Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family
Abstract not provided
Odokonyero, Denis↗
SEARCH · Engineering Papers
Results for “Structured”
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.
RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models
Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.
Rose, Yana [Research Collaboratory for Structural ↗
FAST.Farm Development and Validation of Structural Load Prediction Against Large Eddy Simulations
FAST.Farm is a mid-fidelity engineering tool developed by the National Renewable Energy Laboratory targeted at accurately and efficiently predicting wind turbine power production and structural loading in wind farm settings, including wake interactions between turbines. FAST.Farm is based on several principles of the dynamic wake meandering (DWM) model, but also addresses limitations of previous DWM implementations. Previous FAST.Farm studies have shown the similarities and differences between FAST.Farm and large eddy simulations for rigid turbine cases. The objective of this work is to quantify the ability of FAST.Farm to accurately predict turbine structural response in a small wind farm. This is done by comparing FAST.Farm structural response to SOWFA-OpenFAST results for three laterally-aligned turbines. The purpose of this study is to characterize the similarities and differences between FAST.Farm and a higher fidelity model for predicting turbine structural response in a wind farm for differing atmospheric inflows. Strong statistical agreement was found between FAST.Farm and SOWFA-OpenFAST structural response for the non-waked upstream turbine, and good agreement was found for the downstream turbines for most structural quantities. Higher differences were seen for downstream turbines with low ambient turbulence intensity or yawed turbines, suggesting areas for FAST.Farm wake dynamics modeling improvements. For all cases and turbines, small statistical differences were seen between blade deflections and bending moments, with larger differences for tower-top and tower-base bending moments. Overall, the results establish confidence for applying FAST.Farm to wind farm power and loads analyses and identify areas where further model validations and model improvements should be targeted.
49 EE - Wind and Water Power Program - Wind (EE-4W↗
Local structure, composition, and crystallization mechanism of a model two-phase “composite nanoglass”
We report a detailed study of the local composition and structure of a model, bi-phasic nanoglass with nominal stoichiometry Cu{sub 55}Nb{sub 45}. Three dimensional atom probe data suggest a nanoscale-phase-separated glassy structure having well defined Cu-rich and Nb-rich regions with a characteristic length scale of ≈3 nm. However, extended x-ray absorption fine structure analysis indicates subtle differences in the local environments of Cu and Nb. While the Cu atoms displayed a strong tendency to cluster and negligible structural order beyond the first coordination shell, the Nb atoms had a larger fraction of unlike neighbors (higher chemical order) and a distinctly better-ordered structural environment (higher topological order). This provides the first experimental indication that metallic glass formation may occur due to frustration arising from the competition between chemical ordering and clustering. These observations are complemented by classical as well as ab initio molecular dynamics simulations. Our study indicates that these nanoscale phase-separated glasses are quite distinct from the single phase nanoglasses (studied by Gleiter and others) in the following three respects: (i) they contain at least two structurally and compositionally distinct, nanodispersed, glassy phases, (ii) these phases are separated by comparatively sharp inter-phase boundaries, and (iii) thermally induced crystallization occurs via a complex, multi-step mechanism. Such materials, therefore, appear to constitute a new class of disordered systems that may be called a composite nanoglass.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Using support vector machines to improve elemental ion identification in macromolecular crystal structures
A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Symmetry-mode analysis for local structure investigations using pair distribution function data
Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.
36 MATERIALS SCIENCE↗
RDMA vs. RPC for Implementing Distributed Data Structures
Distributed data structures are key to implementing scalable applications for scientific simulations and data analysis. In this paper we look at two implementation styles for distributed data structures: remote direct memory access (RDMA) and remote procedure call (RPC). We focus on operations that require individual accesses to remote portions of a distributed data structure, e.g., accessing a hash table bucket or distributed queue, rather than global operations in which all processors collectively exchange information. We look at the trade-offs between the two styles through microbenchmarks and a performance model that approximates the cost of each. The RDMA operations have direct hardware support in the network and therefore lower latency and overhead, while the RPC operations are more expressive but higher cost and can suffer from lack of attentiveness from the remote side. We also run experiments to compare the real-world performance of RDMA- and RPC-based data structure operations with the predicted performance to evaluate the accuracy of our model, and show that while the model does not always precisely predict running time, it allows us to choose the best implementation in the examples shown. We believe this analysis will assist developers in designing data structures that will perform well on current network architectures, as well as network architects in providing better support for this class of distributed data structures.
distributed data structures↗
PRINCEPS: A computer-based approach to the structural description and recognition of trends within structural databases, and its application to the Ce-Ni-Si System
Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternary system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.
