Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structural features”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases

Abstract Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate’s C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10’s recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases.

Science & Technology - Other Topics↗
DOE OSTI2026

Automated Bacterial Identification and Morphological Feature Analysis in Low‐Dose Cryo‐EM Using YOLOv11

Bacteria rapidly adapt to environmental cues through morphological and ultrastructural changes that correlate with physiology and behavior. Cryogenic transmission electron microscopy (cryo‐TEM) can capture these phenotypic changes in near‐native, vitrified states, but manual analysis of low‐dose micrographs is labor intensive and limits throughput. Here, we present an end‐to‐end workflow that combines low‐dose cryo‐TEM imaging with a YOLOv11‐based instance‐segmentation model to automatically identify bacteria and quantify key structural features directly from the micrographs. This workflow enables (i) robust bacterial localization and counting from low‐magnification atlas/montage images, (ii) automated measurements of cell‐envelope (outer–inner membrane) thickness and anisotropy from higher‐magnification views, and (iii) detection and quantification of bacteria–flagella interactions, including overlap length and curvature metrics for interacting versus noninteracting flagella. Using Pantoea sp. YR343 grown under distinct media conditions, we show that the automated measurements agree with manual annotations while substantially reducing analysis time. Together, these tools provide a practical framework for scalable bacterial identification and quantitative phenotyping in low‐dose cryo‐TEM datasets and establish a foundation for extending cryo‐TEM image analysis toward higher‐throughput studies of microbial heterogeneity and biointerfaces.

YOLOv11↗
DOE OSTI2021

Neural network potential for Zr–Rh system by machine learning

Zr–Rh metallic glass has enabled its many applications in vehicle parts, sports equipment and so on due to its outstanding performance in mechanical property, but the knowledge of the microstructure determining the superb mechanical property remains yet insufficient. Here, we develop a deep neural network potential of Zr–Rh system by using machine learning, which breaks the dilemma between the accuracy and efficiency in molecular dynamics simulations, and greatly improves the simulation scale in both space and time. Here, the results show that the structural features obtained from the neural network method are in good agreement with the cases in ab initio molecular dynamics simulations. Furthermore, we build a large model of 5400 atoms to explore the influences of simulated size and cooling rate on the melt-quenching process of Zr 77 Rh 23 . Our study lays a foundation for exploring the complex structures in amorphous Zr 77 Rh 23 , which is of great significance for the design and practical application.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Ba 4 RuMn 2 O 10 : A Noncentrosymmetric Polar Crystal Structure with Disordered Trimers

Phase-pure polycrystalline Ba 4 RuMn 2 O 10 was prepared and determined to adopt the noncentrosymmetric polar crystal structure (space group Cmc2 1 ) based on results of second harmonic generation, convergent beam electron diffraction, and Rietveld refinements using powder neutron diffraction data. The crystal structure features zigzag chains of corner-shared trimers, which contain three distorted face-sharing octahedra. The three metal sites in the trimers are occupied by disordered Ru/Mn with three different ratios: Ru1:Mn1 = 0.202(8):0.798(8), Ru2:Mn2 = 0.27(1):0.73(1), and Ru3:Mn3 = 0.40(1):0.60(1), successfully lowering the symmetry and inducing the polar crystal structure from the centrosymmetric parent compounds Ba 4 T 3 O 10 (T = Mn, Ru; space group Cmca). The valence state of Ru/Mn is confirmed to be +4 according to X-ray absorption near-edge spectroscopy. Ba 4 RuMn 2 O 10 is a narrow bandgap (~0.6 eV) semiconductor exhibiting spin-glass behavior with strong magnetic frustration and antiferromagnetic interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Noncoordinating Secondary Sphere Ion Modulates Supramolecular Clustering of Lanthanides

The role of counterions in molecular recognition of lanthanides is underexplored, especially when they exhibit weak interactions with the metal cations. Here, we report a complementary and comprehensive investigation integrating theoretical calculations with X-ray absorption fine structure spectroscopy, dynamic light scattering, and small-angle X-ray scattering to reveal atomic-scale structural features beyond the immediate coordination sphere of a system used for rare-earth element separations. Here, our results indicate the formation of an unusual T-shaped outer-sphere lanthanide complex, containing two ligands and two nitrate ions in the first coordination sphere, whereas the third nitrate is weakly coordinated and resides in the second shell. This unique structural arrangement causes inhomogeneous charge distribution, leading to self-assembly of the complexes into larger nanoclusters through sterically directed electrostatic interactions in the nonpolar medium. Our findings point to the importance of "noncoordinating" anions in defining the degree of supramolecular aggregation and ion cluster assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2016

