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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C222 1 and P3 2 21) at 1.9 Å resolution. The phase problem was solved by molecular replacement using an AlphaFold model as the search model. AaDUF507 is a Y-shaped α-helical protein consisting of an anti-parallel 4-helix bundle base and two helical arms that extend 30-Å from the base. The two crystal structures differ by a 25° rigid body rotation of the C-terminal arm. The tertiary structure exhibits pseudo-twofold symmetry. The structural symmetry mirrors internal sequence similarity: residues 11–57 and 102–148 are 30% identical and 53% similar with an E-value of 0.002. In one of the structures, electron density for an unknown ligand, consistent with nicotinamide or similar molecule, may indicate a functional site. Docking calculations suggest potential ligand binding hot spots in the region between the helical arms. Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Thermofield Theory for Finite-Temperature Electronic Structure

Wave function methods have offered a robust, systematically improvable means to study ground-state properties in quantum many-body systems. Theories like coupled cluster and their derivatives provide highly accurate approximations to the energy landscape at a reasonable computational cost. Analogues of such methods to study thermal properties, though highly desirable, have been lacking because evaluating thermal properties involve a trace over the entire Hilbert space, which is a formidable task. Besides, excited-state theories are generally not as well studied as ground-state ones. In this mini-review, we present an overview of a finite-temperature wave function formalism based on thermofield dynamics to overcome these difficulties. Thermofield dynamics allows us to map the equilibrium thermal density matrix to a pure state, i.e., a single wave function, albeit in an expanded Hilbert space. Ensemble averages become expectation values over this so-called thermal state. Around this thermal state, we have developed a procedure to generalize ground-state wave function theories to finite temperatures. As explicit examples, we highlight formulations of mean-field, configuration interaction, and coupled cluster theories for thermal properties of Fermions in the grand-canonical ensemble. To assess the quality of these approximations, we also show benchmark studies for the one-dimensional Hubbard model, while comparing against exact results. We will see that the thermal methods perform similarly to their ground-state counterparts, while merely adding a prefactor to the asymptotic computational cost. Furthermore, they also inherit all the properties, good or bad, from the ground-state methods, signifying the robustness of our formalism and the scope for future development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Target mass corrections in lepton–nucleus DIS: Theory and applications to nuclear PDFs

Motivated by the wide range of kinematics covered by current and planned deep-inelastic scattering (DIS) facilities, we revisit the formalism, practical implementation, and numerical impact of target mass corrections (TMCs) for DIS on unpolarized nuclear targets. An important aspect is that we only use nuclear and later partonic degrees of freedom, carefully avoiding a picture of the nucleus in terms of nucleons. After establishing that formulae used for individual nucleon targets (p,n), derived in the Operator Product Expansion (OPE) formalism, are indeed applicable to nuclear targets, here we rewrite expressions for nuclear TMCs in terms of re-scaled (or averaged) kinematic variables. As a consequence, we find a representation for nuclear TMCs that is approximately independent of the nuclear target. We go on to construct a single-parameter fit for all nuclear targets that is in good numerical agreement with full computations of TMCs. We discuss in detail qualitative and quantitative differences between nuclear TMCs built in the OPE and the parton model formalisms, as well as give numerical predictions for current and future facilities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

3D domain swapping in the TIM barrel of the α subunit of Streptococcus pneumoniae tryptophan synthase

