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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens

Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Magnetic ground state and perturbations of the distorted kagome Ising metal TmAgGe

Here, we present the magnetic orders and excitations of the distorted kagome intermetallic magnet TmAgGe. Using neutron single crystal diffraction we identify the propagation vectors k = ($\frac{1}{2}$ 0 0) and k = (0 0 0) and determine the magnetic structures of the zero-field and magnetic field-induced phases for H along the $\mathcal{a}$ and [–110] crystal directions. We determine the experimental magnetic field- temperature (H, T)-phase diagram and reproduce it by Monte Carlo simulations of an effective spin exchange Hamiltonian for one distorted kagome layer. Our model includes a strong axial single-ion anisotropy and significantly smaller exchange couplings, which span up to the third-nearest neighbors within the layer. Single crystal inelastic neutron scattering (INS) measurements reveal an almost flat, only weakly dispersive mode around 7 meV that we use alongside bulk magnetization data to deduce the crystal-electric field (CEF) scheme for the Tm 3+ ions. Random phase approximation (RPA) calculations based on the determined CEF wave functions of the two lowest quasidoublets enable an estimation of the interlayer coupling that is compatible with the experimental INS spectra. No evidence for low-energy spin waves associated to the magnetic order was found, which is consistent with the strongly Ising nature of the ground state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
DOE OSTI2020

Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity

Most antibodies isolated from individuals with coronavirus disease 2019 (COVID-19) are specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, COVA1-16 is a relatively rare antibody that also cross-neutralizes SARS-CoV. Here, we determined a crystal structure of the COVA1-16 antibody fragment (Fab) with the SARS-CoV-2 receptor-binding domain (RBD) and negative-stain electron microscopy reconstructions with the spike glycoprotein trimer to elucidate the structural basis of its cross-reactivity. COVA1-16 binds a highly conserved epitope on the SARS-CoV-2 RBD, mainly through a long complementarity-determining region (CDR) H3, and competes with the angiotensin-converting enzyme 2 (ACE2) receptor because of steric hindrance rather than epitope overlap. COVA1-16 binds to a flexible up conformation of the RBD on the spike and relies on antibody avidity for neutralization. These findings, along with the structural and functional rationale for epitope conservation, provide insights for development of more universal SARS-like coronavirus vaccines and therapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Joint inversion of electromagnetic measurements for the determination of water saturation profiles in concrete structures

Highlights: • DC-electrical and dielectric data are combined to estimate concrete saturation degree. • A joint inversion approach of the electromagnetic measurements is proposed. • The sensitivity of the measurements to the saturation model parameters is analysed. • The new joint approach was developed and is applied to synthetic and real data. • The benefits of the joint approach over the inversion of one data type are highlighted. Water saturation profiles in concrete are essential to assess its durability and can be determined using non-destructive techniques, especially the electric and the capacitive methods. In this paper, we propose a new inversion scheme where both resistivity and permittivity measurements are inverted jointly to retrieve the saturation profile. The finite element method is used to model the measurements in 3D, the concrete having a saturation profile with depth, represented by a continuous model taking the form of a Weibull curve with four parameters. A non-linear least-squares optimization based on the Levenberg-Marquardt scheme is developed for the inversion of measurements. Results show that information gathered from both measurements enriches the reconstructed profile, leading to a more reliable estimation of saturation profiles. We believe that the joint inversion method herein developed could lead to the study of more complex phenomena, such as the coupled water-chloride ingress.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Insights into Molecular Magnetism in Metal–Metal Bonded Systems as Revealed by a Spectroscopic and Computational Analysis of Diiron Complexes

