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At least 1,729 records · Page 96
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Basin-Scale Structural Features Database: Spatial Datasets to Support Carbon Storage Resource Assessments

Presentation slides on "Basin-Scale Structural Features Database: Spatial Datasets to Support Carbon Storage Resource Assessments" for CCUS 2025 Annual Meeting. The Basin-Scale Structural Features database contains a series of basin-scale spatial datasets representing structural features, including faults, fractures, folds, and earthquakes. Designed to support carbon storage feasibility and resources assessments for Carbon Capture and Storage (CCS) projects, the database leverages publicly available data resources from authoritative sources (e.g. US Geological Survey, State Geologic Surveys), and aims to help users better understand basin-scale structural features, as well as potential data gaps in areas with sparse information.

basin scale↗
DOE OSTI2021

Defining the Structural Stability Field of Disordered Fluorite Oxides

Fluorite-structured oxides constitute an important class of materials for energy technologies. Despite their high level of structural symmetry and simplicity, these materials can accommodate atomic disorder without losing crystallinity, making them indispensable for uses in environments with high temperature, changing chemical compositions, or intense radiation fields. In this contribution, we present a set of simple rules that predict whether a compound may adopt a disordered fluorite structure. This approach is closely aligned with Pauling’s rules for ionic crystal structures and Goldschmidt’s rules for ionic substitution.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Imaging Complex Subsurface Structures for Geothermal Exploration at Pirouette Mountain and Eleven-Mile Canyon in Nevada

Accurate imaging of subsurface complex structures with faults is crucial for geothermal exploration because faults are generally the primary conduit of hydrothermal flow. It is very challenging to image geothermal exploration areas because of complex geologic structures with various faults and noisy surface seismic data with strong and coherent ground-roll noise. In addition, fracture zones and most geologic formations behave as anisotropic media for seismic-wave propagation. Properly suppressing ground-roll noise and accounting for subsurface anisotropic properties are essential for high-resolution imaging of subsurface structures and faults for geothermal exploration. We develop a novel wavenumber-adaptive bandpass filter to suppress the ground-roll noise without affecting useful seismic signals. This filter adaptively exploits both characteristics of the lower frequency and the smaller velocity of the ground-roll noise than those of the signals. Consequently, this filter can effectively differentiate the ground-roll noise from the signal. We use our novel filter to attenuate the ground-roll noise in seismic data along five survey lines acquired by the U.S. Navy Geothermal Program Office at Pirouette Mountain and Eleven-Mile Canyon in Nevada, United States. We then apply our novel anisotropic least-squares reverse-time migration algorithm to the resulting data for imaging subsurface structures at the Pirouette Mountain and Eleven-Mile Canyon geothermal exploration areas. The migration method employs an efficient implicit wavefield-separation scheme to reduce image artifacts and improve the image quality. Our results demonstrate that our wavenumber-adaptive bandpass filtering method successfully suppresses the strong and coherent ground-roll noise in the land seismic data, and our anisotropic least-squares reverse-time migration produces high-resolution subsurface images of Pirouette Mountain and Eleven-Mile Canyon, facilitating accurate fault interpretation for geothermal exploration.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

Structural Principles in Liquids and Glasses: Bottom-Up or Top-Down

The conventional approach to elucidate the atomic structure of liquid and glass is to start with local structural units made of several atoms, and to use them as building blocks to form a global structure, the bottom-up approach. We propose to add an alternative top-down approach in which we start with a global high-temperature gas state and then apply interatomic potentials to all atoms at once. This causes collective density wave instability in all directions with the same wavelength. These two driving forces, local and global, are in competition and are mutually frustrated. The final structure is determined through the compromise of frustration between these two, which creates the medium-range-order. This even-handed approach on global and local potential energy landscapes explains the distinct natures of short-range order and medium-range order, and strong temperature dependence of various properties of liquid.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Editorial: Structure and mechanism of microbial membrane active transporters