Tryptophan synthase catalyzes the last two steps of tryptophan biosynthesis in plants, fungi and bacteria. It consists of two protein chains, designated α and β, encoded by trpA and trpB genes, that function as an αββα complex. Structural and functional features of tryptophan synthase have been extensively studied, explaining the roles of individual residues in the two active sites in catalysis and allosteric regulation. TrpA serves as a model for protein-folding studies. In 1969, Jackson and Yanofsky observed that the typically monomeric TrpA forms a small population of dimers. Dimerization was postulated to take place through an exchange of structural elements of the monomeric chains, a phenomenon later termed 3D domain swapping. The structural details of the TrpA dimer have remained unknown. Here, the crystal structure of the Streptococcus pneumoniae TrpA homodimer is reported, demonstrating 3D domain swapping in a TIM-barrel fold for the first time. The N-terminal domain comprising the H0–S1–H1–S2 elements is exchanged, while the hinge region corresponds to loop L2 linking strand S2 to helix H2′. The structural elements S2 and L2 carry the catalytic residues Glu52 and Asp63. As the S2 element is part of the swapped domain, the architecture of the catalytic apparatus in the dimer is recreated from two protein chains. The homodimer interface overlaps with the α–β interface of the tryptophan synthase αββα heterotetramer, suggesting that the 3D domain-swapped dimer cannot form a complex with the β subunit. In the crystal, the dimers assemble into a decamer comprising two pentameric rings.

3D domain swapping↗
DOE OSTI2021

Melting Point Depression and Phase Identification of Sugar Alcohols Encapsulated in ZIF Nanopores

Sugar alcohols (SAs) have attractive characteristics as phase-change materials, but their relatively high melting temperature limits their application in the real world. Nanoconfinement can be a useful parameter to reduce the melting temperature to pragmatic ranges. Using molecular dynamics simulations, we investigate the phases and behaviors of encapsulated SA in ZIF-8 and ZIF-11, which cannot be experimentally observed. Based on reliable partial charges for the zeolitic imidazolate framework (ZIF) structures calculated by a density functional theory, structural analysis shows that the SA’s attractive interaction with the ZIF structure frustrates the SA crystallization and also elucidates the second-order phase transition between amorphous phases. A methodology is suggested to determine the phase transition temperature of confined materials and used to quantify the melting temperature depression of the ZIF-confined SAs. We also explored the thermal conductivity of SA-in-ZIF composites. Phonon frequency analysis verifies that the presence of SA molecules enhances the heat transfer by adding heat pathways between the nanoporous structure of ZIFs.

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

Uncovering multiscale structure-property correlations via active learning in scanning tunneling microscopy

Atomic arrangements and local sub-structures fundamentally influence emergent material functionalities. These structures are conventionally probed using spatially resolved studies and the property correlations are deciphered by a researcher based on sequential explorations, thereby limiting the efficiency and scope. Here we demonstrate a multi-scale Bayesian deep-learning based framework that automatically correlates material structure with its electronic properties using scanning tunneling microscopy (STM) measurements in real-time. Its predictions are used to autonomously direct exploration toward regions of the sample that optimize a given material property. This method is deployed on a low-temperature ultra-high vacuum STM to understand the structure-property relationship in a europium-based semimetal, EuZn 2 As 2 , a promising candidate relevant to magnetism-driven topological phenomena. The framework employs a sparse-sampling approach to efficiently construct the scalar-property space using minimal measurements, about 1–10% of the data required in standard hyperspectral methods. Moreover, we formulate the problem hierarchically across length scales, implementing autonomous workflow to locate mesoscopic and atomic structures that correspond to a target material property. This framework offers the choice to design scalar-property from the spectroscopic data to steer sample exploration. Our findings reveal correlations of the electronic properties unique to surface terminations, local defect density, and point defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