A pair of bimetallic compounds featuring Fe–Fe bonds, [Fe( i PrNPPh 2 ) 3 FeR] (R = PMe 3 , ≡N t Bu), have been investigated using High-Frequency Electron Paramagnetic Resonance (HFEPR) as well as field- and temperature-dependent 57 Fe nuclear γ resonance (Mössbauer) spectroscopy. To gain insight into the local site electronic structure, we have concurrently studied a compound containing a single Fe(II) in a geometry analogous to that of one of the dimer sites. Our spectroscopic studies have allowed for the assessment of the electronic structure via the determination of the zero-field splitting and 57 Fe hyperfine parameters for the entire series. We also report on our efforts to correlate structure with physical properties in metal–metal bonded systems using ligand field theory guided by quantum chemical calculations. Through the insight gained in this study, we discuss strategies for the design of single-molecule magnets based on polymetallic compounds linked via direct metal–metal bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Atomically Dispersed Platinum in Surface and Subsurface Sites on MgO Have Contrasting Catalytic Properties for CO Oxidation

Atomically dispersed metals on metal oxide supports are a rapidly growing class of catalysts. Developing an understanding of where and how the metals are bonded to the supports is challenging because support surfaces are heterogeneous, and most reports lack a detailed consideration of these points. In this work, we report two atomically dispersed CO oxidation catalysts having markedly different metal–support interactions: platinum in the first layer of crystalline MgO powder and platinum in the second layer of this support. Structural models have been determined on the basis of data and computations, including those determined by extended X-ray absorption fine structure and X-ray absorption near edge structure spectroscopies, infrared spectroscopy of adsorbed CO, and scanning transmission electron microscopy. The data demonstrate the transformation of surface to subsurface platinum as the temperature of sample calcination increased. Catalyst performance data demonstrate the lower activity but greater stability of the subsurface platinum than of the surface platinum.

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

Structure of pre-miR-31 reveals an active role in Dicer–TRBP complex processing

As an essential posttranscriptional regulator of gene expression, microRNA (miRNA) levels must be strictly maintained. The biogenesis of many miRNAs is mediated by trans-acting protein partners through a variety of mechanisms, including remodeling of the RNA structure. miR-31 functions as an oncogene in numerous cancers, and interestingly, its biogenesis is not known to be regulated by protein-binding partners. Therefore, the intrinsic structural properties of the precursor element of miR-31 (pre-miR-31) can provide a mechanism by which its biogenesis is regulated. We determined the solution structure of pre-miR-31 to investigate the role of distinct structural elements in regulating processing by the Dicer–TRBP complex. We found that the presence or absence of mismatches within the helical stem does not strongly influence Dicer–TRBP processing of the pre-miRNAs. However, both the apical loop size and structure at the Dicing site are key elements for discrimination by the Dicer–TRBP complex. Interestingly, our NMR-derived structure reveals the presence of a triplet of base pairs that link the Dicer cleavage site and the apical loop. Mutational analysis in this region suggests that the stability of the junction region strongly influences processing by the Dicer–TRBP complex. Our results enrich our understanding of the active role that RNA structure plays in regulating miRNA biogenesis, which has direct implications for the control of gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Widespread Negative Longitudinal Piezoelectric Responses in Ferroelectric Crystals with Layered Structures

In this study, we investigate the underlying mechanisms of the universal negative piezoelectricity in low-dimensional layered materials by carrying out first-principles calculations. Two-dimensional layered ferroelectric CuInP 2 S 6 is analyzed in detail as a typical example, but the theory can be applied to any other low-dimensional layered piezoelectrics. Consistent with the theory proposed in [Phys. Rev. Lett. 119, 207601 (2017), the anomalous negative piezoelectricity in CuInP 2 S 6 also results from its negative clamped-ion term, which cannot be compensated by the positive internal-strain part. Here, we focus on a more general rule by proposing that having a negative clamped-ion term should be universal among piezoelectric materials, which is attributed to the “lag of Wannier center” effect. The internal-strain term, which is the change in polarization due to structural relaxation in response to strain, is mostly determined by the spatial structure and chemical bonding of the material. In a low-dimensional layered piezoelectric material such as CuInP 2 S 6 , the internal-strain term is approximately zero. This is because the internal structure of the molecular layers, which are bonded by the weak van der Waals interaction, responds little to the strain. As a result, the magnitude of the dipole, which depends strongly on the dimension and structure of the molecular layer, also has a small response with respect to strain. An equation bridging the internal strain responses in low-dimensional and three-dimensional piezoelectrics is also derived to analytically express this point. This work aims to deepen our understanding about this anomalous piezoelectric effect, especially in low-dimensional layered materials, and provide strategies for discovering materials with novel electromechanical properties.