97 MATHEMATICS AND COMPUTING↗
Rare earth silicates and germanates crystallizing in the wadeite and related structure types
Single crystals of six new alkali lanthanide silicates and germanates were synthesized via the flux growth method. A2CeSi3O9 (A = Rb, Cs) and Cs2CeGe3O9 crystallize in the Wadeite structure with space group P63/m and lattice parameters a = 7.1950(2) Å and c = 10.5109(3) Å for the Rb analogue. K2CeSi3O9 crystallizes in a previously unobserved monoclinic distortion of the Wadeite structure with space group P21/n and lattice parameters a = 7.0801(2) Å, b = 10.458(2) Å, c = 12.238(2) Å and β = 90.07(3)°. Finally, Cs8Dy2Ge16O39 and Cs8Dy2Ge16O38F2 crystallize in two new structure types that are related to each other and to the Wadeite structure. Cs8Dy2Ge16O39 crystallizes in the monoclinic space group P2/c with lattice parameters a = 12.4054(3) Å, b = 7.4310(2) Å, c = 24.5761(6) Å, and β = 90.8849(16)° and Cs8Dy2Ge16O38F2 crystallizes in the orthorhombic space group Pnn2 with lattice parameters a = 12.3489(4) Å, b = 12.4805(5) Å, and c = 7.3802(3) Å. The synthesis and structure of the six compounds are reported and the crystallochemical reasons for the formation of each structure are discussed.
nuclear, materials and chemistry by design, synthe↗
Forging Fast Ion Conducting Nanochannels with Swift Heavy Ions: The Correlated Role of Local Electronic and Atomic Structure
Atomically disordered oxides have attracted significant attention in recent years due to the possibility of enhanced ionic conductivity. However, the correlation between atomic disorder, corresponding electronic structure, and the resulting oxygen diffusivity is not well understood. The disordered variants of the ordered pyrochlore structure in gadolinium titanate (Gd 2 Ti 2 O 7 ) are seen as a particularly interesting prospect due to intrinsic presence of a vacant oxygen site in the unit atomic structure, which could provide a channel for fast oxygen conduction. As such, in the present work, we provide insights into the subangstrom scale on the disordering-induced variations in the local atomic environment and its effect on the electronic structure in high-energy ion irradiation-induced disordered nanochannels, which can be utilized as pathways for fast oxygen ion transport. With the help of an atomic plane-by-plane-resolved analyses, the work shows how the presence of various types of TiO$_x$ polyhedral that exist in the amorphous and disordered crystalline phase modify the electronic structures relative to the ordered pyrochlore phase in Gd 2 Ti 2 O 7 . The correlated molecular dynamics simulations on the disordered structures show a remarkable enhancement in oxygen diffusivity as compared with ordered pyrochlore lattice and make that a suitable candidate for applications requiring fast oxygen conduction.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue
Although aggregation of Aβ amyloid fibrils into plaques in the brain is a hallmark of Alzheimer's Disease (AD), the correlation between amyloid burden and severity of symptoms is weak. One possible reason is that amyloid fibrils are structurally polymorphic and different polymorphs may contribute differentially to disease. However, the occurrence and distribution of amyloid polymorphisms in human brain is poorly documented. Here we seek to fill this knowledge gap by using X-ray microdiffraction of histological sections of human tissue to map the abundance, orientation and structural heterogeneities of amyloid within individual plaques; among proximal plaques and in subjects with distinct clinical histories. A 5 µ x-ray beam was used to generate diffraction data with each pattern arising from a scattering volume of only ~ 450 µ3 , making possible collection of dozens to hundreds of diffraction patterns from a single amyloid plaque. X-ray scattering from these samples exhibited all the properties expected for scattering from amyloid. Amyloid distribution was mapped using the intensity of its signature 4.7 Å reflection which also provided information on the orientation of amyloid fibrils across plaques. Margins of plaques exhibited a greater degree of orientation than cores and orientation around blood vessels frequently appeared tangential. Variation in the structure of Aβ fibrils is reflected in the shape of the 4.7 Å peak which usually appears as a doublet. Variations in this peak correspond to differences between the structure of amyloid within cores of plaques and at their periphery. Examination of tissue from a mismatch case - an individual with high plaque burden but no overt signs of dementia at time of death - revealed a diversity of structure and spatial distribution of amyloid that is distinct from typical AD cases. As a result, we demonstrate the existence of structural polymorphisms among amyloid within and among plaques of a single individual and suggest the existence of distinct differences in the organization of amyloid in subjects with different clinical presentations.