A Novel Process for Converting Coal to High-Value Polyurethane Products

Battelle has demonstrated a patented process for making high-value, polyurethane (PU) foam from coal, based on preparing liquefied coal via direct liquefaction, converting it to polyols as an intermediate via ozonation, and then making PU foams from these polyols. This process represents a breakthrough in innovative utilization of U.S. coals, and is applicable to bituminous as well as sub-bituminous coals. The resulting PU foam products are projected to have an extremely high value (i.e., over $\$5,000$ /ton), with nearly 100% of carbon utilization from coalderived liquid feedstock, and 31.5% to 43.5% of the carbon in the PU foam polyol product being bio-based. The targeted products represent an extremely large (i.e., over $80 billion/year), existing PU foam market, which could expand into making coatings and adhesives. The process can further help reduce petroleum imports, while improving the economics of PU foam production. This work was completed with funding from the National Energy Technology Laboratory (NETL), with cost share from the State of Ohio’s Ohio Development Services Agency (ODSA) and others, and has advanced the process to 10 kg/day continuous scale and thus to Technology Readiness Level (TRL) 5. A total of 48 coal-based polyols were prepared and evaluated. The initial 28 polyols focused on range finding for ideal conditions. The later 20 polyols were produced as part of process optimizations. These optimizations were targeted around a continuous ozonolysis process to evaluate extended time reactions and to create the necessary intermediate for production of 1-gallon samples of polyol. The most unique attribute of Battelle’s polyol is in the utilization of coal’s aromaticity to gain final foam rigidity. Typically, polyols depend on the isocyanate fraction and cross-linking to gain rigidity. By utilizing coal, we were able to maintain rigidity while reducing the overall hydroxyl value of the polyol. This is important as lower hydroxyl value leads to greater percent weight of the coal-based polyol because less isocyanate is required for foaming. This leads to greater foam cost savings. This report provides the details, process, and process cost models of the conversion of coal to polyols and further to PU foams. Battelle’s process begins with coal liquids. These liquids can be obtained by two processes: coal coking or pyrolysis to produce coal tar, and Battelle’s biobased coal-to-liquids (CTL) process to produce heavy syncrude after liquifying >85% coal. After liquification, Battelle utilizes ozonolysis to create functionalization on the polyaromatic coal structure. The functionalization is then converted to the final polyester polyol through transesterification, or to hydroxyamide polyol through amidification. Equivalent or better standard properties have been obtained for 2 lb/ft 3 density rigid, water and freon-alternative blown foams, including compressive strength, density, R-value, and dimensional stability. Target applications for these foams are insulation, packaging, and energy-absorbing foams. Some exploratory testing also showed promise for adhesives applications. A detailed economic analysis showed that Battelle’s polyol process is economical, at a 140 metric tons per day (MTD) polyol production scale. An attractive return on investment (ROI) at competitive pricing validates the process is ready for a pilot-plant demonstration. A scale-up plan is provided.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2022

Emerging Modification Technologies of Lignin-based Activated Carbon toward Advanced Applications

Lignin-based activated carbon (LAC) is a promising high-quality functional material due to high surface area, abundant porous structure, and various functional groups. Modification is the most important step to functionalize LAC by altering its porous and chemical properties. Here, this Review summarizes the state-of-the-art modification technologies of LAC toward advanced applications. Promising modification approaches are reviewed to display their effects on the preparation of LAC. The multiscale changes in the porosity and the surface chemistry of LAC are fully discussed. Advanced applications are then introduced to show the potential of LAC for supercapacitor electrode, catalyst support, hydrogen storage, and carbon dioxide capture. Finally, the mechanistic structure-function relationships of LAC are elaborated. These results highlight that modification technologies play a special role in altering the properties and defining the functionalities of LAC, which could be a promising porous carbon material toward industrial applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structural and biophysical insights into targeting of claudin-4 by a synthetic antibody fragment

Claudins are a 27-member family of ~25 kDa membrane proteins that integrate into tight junctions to form molecular barriers at the paracellular spaces between endothelial and epithelial cells. As the backbone of tight junction structure and function, claudins are attractive targets for modulating tissue permeability to deliver drugs or treat disease. However, structures of claudins are limited due to their small sizes and physicochemical properties—these traits also make therapy development a challenge. Here we report the development of a synthetic antibody fragment (sFab) that binds human claudin-4 and the determination of a high-resolution structure of it bound to claudin-4/enterotoxin complexes using cryogenic electron microscopy. Structural and biophysical results reveal this sFabs mechanism of select binding to human claudin-4 over other homologous claudins and establish the ability of sFabs to bind hard-to-target claudins to probe tight junction structure and function. The findings provide a framework for tight junction modulation by sFabs for tissue-selective therapies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Nanoscale Mass Spectrometry Multimodal Imaging via Tip-Enhanced Photothermal Desorption