Membrane active transporters play essential roles in microbial physiology. They couple energy transduction to conformational changes that drive translocation of nutrients, substrates and ions, as well as molecular communication. The structure and function of microbial membrane active transporters are highly diverse. Typical examples include the primary active transporters in the ATP-binding cassette (ABC) superfamily (Thomas and Tampé, 2020; Davidson et al., 2008; Locher et al., 2002), the secondary active transporters in the Major Facilitator Superfamily (MFS) (Drew et al., 2021; Kaback and Guan, 2019), and the ligand-gated porins in the TonB-dependent transporter (TBDT) family (Klebba et al., 2021). As structural, proteogenomic, and computational methods advance, active transporters are increasingly recognized as dynamic molecular machines whose mechanisms can now be visualized and modeled with remarkable precision, building on decades of biochemical and biophysical discovery that established the foundations of this field. The transporter studies recruited in this Research Topic provide us with new insights into the field including structure-function of sugar transporters in yeast, structural prediction and classification of ABC complexes in Bacillus subtilis, Type VI Secretion System (T6SS) in Bacteroides fragilis, amino acids uptake in Escherichia coli and bacterial spore germination.

mechanism↗
DOE OSTI2020

Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200 ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10– 30°C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40°C and attains a completely closed conformation at 50°C. We also found that the presence of glycan moieties did not influence the observed protein dynamics. Nevertheless, the closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Enhancement of γ/γ’ Microstructured Cobalt Superalloys Produced from Atomized Powder by Creating a Harmonic Structure

A material’s properties must be continuously improved to meet the demands of extreme conditions in high-temperature applications. It is demonstrated that γ-γ’ Co-based superalloys could surpass the yield stress of Ni-based superalloys at high temperature due to the γ-γ’ structure. The powders were subjected to a harmonic modification in order to refine the grain structure on the surface and to activate the sintering process. This study examines how harmonic structure affects microstructure and mechanical properties at high temperatures. Spark Plasma Sintering (SPS) was used for consolidation to maintain the ultrafine grain size microstructure of the powder. Compression tests were conducted from room temperature (RT) to 750 °C to assess the mechanical properties of the material. Yield stress values obtained from harmonic structures are four times higher than those obtained from cast alloys.

36 MATERIALS SCIENCE↗
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 OSTI2023

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the $P$-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Diversity in the Common Fold: Structural Insights into Class D β-Lactamases from Gram-Negative Pathogens

Class D β-lactamases (DBLs) represent a major threat to antibiotic efficacy by hydrolyzing β-lactam drugs, including last-resort carbapenems, thereby driving antimicrobial resistance in Gram-negative bacteria. The enzymes share a structurally conserved two-domain α/β architecture with seven active-site motifs and three flexible extended loops (the P-loop, Ω-loop, and newly designated B-loop) that surround the active site. While each of these loops is known to influence enzyme function, their coordinated roles have not been fully elucidated. To investigate the significance of their interplay, we compared the sequences and crystal structures of 40 DBLs from clinically relevant Gram-negative pathogens and performed molecular dynamics simulations on selected representatives. Combined structural and dynamical analyses revealed a strong correlation between B-loop architecture and carbapenemase activity in the pathogens Klebsiella and Acinetobacter, particularly regarding loop length and spatial organization. These findings emphasize the B-loop’s critical contribution, in concert with the P- and Ω-loops, in tuning active site versatility, substrate recognition, catalytic activity, and structural stability. A deeper understanding of how these motifs and loops govern DBL function may inform the development of novel antibiotics and inhibitors targeting this class of enzymes.

antibiotic resistance↗
DOE OSTI2023

Structural Characterization of TRAF6 N-Terminal for Therapeutic Uses and Computational Studies on New Derivatives

Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source “Turkish DeLight” to be 3.2 Å resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Mesoscale Modeling of Dislocation Cell Structure Evolution and Radiation-Induced Segregation in Additively Manufactured Austenitic Stainless Steel

