day, depending on species, which offers a unique opportunity to record environmental changes over a short duration of time. Shark teeth contain a biomineral phase that is made up of fluorapatite [Ca 5 (PO 4 ) 3 F], and the F distribution within the tooth can be correlated to tooth hardness. Typically, this is determined by bulk acid digestion, energy-dispersive X-ray spectroscopy (EDS), or wavelength-dispersive spectroscopy. Here we present laser-induced breakdown spectroscopy (LIBS) as an alternative and faster approach for determining F distribution within shark teeth. Using a two-volume laser ablation chamber (TwoVol3) with innovative embedded collection optics for LIBS, shark teeth were investigated from sand tiger (Carcharias Taurus), tiger (Galeocerdo Cuvier), and hammerhead sharks (Sphyrnidae). Fluorine distribution was mapped using the CaF 603 nm band (CaF, Β 2 Σ + → X 2 Σ + ) and quantified using apatite reference materials. In addition, F measurements were cross referenced with EDS analyses to validate the findings. Distributions of F (603 nm), Na (589 nm), and H (656 nm) within the tooth correlate well with the expected biomineral composition and expected tooth hardness. This rapid methodology could transform the current means of determining F distribution, particularly when large sample specimens (350 mm 2 , presented here) and large quantities of specimens are of interest.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Inherent issues regarding the use of in situ x-ray diffraction measurements to determine temperature in shock-compressed metals

Temperature determination in shock compressed solids constitutes an important and long-standing scientific need. Since the reduction of Bragg diffracted peaks due to temperature increase, using the Debye-Waller factor, is well established, we examined the use of this approach to determine temperatures in shock compressed gold and platinum by representing the shocked state as a superposition of density and temperature changes. Comparison of the calculated and measured diffraction peaks did not show good agreement, because x-ray diffraction (XRD) profiles in the shock compressed state are not governed solely by density and temperature changes. XRD results are also influenced measurably by shock wave induced microstructural changes. Our results demonstrate that contributions from microstructural changes need to be incorporated and modeled in the theoretical analysis to use XRD measurements for reliable temperature determination in shock compressed solids.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Three-dimensional structure of hybrid magnetic skyrmions determined by neutron scattering

Magnetic skyrmions are topologically protected chiral spin textures which present opportunities for next-generation magnetic data storage and logic information technologies. The topology of these structures originates in the geometric configuration of the magnetic spins, more generally described as the structure. While the skyrmion structure is most often depicted using a two-dimensional projection of the three-dimensional (3D) structure, recent works have emphasized the role of all three dimensions in determining the topology and their response to external stimuli. Here, grazing-incidence small-angle neutron scattering and polarized neutron reflectometry are used to determine the 3D structure of hybrid skyrmions. The structure of the hybrid skyrmions, which includes a combination of Néel-like and Bloch-like components along their length, is expected to significantly contribute to their notable stability, which includes ambient conditions. To interpret the neutron scattering data, micromagnetic simulations of the hybrid skyrmions were performed, and the corresponding diffraction patterns were determined using a Born approximation transformation. The converged magnetic profile reveals the magnetic structure along with the skyrmion depth profile, including the thickness of the Bloch and Néel segments and the diameter of the core.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Auxiliary function approach for determining symmetry energy at suprasaturation densities

Nuclear symmetry energy E sym (ρ) at density ρ is normally expanded or simply parameterized as a function of χ = (ρ – ρ 0 )/3ρ 0 in the form of Esym(ρ) ≈ S + Lχ + 2 –1 K sym χ 2 + 6 –1 J sym χ 3 + … using its magnitude S, slope L, curvature K sym and skewness J sym at the saturation density ρ0 of nuclear matter. Much progress has been made in recent years in constraining especially the S and L parameters using various terrestrial experiments and astrophysical observations. Furthermore, such kind of expansions/parameterizations do not converge at supra-saturation densities where χ is not small enough, hindering an accurate determination of high-density E sym (ρ) even if its characteristic parameters at ρ0 are all well determined by experiments/observations. By expanding the E sym (ρ) in terms of a properly chosen auxiliary function Π sym (χ,Θ sym ) with a parameter Θsym fixed accurately by an experimental E sym (ρ r ) value at a reference density ρr, we show that the shortcomings of the χ-expansion can be completely removed or significantly reduced in determining the high-density behavior of E sym (ρ). In particular, using two significantly different auxiliary functions, we show that the new approach effectively incorporates higher χ-order contributions and converges to the same E sym (ρ) much faster than the conventional χ-expansion at densities ≲3ρ 0 . Several quantitative demonstrations using Monte Carlo simulations are given.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Determination of β -decay feeding patterns of 88 Rb and 88 Kr using the Modular Total Absorption Spectrometer at ORNL HRIBF

We report precise determination of ground-state feeding in the β decay of fission products is an important but challenging component in modeling reactor antineutrino flux and reactor decay heat. The Modular Total Absorption Spectrometer (MTAS) is a versatile NaI(Tl) detector array that determines the true β-decay pattern free from the pandemonium effect, including precise ground-state feeding intensities. In this paper, we report MTAS results of the β feeding intensities of 88 Rb and 88 Kr, fission products with large cumulative yields in nuclear reactors. By comparing MTAS results with previous measurements, 88 Rb provides a validation of MTAS's ability to determine ground-state feedings in β decays, while the precision of 88 Kr ground-state feeding is improved when compared with the Evaluated Nuclear Structure Data File (ENSDF). The investigation of sources that contribute to β feeding branching uncertainties in MTAS experiments is discussed in detail. Lastly, the deconvolution of 88 Rb decay spectra suggests that MTAS can distinguish an allowed β spectral shape from a first forbidden unique β spectral shape.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