Insights into RNA binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome

Cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. Among cisplatin targets, cellular RNAs remain the most poorly characterized molecules. Although cisplatin was shown to inactivate essential RNAs, including ribosomal, spliceosomal and telomeric RNAs, cisplatin binding sites in most RNA molecules are unknown, and therefore it remains challenging to study how modifications of RNA by cisplatin contributes to its toxicity. Here we report a 2.6Å-resolution X-ray structure of cisplatin-modified 70S ribosome, which describes cisplatin binding to the ribosome and provides the first nearly atomic model of cisplatin–RNA complex. We observe nine cisplatin molecules bound to the ribosome and reveal consensus structural features of the cisplatin-binding sites. Two of the cisplatin molecules modify conserved functional centers of the ribosome—the mRNA-channel and the GTPase center. In the mRNA-channel, cisplatin intercalates between the ribosome and the messenger RNA, suggesting that the observed inhibition of protein synthesis by cisplatin is caused by impaired mRNA-translocation. Furthermore, our structure provides an insight into RNA targeting and inhibition by cisplatin, which can help predict cisplatin-binding sites in other cellular RNAs and design studies to elucidate a link between RNA modifications by cisplatin and cisplatin toxicity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1973

Application of ERTS-1 imagery to detecting and mapping modern erosion features and to monitoring erosional changes, in southern Arizona

The author has identified the following significant results. The chief results during the reporting period were three 1:1,000,000 scale maps made from one ERTS-1 frame (1085-17330, 16 October 1972) showing: (1) the three most important types of materials in terms of the modern erosion problem: the readily erodible soils, gravel piedmonts and basin-fill areas, and consolidated rocks; (2) alluvial fans (dissected and relatively undissected); and (3) (as an additional bonus) linear structural features. Eight key areas (small parts of the whole study area) were selected for detailed study, and mapping was started in two of them, by interpretation of ultrahigh (U-2 and RB-57) airphotos, supplemented by field studies. In these areas detailed mapping was done not only on the modern erosion phenomena (arroyos, gullies, modern flood plains and terraces, and areas of sheet erosion and deposition), but also other features pertinent to the erosion problem, such as slope-local relief, landforms rock units, soil particle size and erodibility, and classes of vegetative cover.

Morrison, R. B.↗
DOE OSTI2018

Cadmium(II) complexes with monoiodo- and dibromodipyrromethenes: synthesis, molecular structure, spectral-luminescent properties, and stability in solutions

Cadmium(II) chelates with 4-iodo-, 5,5´-, and 4,4´-dibromo-2,2´-dipyrromethenes (HL{sup 1}, HL{sup 2}, and HL{sup 3}, respectively) with the composition of [CdL{sub 2}] were synthesized. The influence of structural features of their molecules and properties of the medium on the characteristics of absorption and fluorescence spectra, and also on the thermodynamic stability constants in solutions was evaluated. The results of quantum chemical calculations revealed that the additional coordination interactions between the bromine atoms at the α-positions of dipyrromethene ligands and the complexing atom are possible in the molecular structure of α,α´- dibromosubstituted dipyrromethenate [Cd(L{sup 2}){sub 2}] in contrast with β-halogenated analogues [Cd(L{sup 1}){sub 2}] and [Cd(L{sup 3}){sub 2}].

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

Local measurement of bulk thermal diffusivity using photothermal radiometry

Here, an experimental methodology using photothermal radiometry is developed for the accurate measurement of bulk thermal diffusivity of nuclear fuels and materials irradiated to high doses. Under these conditions, nuclear fuels, such as uranium oxide, and moderator materials, such as graphite, become friable, which requires characterization techniques that can accommodate irregularly shaped fragments. Photothermal radiometry, a good candidate for this application, involves locally heating a sample by using a laser and measuring the temperature field by monitoring blackbody radiation. The interaction volume for this study, less than a millimeter, is carefully chosen to sample a statistically significant number of large-scale structural features, such as pores and gas filled bubbles, and is small enough that the sample fragments can be treated as a thermal half-space. The thermal diffusivity standards considered in this study cover a range of thermal diffusivities representative of both fresh and spent nuclear fuels. We also consider a sample having a porous microstructure representative of large-scale structures found in materials irradiated to high doses. Our measurement methodology circumvents complex thermal wave models that address optical diffraction, nonlinear transfer function associated with blackbody radiation, and finite sample size effects. Consequently, the large measurement uncertainty associated with modeling these effects can be avoided. While the emphasis here is on nuclear fuels and materials, this measurement approach is well suited to measure thermal transport in a variety of technologically important materials associated with advanced synthesis techniques. Examples range from small, exotic single crystals grown using hydrothermal growth techniques to additively manufactured components having complex geometries.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Social network structure and the spread of complex contagions from a population genetics perspective