Materials ranging from adhesives, pharmaceuticals, lubricants, and personal care products are traditionally studied using macroscopic characterization techniques. However, their functionality is in reality defined by details of chemical organization on often noncrystalline matter with characteristic length scales on the order of microns to nanometers. Additionally, these materials are traditionally difficult to analyze using standard vacuum-based approaches that provide nanoscale chemical characterization due to their volatile and beam-sensitive nature. Therefore, approaches that operate under ambient conditions need to be developed that allow probing of nanoscale chemical phenomena and correlated functionality. Here, we demonstrate a tool for probing and visualizing local chemical environments and correlating them to material structure and functionality using advanced multimodal chemical imaging on a combined atomic force microscopy (AFM) and mass spectrometry (MS) system using tip-enhanced photothermal desorption with atmospheric pressure chemical ionization (APCI). We demonstrate enhanced performance metrics of the technique for correlated imaging and point sampling and illustrate the applicability for the analysis of trace chemicals on a human hair, additives in adhesives on paper, and pharmaceuticals samples notoriously difficult to analyze in a vacuum environment. Overall, this approach of correlating local chemical environments to structure and functionality is key to advancing research in many fields ranging from biology, to medicine, to material science.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Hydrogen in disordered titania: connecting local chemistry, structure, and stoichiometry through accelerated exploration

Hydrogen incorporation in native surface oxides of metal alloys often controls the onset of metal hydriding, with implications for materials corrosion and hydrogen storage. A key representative example is titania, which forms as a passivating layer on a variety of titanium alloys for structural and functional applications. These oxides tend to be structurally diverse, featuring polymorphic phases, grain boundaries, and amorphous regions that generate a disparate set of unique local environments for hydrogen. Here, we introduce a workflow that can efficiently and accurately navigate this complexity. First, a machine learning force field, trained on ab initio molecular dynamics simulations, was used to generate amorphous configurations. Density functional theory calculations were then performed on these structures to identify local oxygen environments, which were compared against experimental observations. Second, to classify subtle differences across the disordered configuration space, we employ a graph-based sampling procedure. Finally, local hydrogen binding energies and hopping kinetics are computed using exhaustive density functional theory calculations on representative configurations. Here, we leverage this methodology to show that hydrogen binding energetics are described by local oxygen coordination, which in turn is affected by stoichiometry, and form the basis of hopping kinetics and diffusion. Together these results imply that hydrogen incorporation and transport in TiO x can be tailored through compositional engineering, with implications for improving the performance and durability of titanium-derived alloys in hydrogen environments.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Extracting structural motifs from pair distribution function data of nanostructures using explainable machine learning

Characterization of material structure with X-ray or neutron scattering using e.g. Pair Distribution Function (PDF) analysis most often rely on refining a structure model against an experimental dataset. However, identifying a suitable model is often a bottleneck. Recently, automated approaches have made it possible to test thousands of models for each dataset, but these methods are computationally expensive and analysing the output, i.e. extracting structural information from the resulting fits in a meaningful way, is challenging. Our Machine Learning based Motif Extractor (ML-MotEx) trains an ML algorithm on thousands of fits, and uses SHAP (SHapley Additive exPlanation) values to identify which model features are important for the fit quality. We use the method for 4 different chemical systems, including disordered nanomaterials and clusters. ML-MotEx opens for a type of modelling where each feature in a model is assigned an importance value for the fit quality based on explainable ML.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Radiation of the plant pyridoxal 5'-phosphate (PLP)-dependent aromatic L -amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic L -amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. In this paper, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A glossary of plant cell structures: Current insights and future questions

Abstract In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.

Biochemistry & Molecular Biology↗
DOE OSTI2025

GPU acceleration of hybrid functional calculations in the SPARC electronic structure code

We present a Graphics Processing Unit (GPU)-accelerated version of the real-space SPARC electronic structure code for performing hybrid functional calculations in generalized Kohn–Sham density functional theory. In particular, we develop a batch variant of the recently formulated Kronecker product-based linear solver for the simultaneous solution of multiple linear systems. We then develop a modular, math kernel based implementation for hybrid functionals on NVIDIA architectures, where computationally intensive operations are offloaded to the GPUs, while the remaining workload is handled by the central processing units (CPUs). Considering bulk and slab examples, we demonstrate that GPUs enable up to 8× speedup in node-hours and 80× in core-hours compared to CPU-only execution, reducing the time to solution on V100 GPUs to around 300 s for a metallic system with over 6000 electrons, and significantly reducing the computational resources required for a given wall time.

