Search NASA⌕ Search

SEARCH · Search NASA

Results for “Structures”

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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Interplay of Binary and Quantitative Structure on the Stability of Mutualistic Networks

Synopsis Understanding how the structure of biological systems impacts their resilience (broadly defined) is a recurring question across multiple levels of biological organization. In ecology, considerable effort has been devoted to understanding how the structure of interactions between species in ecological networks is linked to different broad resilience outcomes, especially local stability. Still, nearly all of that work has focused on interaction structure in presence-absence terms and has not investigated quantitative structure, i.e., the arrangement of interaction strengths in ecological networks. We investigated how the interplay between binary and quantitative structure impacts stability in mutualistic interaction networks (those in which species interactions are mutually beneficial), using community matrix approaches. We additionally examined the effects of network complexity and within-guild competition for context. In terms of structure, we focused on understanding the stability impacts of nestedness, a structure in which more-specialized species interact with smaller subsets of the same species that more-generalized species interact with. Most mutualistic networks in nature display binary nestedness, which is puzzling because both binary and quantitative nestedness are known to be destabilizing on their own. We found that quantitative network structure has important consequences for local stability. In more-complex networks, binary-nested structures were the most stable configurations, depending on the quantitative structures, but which quantitative structure was stabilizing depended on network complexity and competitive context. As complexity increases and in the absence of within-guild competition, the most stable configurations have a nested binary structure with a complementary (i.e., anti-nested) quantitative structure. In the presence of within-guild competition, however, the most stable networks are those with a nested binary structure and a nested quantitative structure. In other words, the impact of interaction overlap on community persistence is dependent on the competitive context. These results help to explain the prevalence of binary-nested structures in nature and underscore the need for future empirical work on quantitative structure.

Zoology↗
DOE OSTI2020

Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures

The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets: 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF1% value of 6.2 compared to apo structures with 3.5. Docking of native ligands to the refined structures shows an average ligand root mean square deviation (RMSD) of 1.97 Å (DUD-E dataset and Gunasekaran dataset) relative to ligands in the holo crystal structures, which is comparable to the self-docking (i.e., docking of the native ligand back to its crystal structure receptor) average, 1.34 Å (DUD-E dataset) and 1.36 Å (Gunasekaran dataset). On the other hand, docking to the apo structures yields an average ligand RMSD of 3.65 Å (DUD-E) and 2.90 Å (Gunasekaran). These results indicate that our method is robust and can be useful to improve virtual screening performance of apo structures.

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

Effects of Al:Si and (Al+Na):Si Ratios on the Properties of the International Simple Glass, Part II: Structure

High-alumina containing high-level waste (HLW) will be vitrified at the Waste Treatment Plant at the Hanford Site. The resulting glasses, high in alumina, will have distinct composition-structure-property (C-S-P) relationships compared to previously studied HLW glasses. These C-S-P relationships determine the processability and product durability of glasses and therefore must be understood. The main purpose of this study is to understand the detailed structural changes caused by Al:Si and (Al+Na):Si substitutions in a simplified nuclear waste model glass (ISG, International Simple Glass) by combining experimental structural characterizations and molecular dynamics (MD) simulations. The structures of these two series of glasses were characterized by neutron total scattering and 27Al, 23Na, 29Si, and 11B solid-state nuclear magnetic resonance (NMR) spectroscopy. Additionally, MD simulations were used to generate atomistic structural models of the borosilicate glasses and simulation results were validated by the experimental structural data. Short-range (e.g., bond distance, coordination number, etc.) and medium-range (e.g., oxygen speciation, network connectivity, polyhedral linkages) structural features of the borosilicate glasses were systematically investigated as a function of the degree of substitution. The results show that bond distance and coordination number of the cation-oxygen pairs are relatively insensitive to Al:Si and (Al+Na):Si substitutions with the exception of the B-O pair. Additionally, the Al:Si substitution results in an increase of tri-bridging oxygen species, while (Al+Na):Si substitution creates non-bridging oxygen species. Charge compensator preferences were found for Si-[NBO] (Na+), [3]B-[NBO] (Na+), [4]B (mostly Ca2+), [4]Al (nearly equally split Na+ and Ca2+), and [6]Zr (mostly Ca2+). The network former-BO-network former linkages preferences were also tabulated; Si-O-Al and Al-O-Al were preferred at the expense of lower Si-O-[3]B and [3]B-O-[3]B linkages. These results provide insights on the structural origins of property changes such as glass transition temperature caused by the substitutions, providing a basis for future improvements of theoretical and computer simulation models.

Lu, Xiaonan↗
DOE OSTI2020

Enumeration as a Tool for Structure Solution: A Materials Genomic Approach to Solving the Cation-Ordered Structure of Na 3 V 2 (PO 4 ) 2 F 3

While powder diffraction methods are routinely utilized to optimize structural models for compounds whose crystal structures are known, the determination of unknown structures is far more challenging. When the unknown structure is large, structure solution can become a virtually intractable problem using standard structure solution methodologies, especially when the space group cannot be unambiguously resolved. One such system is the promising Na-ion battery cathode material Na 3 V 2 (PO 4 ) 2 F 3 whose high temperature and room temperature structures were previously solved, but whose more complex low-temperature structure could not be determined. Here, a novel materials genomic approach is demonstrated for the solution of the unknown 100 K structure of Na 3 V 2 (PO 4 ) 2 F 3 in which enumeration methods are first used to generate a large number (~3,000) of trial structures based on plausible orderings of Na ions and then automated Rietveld refinements are carried out to optimize each of these trial structures. Based on both the analysis of the ensemble of optimized trial structures and the density functional theory energy minimization of selected trial structures, the 100 K structure of Na 3 V 2 (PO 4 ) 2 F 3 is best described as belonging to the space group A2 1 am with unit cell dimensions of a = 9.01928(4), b = 27.1379(1), c = 10.73307(5). The 100 K unit cell has a large volume of 2627.07(2) Å 3 with Z = 12 and 33 independent crystallographic sites (9 Na, 3 V, 3 P, 12 O, and 6 F) that is 3x and 6x larger than the room- and high-temperature polymorphs of this phase, respectively. Finally, the novel methods described here will be generally applicable for the solution of the complex cation-ordered structures that commonly occur for battery materials.

36 MATERIALS SCIENCE↗
DOE OSTI2026

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 ↗
DOE OSTI2020

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↗
DOE OSTI2023

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↗
DOE OSTI2019

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↗
DOE OSTI2020

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↗
DOE OSTI2021

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↗
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↗