Structural alloys under irradiation develop radiation-induced segregation (RIS) at point defect sinks, which lead to undesired changes in the alloy's properties. Additively manufactured austenitic stainless steels are expected to yield a distinct response to irradiation damage owing to their unique as-printed dislocation cell structure. In this talk, we present the development of a mesoscale model for dislocation cell structure evolution coupled with RIS using the MOOSE framework. The evolution of network dislocations within spatially distinct cells and cell walls are modeled using climb-mediated edge annihilation and generation processes. Starting with initial microstructures of as-printed non-equilibrium segregations at dislocation cell walls, our 2D and 3D simulations explore the effects of irradiation temperature, dose rate, dislocation sink bias, and specimen thickness on microstructure evolution. The results will be compared against experimental characterizations of in-situ and ex-situ ion-irradiated samples, and the implications of evolving cell structure on irradiation damage response will be discussed.

additive manufacturing↗
DOE OSTI2024

Structural insights into binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean

Tetrahydrofolate and its derivatives participate in one-carbon transfer reactions in all organisms. The cellular form of tetrahydrofolate (THF) is modified by multiple glutamate residues and polyglutamylation plays a key role in organellar and cellular folate homeostasis. In addition, polyglutamylation of THF is known to increase the binding affinity to enzymes in the folate cycle, many of which can utilize polyglutamylated THF as a substrate. Here, we use X-ray crystallography to provide a high-resolution view of interactions between the enzyme serine hydroxymethyltransferase (SHMT), which provides one carbon precursors for the folate cycle, and a polyglutamylated form of THF. Our 1.7 Å crystal structure of soybean SHMT8 in complex with diglutamylated 5-formyl-THF reveals, for the first time, a structural rearrangement of a loop at the entrance to the folate binding site accompanied by the formation of novel specific interactions between the enzyme and the diglutamyl tail of the ligand. Biochemical assays show that additional glutamate moieties on the folate ligand increase both enzyme stability and binding affinity. Together these studies provide new information on SHMT structure and function and inform the design of anti-folate agents.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Non-Invasive Biophysical Techniques to Monitor the Structural Plasticity of the Photosynthetic Machinery of Live Diatom Cells

The photosynthetic performance of diatoms depends largely on the organization and structural flexibility of their thylakoid membranes, the densely packed, highly organized membrane vesicles in which light reactions of photosynthesis occur. Different regulatory mechanisms that fine tune the photosynthetic functions affect the organization of the photosynthetic machinery at different levels of structural complexity, from the level of individual protein complexes to the macroarray of membrane proteins and the remodeling of the entire thylakoid membrane system. To monitor these reorganizations, non-invasive techniques are of special value. In this chapter, we focus our attention on three of these techniques, which have been demonstrated to provide unique and useful information on the structure and structural and functional plasticity of live diatom cells: (i) circular dichroism (CD) spectroscopy, which has provided unique information on the chiral (macro-)organization of protein complexes and on their rapid, reversible reorganizations, fine-tuning the light-harvesting processes, as well as on variations in the short-range excitonic interactions in the antenna complexes; (ii) small-angle neutron scattering (SANS), which has been used to determine the periodic organization of the thylakoid membranes and to monitor reversible ultrastructural changes on the time-scale of minutes, induced by variations in the environmental conditions such as changes in temperature or light intensity; and (iii) electrochromic shift absorbance transients (ΔA ECS ), a spectroscopic tool which has been shown to be capable of identifying distinct functional groups of the light-harvesting carotenoid fucoxanthin in different diatoms and in cells exposed to different light intensities. Future use of these techniques will most certainly contribute to the deeper understanding of key regulatory mechanisms of photosynthesis in diatoms.

Szabo, Milan↗
DOE OSTI2026

Microstructure‐Informed Analysis Framework for Lattice Structures: Guiding Topology‐Material Synergy in Titanium Alloys