59 BASIC BIOLOGICAL SCIENCES↗
Electrochemical properties and structural evolution of O3-type layered sodium mixed transition metal oxides with trivalent nickel
The electrochemical properties of NaNi 0.5 Co 0.5 O 2 and NaNi 0.5 Fe 0.5 O 2 and their structural transitions as a function of Na extraction associated with redox reactions are investigated. Synthesized in the O3-type layered structure, both materials show reasonable electrochemical activities at room temperature, delivering approximately 0.5 Na per formula unit at C/10 discharge. More Na can be reversibly cycled in NaNi 0.5 Co 0.5 O 2 at elevated temperature and/or in an extended voltage window, while NaNi 0.5 Fe 0.5 O 2 shows significant capacity fading at a high voltage cutoff which is likely due to Fe 4+ migration. In situ X-ray diffraction shows that the structural changes in the two materials upon desodiation are very different. NaNi 0.5 Co 0.5 O 2 goes through many different two-phase reactions including three different O3-type and three different P3-type structures during cycling, producing a voltage profile with multiple plateau-like features. In contrast, NaNi 0.5 Fe 0.5 O 2 has a smooth voltage profile and shows the typical O3–P3 phase transition without lattice distortion seen in other materials. Finally, this different structural evolution upon desodiation and re-sodiation can be explained by the electronic structure of the mixed transition metals and how it perturbs the ordering between Na ions differently.
36 MATERIALS SCIENCE↗
Coherent high-power RF wakefield generation by electron bunch trains in a metamaterial structure
In this paper, we present an experimental study of coherent high-power wakefield generation in a metamaterial (MTM) structure at 11.7 GHz by 65 MeV electron bunch trains at the Argonne Wakefield Accelerator (AWA), following a previous experiment, the Stage-I experiment, at the AWA. Both the Stage-II experiment, reported in this paper, and the Stage-I experiment were conducted using MTM structures, which are all-metal periodic structures with the period being much smaller than the wavelength. Differences between the two experiments include (1) structure length (Stage-I 8 cm and Stage-II 20 cm); (2) number of bunches used to excite the structure (Stage-I with two bunches, up to 85 nC of total charge; Stage-II with eight bunches, up to 224 nC of total charge); and (3) highest peak power measured (Stage-I 80 MW in a 2 ns pulse and Stage-II 380 MW in a 10 ns pulse). High-power radio frequency pulses were generated by reversed Cherenkov radiation of the electron beam due to the negative group velocity in the MTM structures. Because the radiation is coherent, a train of bunches with a proper spacing can build up to achieve a high peak power. The observed output power levels are very promising for future applications in direct collinear wakefield acceleration or in transfer to a second accelerator for two-beam acceleration.
