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Results for “structural complexity”

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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Accurate and rapid acoustic damage characterization in complex structures using sparse sensor networks and deep learning models

Damage diagnosis in critical components is essential for ensuring the safety and reliability of operations across industries, spanning manufacturing, aerospace, and energy. Traditional acoustic nondestructive testing methods primarily focus on detecting defects through the direct scattering of single-mode incident waves from the damage, which limit their applicability to simple structures and small inspection areas. Our earlier research demonstrated that machine learning algorithms combined with sparse sensor networks can identify critical defect signatures even from multiply scattered, multi-mode acoustic signals, indicating the potential for improved defect inspection in complex, real-world structures. In this work, we demonstrate the successful implementation of this approach in a fixed sensor configuration to rapidly and accurately detect simulated defects in a geometrically complex, real-world structure, a brake rotor hub. Three different types of defects were physically simulated on the surface of the hub, and the collected data were used to train an autoencoder-based deep learning model. Two models were tested, one using single measurements and the other using multiple measurements taking advantage of the spatial distribution of the sensor network. After training, the multi-measurement model achieved 100 % accuracy in identifying, classifying, and locating unseen, unique damages. This work illustrates the potential of the proposed method for a wide range of industrial applications.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly’s global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE–p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.

Biochemistry & Molecular Biology↗
DOE OSTI2024

High-Resolution Tandem Mass Spectrometry-Based Analysis of Model Lignin–Iron Complexes: Novel Pipeline and Complex Structures

Understanding the chemical nature of soil organic carbon (SOC) with great potential to bind iron (Fe) minerals is critical for predicting the stability of SOC. Organic ligands of Fe are among the top candidates for SOCs able to strongly sorb on Fe minerals, but most of them are still molecularly uncharacterized. To shed insights into the chemical nature of organic ligands in soil and their fate, this study developed a protocol for identifying organic ligands using ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) and metabolomic tools. The protocol was used for investigating the Fe complexes formed by model compounds of lignin-derived organic ligands, namely, caffeic acid (CA), p-coumaric acid (CMA), vanillin (VNL), and cinnamic acid (CNA). Isotopologue analysis of 54/56 Fe was used to screen out the potential UHPLC-HRMS (m/z) features for complexes formed between organic ligands and Fe, with multiple features captured for CA, CMA, VNL, and CNA when 35/37 Cl isotopologue analysis was used as supplementary evidence for the complexes with Cl. MS/MS spectra, fragment analysis, and structure prediction with SIRIUS were used to annotate the structures of mono/bidentate mono/biligand complexes. The analysis determined the structures of monodentate and bidentate complexes of FeL x Cl y (L: organic ligand, x = 1–4, y = 0–3) formed by model compounds. The protocol developed in this study can be used to identify unknown organic ligands occurring in complex environmental samples and shed light on the molecular-level processes governing the stability of the SOC.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Complex structure due to As bonding and interplay with electronic structure in superconducting BaNi 2 As 2

BaNi 2 As 2 is a superconductor chemically related to the Fe-based superconductors, with a complex and poorly understood structural phase transition. We show, based on first-principles calculations, that, in fact, there are two distinct competing structures. These structures are different from the electronic, transport, and bonding points of view but are close in energy. These arise due to complex As bonding patterns and drive distortions of the Ni layers. This is supported by photoemission experiments. This is very distinct from views of the distortion as being primarily driven by electrons at the Fermi surface as in a classical charge density wave, or by correlated electron physics associated with the Ni d electrons and the Ni d orbitals. The structural distortion, although connected with As does lead to an interplay of electronic and structural behavior including induced anisotropic electronic transport. Here, the local bonding nature of the instabilities and the competition between distortions is discussed in the context of the complex behavior observed in BaNi 2 As 2 samples.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Zintl Ions within Framework Channels: The Complex Structure and Low-Temperature Transport Properties of Na 4 Ge 13

Single crystals of a complex Zintl compound with the composition Na 4 Ge 13 were synthesized for the first time using a high-pressure/high-temperature approach. Single-crystal diffraction of synchrotron radiation revealed a hexagonal crystal structure with P6/m space group symmetry that is composed of a three-dimensional sp 3 Ge framework punctuated by small and large channels along the crystallographic c axis. Na atoms are inside hexagonal prism-based Ge cages along the small channels, while the larger channels are occupied by layers of disordered sixfold Na rings, which are in turn filled by disordered [Ge 4 ] 4– tetrahedra. This compound is the same as “Na 1–x Ge 3+z ” reported previously, but the availability of single crystals allowed for more complete structural determination with a formula unit best described as Na 4 Ge 12 (Ge 4 ) 0.25 . The compound is the first known example of a guest–host structure where discrete Zintl polyanions are confined inside the channels of a three-dimensional covalent framework. These features give rise to temperature-dependent disorder, as confirmed by first-principles calculations and physical properties measurements. Here, the availability of single-crystal specimens allowed for measurement of the intrinsic low-temperature transport properties of this material and revealed its semiconductor behavior, which was corroborated by theoretical calculations.