2-dimensional systems↗
DOE OSTI2021

Uranium (VI) Adsorbate Structures on Portlandite [Ca(OH)2] Type Surfaces Determined by Computational Modelling and X-ray Absorption Spectroscopy

Portlandite [Ca(OH) 2 ] is a potentially dominant solid phase in the high pH fluids expected within the cementitious engineered barriers of Geological Disposal Facilities (GDF). This study combined X-ray Absorption Spectroscopy with computational modelling in order to provide atomic-scale data which improves our understanding of how a critically important radionuclide (U) will be adsorbed onto this phase under conditions relevant to a GDF environment. Such data are fundamental for predicting radionuclide mass transfer. Surface coordination chemistry and speciation of uranium with portlandite [Ca(OH) 2 ] under alkaline groundwater conditions (ca. pH 12) were determined by both in situ and ex situ grazing incidence extended X-ray absorption fine structure analysis (EXAFS) and by computational modelling at the atomic level. Free energies of sorption of aqueous uranyl hydroxides, [UO 2 (OH) n ] 2–n (n = 0–5) with the (001), (100) and (203) or (101) surfaces of portlandite are predicted from the potential of mean force using classical molecular umbrella sampling simulation methods and the structural interactions are further explored using fully periodic density functional theory computations. Although uranyl is predicted to only weakly adsorb to the (001) and (100) clean surfaces, there should be significantly stronger interactions with the (203/101) surface or at hydroxyl vacancies, both prevalent under groundwater conditions. The uranyl surface complex is typically found to include four equatorially coordinated hydroxyl ligands, forming an inner-sphere sorbate by direct interaction of a uranyl oxygen with surface calcium ions in both the (001) and (203/101) cases. In contrast, on the (100) surface, uranyl is sorbed with its axis more parallel to the surface plane. The EXAFS data are largely consistent with a surface structural layer or film similar to calcium uranate, but also show distinct uranyl characteristics, with the uranyl ion exhibiting the classic dioxygenyl oxygens at 1.8 Å and between four and five equatorial oxygen atoms at distances between 2.28 and 2.35 Å from the central U absorber. These experimental data are wholly consistent with the adsorbate configuration predicted by the computational models. These findings suggest that, under the strongly alkaline conditions of a cementitious backfill engineered barrier, there would be significant uptake of uranyl by portlandite to inhibit the mobility of U(VI) from the near field of a geological disposal facility.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Atomic structures of interfacial solute gateways to θ' precipitates in Al-Cu alloys

Many materials employed in critical structural applications depend upon metastable strengthening precipitates that transform or dissolve at elevated temperatures. Herein, aberration-corrected scanning transmission electron microscopy and first-principles calculations are used to accurately determine the atomic structure of the highly mobile, semi-coherent precipitate interfaces that control this process in the classic θ' (Al 2 Cu) precipitate in the Al-Cu system. Semi-coherent {110} interfaces are found to be composed of an array of unexpected misfit dislocations that are arranged in two different structural units. Dislocations accommodate nearly all of the misfit between the Al matrix and strengthening phase. Cu is observed to segregate to the compressed edge of the dislocation cores at specific sites in this interface. First-principles calculations revealed the energetic landscape that facilitates these sites to become entry and exit gateways of Cu atoms in this semi-coherent interface. In conclusion, this investigation reveals critical features within semi-coherent interfaces that determine the thermal stability of precipitation-hardened alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Thermodynamics of CeSiO 4 : Implications for Actinide Orthosilicates