36 MATERIALS SCIENCE↗
Revealing the structure of light pseudoscalar mesons at the electron–ion collider
The questions of how the bulk of the Universe's visible mass emerges and how it is manifest in the existence and properties of hadrons are profound, and probe the heart of strongly interacting matter. Paradoxically, the lightest pseudoscalar mesons appear to be key to a further understanding of the emergent mass and structure mechanisms. These mesons, namely, the pion and kaon, are the Nambu-Goldstone boson modes of quantum chromodynamics (QCD). Unravelling their partonic structure and the interplay between emergent and Higgs-boson mass mechanisms is a common goal of three interdependent approaches - continuum QCD phenomenology, lattice-regularised QCD, and the global analysis of parton distributions - linked to experimental measurements of hadron structure. Experimentally, the anticipated electron-ion collider will enable a revolution in our ability to study pion and kaon structures, accessed by scattering from the 'meson cloud' of the proton through the Sullivan process. With the goal of enabling a suite of measurements that can address these questions, we examine key reactions that identify the critical detector-system requirements needed to map tagged pion and kaon cross-sections over a wide range of kinematics. The excellent prospects for extracting pion structural, functional, and form-factor data are outlined, and similar prospects for kaon structures are discussed in the context of a worldwide programme. Finally, the successful completion of the programme outlined herein will deliver deep, far-reaching insights into the emergence of pions and kaons, their properties, and their role as QCD's Goldstone boson modes.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Structural and magnetic phase transitions in CeCu 6 - x T x ( T = Ag , Pd )
The structural and the magnetic properties of CeCu6-xAgx (0≤x≤0.85) and CeCu6-xPdx (0≤x≤0.4) have been studied using neutron diffraction, resonant ultrasound spectroscopy (RUS), x-ray diffraction measurements, and first principles calculations. The structural and magnetic phase diagrams of CeCu6-xAgx and CeCu6-xPdx as a function of Ag/Pd composition are reported. The end member, CeCu6, undergoes a structural phase transition from an orthorhombic (Pnma) to a monoclinic (P21/c) phase at 240 K. In CeCu6-xAgx, the structural phase transition temperature (Ts) decreases linearly with Ag concentration and extrapolates to zero at xS ≈0.1. The structural transition in CeCu6-xPdx remains unperturbed with Pd substitution within the range of our study. The lattice constant b slightly decreases with Ag/Pd doping, whereas a and c increase with an overall increase in the unit cell volume. Both systems, CeCu6-xAgx and CeCu6-xPdx, exhibit a magnetic quantum critical point (QCP), at x≈0.2 and x≈0.05, respectively. Near the QCP, long range antiferromagnetic ordering takes place at an incommensurate wave vector (δ10 δ2), where δ1~0.62,δ2~0.25,x=0.125 for CeCu6-xPdx and δ1~0.64,δ2~0.3,x=0.3 for CeCu6-xAgx. The magnetic structure consists of an amplitude modulation of the Ce moments which are aligned along the c axis of the orthorhombic unit cell.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Generation of High-Power, Reversed-Cherenkov Wakefield Radiation in a Metamaterial Structure
Here, we present the first demonstration of high-power, reversed-Cherenkov wakefield radiation by electron bunches passing through a metamaterial structure. The structure supports a fundamental transverse magnetic mode with a negative group velocity leading to reversed-Cherenkov radiation, which was clearly verified in the experiments. Single 45 nC electron bunches of 65 MeV traversing the structure generated up to 25 MW in 2 ns pulses at 11.4 GHz, in excellent agreement with theory. Two bunches of 85 nC with appropriate temporal spacing generated up to 80 MW by coherent wakefield superposition, the highest rf power that metamaterial structures ever experienced without damage. These results demonstrate the unique features of metamaterial structures that are very attractive for future high-gradient wakefield accelerators, including two-beam and collinear accelerators. Advantages include the high shunt impedance for high-power generation and high-gradient acceleration, the simple and rugged structure, and a large parameter space for optimization.
43 PARTICLE ACCELERATORS↗
Atomic and micro-structure features of nanoporous aluminosilicate glasses from reactive molecular dynamics simulations
Not provided.
Materials Science↗
Flight-vehicle materials, structures, and dynamics - Assessment and future directions. Vol. 5 - Structural dynamics and aeroelasticity
Various papers on flight vehicle materials, structures, and dynamics are presented. Individual topics addressed include: general modeling methods, component modeling techniques, time-domain computational techniques, dynamics of articulated structures, structural dynamics in rotating systems, structural dynamics in rotorcraft, damping in structures, structural acoustics, structural design for control, structural modeling for control, control strategies for structures, system identification, overall assessment of needs and benefits in structural dynamics and controlled structures. Also discussed are: experimental aeroelasticity in wind tunnels, aeroservoelasticity, nonlinear aeroelasticity, aeroelasticity problems in turbomachines, rotary-wing aeroelasticity with application to VTOL vehicles, computational aeroelasticity, structural dynamic testing and instrumentation.
Noor, Ahmed K.↗