Kohn-Sham density functional theory↗
DOE OSTI2022

Towards mapping biodiversity from above: Can fusing lidar and hyperspectral remote sensing predict taxonomic, functional, and phylogenetic tree diversity in temperate forests?

Abstract Aim Rapid global change is impacting the diversity of tree species and essential ecosystem functions and services of forests. It is therefore critical to understand and predict how the diversity of tree species is spatially distributed within and among forest biomes. Satellite remote sensing platforms have been used for decades to map forest structure and function but are limited in their capacity to monitor change by their relatively coarse spatial resolution and the complexity of scales at which different dimensions of biodiversity are observed in the field. Recently, airborne remote sensing platforms making use of passive high spectral resolution (i.e., hyperspectral) and active lidar data have been operationalized, providing an opportunity to disentangle how biodiversity patterns vary across space and time from field observations to larger scales. Most studies to date have focused on single sites and/or one sensor type; here we ask how multiple sensor types from the National Ecological Observatory Network’s Airborne Observation Platform (NEON AOP) perform across multiple sites in a single biome at the NEON field plot scale (i.e., 40 m × 40 m). Location Eastern USA. Time period 2017–2018. Taxa studied Trees. Methods With a fusion of hyperspectral and lidar data from the NEON AOP, we assess the ability of high resolution remotely sensed metrics to measure biodiversity variation across eastern US temperate forests. We examine how taxonomic, functional, and phylogenetic measures of alpha diversity vary spatially and assess to what degree remotely sensed metrics correlate with in situ biodiversity metrics. Results Models using estimates of forest function, canopy structure, and topographic diversity performed better than models containing each category alone. Our results show that canopy structural diversity, and not just spectral reflectance, is critical to predicting biodiversity. Main conclusions We found that an approach that jointly leverages spectral properties related to leaf and canopy functional traits and forest health, lidar derived estimates of forest structure, fine‐resolution topographic diversity, and careful consideration of biogeographical differences within and among biomes is needed to accurately map biodiversity variation from above.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

High-throughput characterization of Ag–V–O nanostructured thin-film materials libraries for photoelectrochemical solar water splitting

Ag–V–O thin-film materials libraries, with both composition (Ag 22-77 V 23-78 O x ) and thickness (123–714 nm) gradients were fabricated using combinatorial reactive magnetron co-sputtering aiming on establishing relations between composition, structure, and functional properties. As-deposited libraries were annealed in air at 300 °C for 10 h. High-throughput characterization methods of composition, structure and functional properties were used to identify photoelectrochemically active regions. The phases AgV 6 O 15 , Ag 2 V 4 O 11 , AgVO 3 , and Ag 4 V 2 O 7 were observed throughout the composition gradient. The photoelectrochemical properties of Ag–V–O films are dependent on composition and morphology. An enhanced photocurrent density (~300–554 μA/cm 2 ) was obtained at 30 to 45 at.% Ag along the thickness gradient. Thin films of these compositions show a nanowire morphology, which is an important factor for the enhancement of photoelectrochemical performance. The photoelectrochemically active regions were further investigated by high-throughput synchrotron-X-ray diffraction and transmission electron microscopy (Ag 32 V 68 O x ) which confirmed the presence of Ag 2 V 4 O 11 as the dominating phase along with the minor phases AgV 6 O 15 and AgVO 3 . This enhanced photoactive region shows bandgap values of ~2.30 eV for the direct and ~1.87 eV for the indirect bandgap energies. Finally, the porous nanostructured films improve charge transport and are hence of interest for photoelectrochemical water splitting.

36 MATERIALS SCIENCE↗