Zircon (ZrSiO 4 : I4 1 /amd) can accommodate actinides, such as thorium, uranium, and plutonium. The zircon structure has been determined for several of the end member compositions of other actinides, such as plutonium and neptunium. However, the thermodynamic properties of these actinide zircon structure-types are largely unknown due to the difficulties in synthesizing these materials and handling transuranium actinides. Thus, we have completed a thermodynamic study of cerium orthosilicate, stetindite (CeSiO 4 ), a surrogate of PuSiO 4 . For the first time, the standard enthalpy of formation of CeSiO 4 was obtained by high temperature oxide melt solution calorimetry to be -1971.9 ± 3.6 kJ/mol. Stetindite is energetically metastable with respect to CeO 2 and SiO 2 by 27.5 ± 3.1 kJ/mol. The metastability explains the rarity of the natural occurrence of stetindite and the difficulty of its synthesis. Applying the obtained enthalpy of formation of CeSiO 4 from this work, along with those previously reported for USiO 4 and ThSiO 4 , we developed an empirical energetic relation for actinide orthosilicates. Here, the predicted enthalpies of formation of AnSiO 4 are then made with a discussion of future strategies to efficiently immobilize Pu or minor actinides in the zircon structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials

The rigid constraints of chemistry-dictated by quantum mechanics and the discrete nature of the atom-limit the set of observable atomic crystal structures. What structures are possible in the absence of these constraints? Here, we systematically crystallize one-component systems of particles interacting with isotropic multiwell pair potentials. We investigate two tunable families of pairwise interaction potentials. Our simulations self-assemble a multitude of crystal structures ranging from basic lattices to complex networks. Sixteen of the structures have natural analogs spanning all coordination numbers found in inorganic chemistry. Fifteen more are hitherto unknown and occupy the space between covalent and metallic coordination environments. The discovered crystal structures constitute targets for self-assembly and expand our understanding of what a crystal structure can look like.

crystal structures↗
DOE OSTI2021

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Abstract Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Sehnal, David↗
DOE OSTI2026

A Review of Polymeric Nanoparticle Design, Synthesis, and Biomedical Applications

Polymeric nanoparticles (PNPs) are solid particles that contain macromolecular polymers ranging in size from 1-1000 nm. They have a wide variety of structures that are determined by their identity as either natural biopolymers, synthetic polymers or a combination of both. In the design of PNPs, the polymeric system, size, internal structure, additional molecules, and synthetic pathway can be engineered, allowing for a multitude of properties including differing responses to physiological environments and the incorporation of a drug. The easily accessible fine tuning of PNPs allows for a multitude of applications in medicine. PNPs allow for increased pharmacokinetics, efficacy, safety, and targeting strength when utilized as carriers for drugs. Currently there are a wide range of PNPs approved by the Food and Drug Administration for use in clinical settings and many more being investigated in clinical studies. There is also research that is being conducted for the usage of PNPs in controlled drug delivery systems and as carriers through the blood brain barrier to aid in treating neurological diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

A sharp interface Lagrangian-Eulerian method for flexible-body fluid-structure interaction