Ideas, behaviors, and opinions spread through social networks. If the probability of spreading to a new individual is a non-linear function of the fraction of the individuals’ affected neighbors, such a spreading process becomes a “complex contagion”. This non-linearity does not typically appear with physically spreading infections, but instead can emerge when the concept that is spreading is subject to game theoretical considerations (e.g. for choices of strategy or behavior) or psychological effects such as social reinforcement and other forms of peer influence (e.g. for ideas, preferences, or opinions). Here we study how the stochastic dynamics of such complex contagions are affected by the underlying network structure. Motivated by simulations of complex contagions on real social networks, we present a framework for analyzing the statistics of contagions with arbitrary non-linear adoption probabilities based on the mathematical tools of population genetics. The central idea is to use an effective lower-dimensional diffusion process to approximate the statistics of the contagion. This leads to a tradeoff between the effects of ”selection” (microscopic tendencies for an idea to spread or die out), random drift, and network structure. Our framework illustrates intuitively several key properties of complex contagions: stronger community structure and network sparsity can significantly enhance the spread, while broad degree distributions dampen the effect of selection compared to random drift. Finally, we show that some structural features can exhibit critical values that demarcate regimes where global contagions become possible for networks of arbitrary size. Our results draw parallels between the competition of genes in a population and memes in a world of minds and ideas. Our tools provide insight into the spread of information, behaviors, and ideas via social influence, and highlight the role of macroscopic network structure in determining their fate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A valine-to-lysine substitution at position 210 induces structural conversion of prion protein into a β-sheet rich oligomer

Highlights: • A V210I mutation has been associated with pathogenic conversion of PrP to PrP{sup Sc}. • A V210K mutation (but not the V210I mutation) impacts on the PrP structure. • The resulting structure adopts a β-sheet-rich oligomer with low stability. • A lysine substitution in the hydrophobic core induces the α→β conversion in vitro. Prion diseases are fatal neurodegenerative diseases associated with structural conversion of α-helical prion protein (PrP) into its β-sheet rich isoform (PrP{sup Sc}). Previous genetic analyses have indicated that several amino acid residues involved in the hydrophobic core of PrP (such as V180, F198, and V210) play a critical role in the development of prion diseases. To understand how these hydrophobic residues would contribute to the α-to-β conversion process of PrP, we substituted the V210 residue with bulkier (V210F, V210I, and V210L), smaller (V210A), and charged amino acids (V210K) and characterized its effects. Interestingly, although most of the mutations had little or no effect on the biochemical properties of PrP, the V210K mutation induced structural conversion of PrP into a β-structure. The β-inducing effect was prominent and observed even under a physiological condition (i.e., in the absence of denaturant, acidic pH, reducing agent, and high temperature) in contrast to the disease-associated mutations in the PrP gene. We also examined structural features of V210K PrP using guanidine-hydrochloride unfolding, dynamic light scattering, 8-anilino-1-naphthalene sulfonate fluorescence, and electron microscopy, and revealed that V210K PrP assembles into a non-fibrillar β-rich oligomer. Thus, the α-to-β conversion can be induced by introduction of a charged residue into the hydrophobic core, which provide novel insight into the structural dynamics of PrP.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Charge density wave memory in a cuprate superconductor

Although CDW correlations are a ubiquitous feature of the superconducting cuprates, their disparate properties suggest a crucial role for pinning the CDW to the lattice. Here, we report coherent resonant X-ray speckle correlation analysis, which directly determines the reproducibility of CDW domain patterns in La 1.875 Ba 0.125 CuO 4 (LBCO 1/8) with thermal cycling. While CDW order is only observed below 54 K, where a structural phase transition creates inequivalent Cu-O bonds, we discover remarkably reproducible CDW domain memory upon repeated cycling to far higher temperatures. That memory is only lost on cycling to 240(3) K, which recovers the four-fold symmetry of the CuO 2 planes. We infer that the structural features that develop below 240 K determine the CDW pinning landscape below 54 K. This opens a view into the complex coupling between charge and lattice degrees of freedom in superconducting cuprates.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Plasmonic spectral tunability of conductive ternary nitrides