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

On the complex structure of the optical spectra of a tetragonal calomel single crystal in a wide energy range

The spectral complex of optical functions of the calomel Hg{sub 2}Cl{sub 2} single crystal is determined in the range 0–20 eV at 300 K in unpolarized light. The spectra of the imaginary part of the permittivity ε{sub 2}(E), the bulk–Imε{sup –1} and the surface–Im(1 + ε){sup –1} electron energy losses are decomposed into elementary bands. Their main parameters, including energies and oscillator strengths of the transition bands are determined. Calculations are performed on the basis of the experimental reflectance spectrum of the crystal cleavage. Computer programs based on Kramers–Kronig relations, analytical formulas, and the advanced parameterfree method of combined Argand diagrams are used. The main features of the spectral set of optical functions and the parameters of expansion band components ε{sub 2}(E),–Imε{sup –1}, and–Im(1 + ε){sup –1} are determined.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Tree mortality during long-term droughts is lower in structurally complex forest stands

Increasing drought frequency and severity in a warming climate threaten forest ecosystems with widespread tree deaths. Canopy structure is important in regulating tree mortality during drought, but how it functions remains controversial. Here, we show that the interplay between tree size and forest structure explains drought-induced tree mortality during the 2012-2016 California drought. Through an analysis of over one million trees, we find that tree mortality rate follows a “negative-positive-negative” piecewise relationship with tree height, and maintains a consistent negative relationship with neighborhood canopy structure (a measure of tree competition). Trees overshadowed by tall neighboring trees experienced lower mortality, likely due to reduced exposure to solar radiation load and lower water demand from evapotranspiration. Our findings demonstrate the significance of neighborhood canopy structure in influencing tree mortality and suggest that re-establishing heterogeneity in canopy structure could improve drought resiliency. Our study also indicates the potential of advances in remote-sensing technologies for silvicultural design, supporting the transition to multi-benefit forest management.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry

Bile acids (BAs) play an integral role in digestion through the absorption of nutrients, emulsification of fats and fat-soluble vitamins, and maintenance of cholesterol levels. Metabolic disruption, diabetes, colorectal cancer, and numerous other diseases have been linked with BA disruption, making improved BA analyses essential. To date, most BA measurements are performed using liquid chromatography separations in conjunction with mass spectrometry measurements (LC-MS). However, 10–40 min LC gradients are often used for BA analyses and these may not even be sufficient for distinguishing all the important isomers present in the human body. Ion mobility spectrometry (IMS) is a promising tool for BA evaluations due to its ability to quickly separate isomeric molecules with subtle structural differences. In this study, we utilized drift tube IMS (DTIMS) coupled with MS to characterize 56 different unlabeled BA standards and 16 deuterated versions. In the DTIMS-MS analyses of 12 isomer groups, BAs with smaller m/z values were easily separated in either their deprotonated or sodiated forms (or both). However, as the BAs grew in m/z value, they became more difficult to separate with two isomer groups being inseparable. Metal ions such as copper and zinc were then added to the overlapping BAs, and due to different binding sites, the resulting complexes were separable. Thus, the rapid structural measurements possible with DTIMS-MS show great potential for BAs measurements with and without prior LC separations.

Zheng, Xueyun↗
DOE OSTI2023

Anatomy of an agricultural antagonist: Feeding complex structure and function of three xylem sap‐feeding insects illuminated with synchrotron‐based 3D imaging

Abstract Many insects feed on xylem or phloem sap of vascular plants. Although physical damage to the plant is minimal, the process of insect feeding can transmit lethal viruses and bacterial pathogens. Disparities between insect‐mediated pathogen transmission efficiency have been identified among xylem sap‐feeding insects; however, the mechanistic drivers of these trends are unclear. Identifying and understanding the structural factors and associated integrated functional components that may ultimately determine these disparities are critical for managing plant diseases. Here, we applied synchrotron‐based X‐ray microcomputed tomography to digitally reconstruct the morphology of three xylem sap‐feeding insect vectors of plant pathogens: Graphocephala atropunctata (blue‐green sharpshooter; Hemiptera, Cicadellidae) and Homalodisca vitripennis (glassy‐winged sharpshooter; Hemiptera, Cicadellidae), and the spittlebug Philaenus spumarius (meadow spittlebug; Hemiptera, Aphrophoridae). The application of this technique revealed previously undescribed anatomical features of these organisms, such as key components of the salivary complex. The visualization of the 3D structure of the precibarial valve led to new insights into the mechanism of how this structure functions. Morphological disparities with functional implications between taxa were highlighted as well, including the morphology and volume of the cibarial dilator musculature responsible for extracting xylem sap, which has implications for force application capabilities. These morphological insights will be used to target analyses illuminating functional differences in feeding behavior.