This paper introduces a sharp-interface approach to simulating fluid-structure interaction (FSI) involving flexible bodies described by general nonlinear material models and across a broad range of mass density ratios. This new flexible-body immersed Lagrangian-Eulerian (ILE) scheme extends our prior work on integrating partitioned and immersed approaches to rigid-body FSI. Our numerical approach incorporates the geometrical and domain solution flexibility of the immersed boundary (IB) method with an accuracy comparable to body-fitted approaches that sharply resolve flows and stresses up to the fluid-structure interface. Unlike many IB methods, our ILE formulation uses distinct momentum equations for the fluid and solid subregions with a Dirichlet-Neumann coupling strategy that connects fluid and solid subproblems through simple interface conditions. As in earlier work, we use approximate Lagrange multiplier forces to treat the kinematic interface conditions along the fluid-structure interface. This penalty approach simplifies the linear solvers needed by our formulation by introducing two representations of the fluid-structure interface, one that moves with the fluid and another that moves with the structure, that are connected by stiff springs. This approach also enables the use of multi-rate time stepping, which allows us to use different time step sizes for the fluid and structure subproblems. Our fluid solver relies on an immersed interface method (IIM) for discrete surfaces to impose stress jump conditions along complex interfaces while enabling the use of fast structured-grid solvers for the incompressible Navier-Stokes equations. The dynamics of the volumetric structural mesh are determined using a standard finite element approach to large-deformation nonlinear elasticity via a nearly incompressible solid mechanics formulation. This formulation also readily accommodates compressible structures with a constant total volume, and it can handle fully compressible solid structures for cases in which at least part of the solid boundary does not contact the incompressible fluid. Selected grid convergence studies demonstrate second-order convergence in volume conservation and in the pointwise discrepancies between corresponding positions of the two interface representations as well as between first and second-order convergence in the structural displacements. The time stepping scheme is also demonstrated to yield second-order convergence. To assess and validate the robustness and accuracy of the new algorithm, comparisons are made with computational and experimental FSI benchmarks. Test cases include both smooth and sharp geometries in various flow conditions. Furthermore, we also demonstrate the capabilities of this methodology by applying it to model the transport and capture of a geometrically realistic, deformable blood clot in an inferior vena cava filter.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Persistent Structure and Frustrated Magnetism in High Entropy Rare-Earth Zirconates

The configurational complexity and distinct local atomic environments of high entropy oxides remain largely unexplored, leaving structure-property relationships and the hypothesis that the family offers rich tunability for applications ambiguous. This work investigates the influence of cation size and materials synthesis in determining the resulting structure and magnetic properties of a family of high entropy rare-earth zirconates (HEREZs, nominal composition RE 2 Zr 2 O 7 with RE = rare-earth element combinations including Eu, Gd, Tb, Dy, Ho, La, or Sc). Here, the structural characterization of the series is examined through synchrotron X-ray diffraction and pair distribution function analysis, and electron microscopy, demonstrating average defect-fluorite structures with considerable local disorder, in all samples. The surface morphology and particle sizes are found to vary significantly with preparation method, with irregular micron-sized particles formed by high temperature sintering routes, spherical nanoparticles resulting from chemical co-precipitation methods, and porous nanoparticle agglomerates resulting from polymer steric entrapment synthesis. In agreement with the disordered cation distribution found across all samples, magnetic measurements indicate that all synthesized HEREZs show frustrated magnetic behavior, as seen in a number of single-component RE 2 Zr 2 O 7 pyrochlore oxides. These findings advance the understanding of the local structure of high entropy oxides and demonstrate strategies for designing nanostructured morphologies in the class.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Selecting Suitable Near-Native Lignins for Research

There are several methods to isolate near-native lignins, including milled-wood lignin, enzymatic lignin, cellulolytic enzyme lignin, and enzymatic mild-acidolysis lignin. Which one is the most representative of the native lignin? Herein, near-native lignins were isolated from different plant groups and structurally analyzed to determine how well these lignins represented their native lignin counterparts. Analytical methods were applied to understand the molecular weight, monomer composition, and distribution of interunit linkages in the structure of the lignins. The results indicated that either enzymatic lignin or cellulolytic enzyme lignin may be used to represent native lignin in softwoods and hardwoods. None of the lignins, however, appeared to represent native lignins in grasses (monocot plants) because of substantial syringyl/guaiacyl differences. Furthermore, complicating the understanding of grass lignin structure, large amounts of hydroxycinnamates acylate their polysaccharides and, when released, are often conflated with actual lignin monomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