In this work we discuss a microstructure‐informed analysis framework for lattice structures that maps the material's microstructural response to guide topology selection and mechanical performance optimization. By coupling geometrical topology with intrinsic material behavior, we demonstrate how anisotropic microstructural response can inform the design of optimized lattice structures. To illustrate this concept, we focus on two distinct classes of titanium alloys: Ti5553 (Ti‐5Al‐5Mo‐5V‐3Cr wt%), which exhibits a predominantly ‐phase microstructure, and Ti64 (Ti‐6Al‐4V wt%), which features a dual‐phase structure. These alloys exhibit markedly different mechanical responses under multiaxial loading in “fully dense” solid form. The strut‐level stress analysis of these alloys reveals how specific microstructural characteristics can guide the selection of appropriate lattice topologies. Two representative lattice configurations, one stretching‐dominated and one bending‐dominated, are evaluated under identical loading conditions to explore how microstructure‐driven design can lead to topology choices that are better suited to accommodate shear or other critical local stress states, thereby enhancing mechanical performance. A strut‐level mechanics‐based analysis is performed to evaluate shear stress distribution and highlight the role of topology‐microstructure synergy and compatibility in determining overall lattice behavior. The findings emphasize the importance of designing structures that are both load‐aware and microstructure‐responsive, enabling more effective material utilization in advanced engineering applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Universal Electronic‐Structure Relationship Governing Intrinsic Magnetic Properties in Permanent Magnets

An electronic-structure-centered perspective is presented on permanent-magnet (PM) design, highlighting two key levers, that is, saturation magnetization (M s ), governed by 3d-band filling and exchange physics, and magnetocrystalline anisotropy energy (MAE), arising from spin-orbit coupling (SOC) on anisotropic orbital populations. Reviewing current practices, including DFT-based MAE/J ij extraction, atomistic-spin and micromagnetic modeling, and high-throughput machine learning (ML) pipelines, three bottlenecks limiting predictive discovery is identified that is i) electronic-structure accuracy for small MAE (sensitive to functional choice, Hubbard U, and many-body effects), ii) finite-temperature and kinetic realism (phonon/magnon renormalization, ordering kinetics), and iii) descriptor and multiscale decoupling (lack of SOC-weighted and orbital-resolved fingerprints). Deep dives into the electronic-structure of Nd─Fe─B and Fe─N show how these fingerprints govern magnetic performance, motivating DFT- and quantum-mechanics-based descriptors for discovery. Unbiased, structure-driven exploration, coupled with high-throughput simulations, ML, generative AI, and reasoning models, accelerates candidate identification and propagates insights across scales. Addressing supply-chain risks, on future needs of designing “critical-element-free” magnets with tailored microstructure and high energy products is emphasized. By integrating electronic fingerprints, AI reasoning, and multiscale modeling, a practical roadmap is provided for rare-earth-lean or rare-earth free, high-performance, sustainable PMs.

Singh, Prashant [Ames Laboratory, and Iowa State U↗
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 OSTI2022

Not All Aggregates Are Made the Same: Distinct Structures of Solution Aggregates Drastically Modulate Assembly Pathways, Morphology, and Electronic Properties of Conjugated Polymers

Abstract Tuning structures of solution‐state aggregation and aggregation‐mediated assembly pathways of conjugated polymers is crucial for optimizing their solid‐state morphology and charge‐transport property. However, it remains challenging to unravel and control the exact structures of solution aggregates, let alone to modulate assembly pathways in a controlled fashion. Herein, aggregate structures of an isoindigo–bithiophene‐based polymer (PII‐2T) are modulated by tuning selectivity of the solvent toward the side chain versus the backbone, which leads to three distinct assembly pathways: direct crystallization from side‐chain‐associated amorphous aggregates, chiral liquid crystal (LC)‐mediated assembly from semicrystalline aggregates with side‐chain and backbone stacking, and random agglomeration from backbone‐stacked semicrystalline aggregates. Importantly, it is demonstrated that the amorphous solution aggregates, compared with semicrystalline ones, lead to significantly improved alignment and reduced paracrystalline disorder in the solid state due to direct crystallization during the meniscus‐guided coating process. Alignment quantified by the dichroic ratio is enhanced by up to 14‐fold, and the charge‐carrier mobility increases by a maximum of 20‐fold in films printed from amorphous aggregates compared to those from semicrystalline aggregates. This work shows that by tuning the precise structure of solution aggregates, the assembly pathways and the resulting thin‐film morphology and device properties can be drastically tuned.

36 MATERIALS SCIENCE↗