3D imaging↗
DOE OSTI2016

A bio-facilitated synthetic route for nano-structured complex electrode materials

Here, we investigate an energy-efficient synthesis that merges the bio-templated technique and solid-state reactions to produce nano-structured lithiated polyanions. With the aid of bio-templates based on an M13 virus, the thermal budget of an annealing process can be reduced, and the nano-structured characteristics of the precursors are preserved in the product. This method enables us to successfully prepare monoclinic LiMnBO 3 with an average particle size of 20 nm in a 1 h annealing process, showing improved electrochemical properties compared with the conventionally synthesized one. Thus, we consider that this bio-facilitated method can open up an environmentally-friendly pathway to produce nano-structured electrode materials with an enhanced performance.

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

Structural complexity of simple Fe 2 O 3 at high pressures and temperatures

Although chemically very simple, Fe 2 O 3 is known to undergo a series of enigmatic structural, electronic and magnetic transformations at high pressures and high temperatures. So far, these transformations have neither been correctly described nor understood because of the lack of structural data. Here we report a systematic investigation of the behaviour of Fe 2 O 3 at pressures over 100 GPa and temperatures above 2,500 K employing single crystal X-ray diffraction and synchrotron Mössbauer source spectroscopy. Crystal chemical analysis of structures presented here and known Fe(II, III) oxides shows their fundamental relationships and that they can be described by the homologous series nFeO·mFe 2 O 3 . Decomposition of Fe 2 O 3 and Fe 3 O 4 observed at pressures above 60 GPa and temperatures of 2,000 K leads to crystallization of unusual Fe 5 O 7 and Fe 25 O 32 phases with release of oxygen. Lastly, our findings suggest that mixed-valence iron oxides may play a significant role in oxygen cycling between earth reservoirs.

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

Structural Complexities in Sodium Ion Conductive Antiperovskite Revealed by Cryogenic Transmission Electron Microscopy

Here we use low-dose cryogenic transmission electron microscopy (cryo-TEM) to investigate the atomic-scale structure of antiperovskite Na 2 NH 2 BH 4 crystals by preserving the room-temperature cubic phase and carefully monitoring the electron dose. Via quantitative analysis of electron beam damage using selected area electron diffraction, we find cryogenic imaging provides 6-fold improvement in beam stability for this solid electrolyte. Cryo-TEM images obtained from flat crystals revealed the presence of a new, long-range-ordered supercell with a cubic phase. The supercell exhibits doubled unit cell dimensions of 9.4 Å × 9.4 Å as compared to the cubic lattice structure revealed by X-ray crystallography of 4.7 Å × 4.7 Å. The comparison between the experimental image and simulated potential map indicates the origin of the supercell is a vacancy ordering of sodium atoms. This work demonstrates the potential of using cryo-TEM imaging to study the atomic-scale structure of air- and electron-beam-sensitive antiperovskite-type solid electrolytes.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Dlx5 Homeodomain: DNA Complex: Structure, Binding and Effect of Mutations Related to Split Hand and Foot Malformation Syndrome

The Dlx5 homeodomain is a transcription factor related to the Drosophila Distal-less gene that is associated with breast and lung cancer, lymphoma, Rett syndrome and osteoporosis in humans. Mutations in the DLX5 gene have been linked to deficiencies in craniofacial and limb development in higher eukaryotes, including Split Hand and Foot Malformation-1 (SHFM-1) in humans. Our characterization of a Dlx5 homeodomain–(CGACTAATTAGTCG) 2 complex by NMR spectroscopy paved the way for determination of its crystal structure at 1.85 Å resolution that enabled rationalization of the effects of disease-related mutations on the protein function. A remarkably subtle mutation, Q186H, is linked to SHFM-1; this change likely affects affinity of DNA binding by disrupting water-mediated interactions with the DNA major groove. A more subtle effect is implicated for the Q178P mutation, which is not in direct contact with the DNA. Our data indicate that these mutations diminish the ability of the Dlx5 homeodomain to recognize and bind target DNAs, and likely destabilize the formation of functional complexes.

59 BASIC BIOLOGICAL SCIENCES↗