Conductive binary transition metal nitrides, such as TiN and ZrN, have emerged as a category of promising alternative plasmonic materials. In this work, we show that ternary transition metal nitrides such as Ti{sub x}Ta{sub 1−x}N, Ti{sub x}Zr{sub 1−x}N, Ti{sub x}Al{sub 1−x}N, and Zr{sub x}Ta{sub 1−x}N share the important plasmonic features with their binary counterparts, while having the additional asset of the exceptional spectral tunability in the entire visible (400–700 nm) and UVA (315–400 nm) spectral ranges depending on their net valence electrons. In particular, we demonstrate that such ternary nitrides can exhibit maximum field enhancement factors comparable with gold in the aforementioned broadband range. We also critically evaluate the structural features that affect the quality factor of the plasmon resonance and we provide rules of thumb for the selection and growth of materials for nitride plasmonics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Crystal-chemical characteristics of nontronites from bottom sediments of Pacific ocean

A crystal-chemical analysis of the nontronite samples formed in deep-water sediments of the underwater Juan-de-Fuca ridge in the Pacific ocean has been performed using powder X-ray diffraction, IR spectroscopy, and Mössbauer spectroscopy. A comparison with the previously investigated nontronites from different regions of the Sea of Okhotsk showed that the structural features of these formations are due to the difference in the physicochemical parameters of their crystallization. The values of the basal interplanar spacing d{sub 001} (within 11–13 Å) in the samples analyzed are determined by the degree of hydration and cation filling of the interlayer space, while the differences in the IR spectra are due to isomorphic substitutions in the structure. The character of cation distribution and the nature and concentration of stacking faults in nontronite structures are determined. The differences in the composition, structure, and properties of nontronites of different origin are confirmed by theoretical calculations of their structural parameters.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Microstructure of Si Crystals Subjected to Irradiation with High-Energy H{sup +} Ions and Heat Treatment by High-Resolution Three-Crystal X-Ray Diffraction and Transmission Electron Microscopy

The structural features of the formation of radiation defects in proton-implanted layers of silicon plates during their heat treatment have been studied. New data on the nature, the characteristics, and the microdefect concentration in Si crystals irradiated with protons with energies 100 + 200 + 300 keV with the total dose 2 × 10{sup 16} cm{sup –2} and the evolution of the defect structure during heat treatment have been obtained by high-resolution three-crystal X-ray diffraction and transmission electron microscopy over wide temperature range from 200 to 1100°C.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Structural characterization of the novel aminoglycoside phosphotransferase AphVIII from Streptomyces rimosus with enzymatic activity modulated by phosphorylation

Aminoglycoside phosphotransferases represent a broad class of enzymes that promote bacterial resistance to aminoglycoside antibiotics via the phosphorylation of hydroxyl groups in the latter. Here we report the spatial structure of the 3′-aminoglycoside phosphotransferase of novel VIII class (AphVIII) solved by X-ray diffraction method with a resolution of 2.15 Å. Deep analysis of APHVIII structure and its comparison with known structures of aminoglycoside phosphotransferases of various types reveals that AphVIII has a typical two-domain fold and, however, possesses some unique characteristics that distinguish the enzyme from its known homologues. The most important difference is the presence of the activation loop with unique Ser146 residue. We demonstrate that in the apo-state of the enzyme the activation loop does not interact with other parts of the enzyme and seems to adopt catalytically competent state only after substrate binding. - Highlights: • 3D structure of the novel aminoglycoside phosphotransferase AphVIII was obtained. • AphVIII activation loop is clearly identified in the electron density. • AphVIII has some unique structural features in its substrate C-ring binding pocket.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Electronic structure and optical properties of the HoCoSi and ErNiSi compounds

The electronic structure and the optical properties of the HoCoSi and ErNiSi compounds are studied. Spin-polarized band calculations are performed in the local electron density approximation corrected for the strong electron–electron interactions in the 4f shell of a rare-earth ion (LSDA + U method [11]). The optical constants are measured by ellipsometry in a wide wavelength range, and the frequency dependences of a number of spectral parameters are determined. The calculated densities of states are used to interpret the structural features of the interband optical conductivities of the intermetallic compounds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