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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The XtalOpt Evolutionary Algorithm for Crystal Structure Prediction

Significant progress has been made in the field of a priori crystal structure prediction, with a number of recent remarkable success stories. Herein, we briefly outline the methods that have been developed for finding the global minimum structure and interesting local minima without the need for experimental information. Focus is placed on describing the XTALOPT evolutionary algorithm (EA) developed in our group towards this end. XTALOPT is published under well-known open-source licenses, and the EA searches can be analyzed via the AVOGADRO chemical editor and visualizer. We describe new algorithmic developments that have made it possible to predict the structures of ever-more complex crystalline lattices. Benchmark tests, which clearly illustrate how the new developments improve the success rate and accelerate the discovery of the global minimum structure, are carried out. Lastly, we describe how XTALOPT has been employed to predict novel ternary hydrides that have the propensity for high-temperature superconductivity under pressure.

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

Site Diversity and Mechanism of Metal–Exchanged Zeolite Catalyzed Non–Oxidative Propane Dehydrogenation

Metal-exchanged zeolites are well-known propane dehydrogenation (PDH) catalysts; however, the structure of the active species remains unresolved. In this review, existing PDH catalysts are first surveyed, and then the current understanding of metal-exchanged zeolite catalysts is described in detail. The case of Ga/H-ZSM-5 is employed to showcase that advances in the understanding of structure–activity relations are often accompanied by technological or conceptional breakthroughs. The understanding of Ga speciation at PDH conditions has evolved owing to the advent of in situ/operando characterizations and to the realization that the local coordination environment of Ga species afforded by the zeolite support has a decisive impact on the active site structure. In situ/operando quantitative characterization of catalysts, rigorous determination of intrinsic reaction rates, and predictive computational modeling are all significant in identifying the most active structure in these complex systems. The reaction mechanism could be both intricately related to and nearly independent of the details of the assumed active structure, as in the two main proposed PDH mechanisms on Ga/H-ZSM-5, that is, the carbenium mechanism and the alkyl mechanism. Perspectives on potential approaches to further elucidate the active structure of metal-exchanged zeolite catalysts and reaction mechanisms are discussed in the final section.

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

Pseudouridine synthase 7 is an opportunistic enzyme that binds and modifies substrates with diverse sequences and structures

Pseudouridine (Ψ) is a ubiquitous RNA modification incorporated by pseudouridine synthase (Pus) enzymes into hundreds of noncoding and protein-coding RNA substrates. Here, in this study, we determined the contributions of substrate structure and protein sequence to binding and catalysis by pseudouridine synthase 7 (Pus7), one of the principal messenger RNA (mRNA) modifying enzymes. Pus7 is distinct among the eukaryotic Pus proteins because it modifies a wider variety of substrates and shares limited homology with other Pus family members. We solved the crystal structure of Saccharomyces cerevisiae Pus7, detailing the architecture of the eukaryotic-specific insertions thought to be responsible for the expanded substrate scope of Pus7. Additionally, we identified an insertion domain in the protein that fine-tunes Pus7 activity both in vitro and in cells. These data demonstrate that Pus7 preferentially binds substrates possessing the previously identified UGUAR (R = purine) consensus sequence and that RNA secondary structure is not a strong requirement for Pus7-binding. In contrast, the rate constants and extent of Ψ incorporation are more influenced by RNA structure, with Pus7 modifying UGUAR sequences in less-structured contexts more efficiently both in vitro and in cells. Although less-structured substrates were preferred, Pus7 fully modified every transfer RNA, mRNA, and nonnatural RNA containing the consensus recognition sequence that we tested. Our findings suggest that Pus7 is a promiscuous enzyme and lead us to propose that factors beyond inherent enzyme properties (e.g., enzyme localization, RNA structure, and competition with other RNA-binding proteins) largely dictate Pus7 substrate selection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evolution of dislocation substructures in metals via high-strain-rate nanoindentation

Deformation at high strain rates often results in high stresses on many engineering materials, potentially leading to catastrophic failure without proper design. High-strain-rate mechanical testing is thus needed to improve the design of future structural materials for a wide range of applications. Although several high-strain-rate mechanical testing techniques have been developed to provide a fundamental understanding of material responses and microstructural evolution under high-strain-rate deformation conditions, these tests are often very time consuming and costly. In this work, we utilize a high-strain-rate nanoindentation testing technique and system in combination with transmission electron microscopy to reveal the deformation mechanisms and dislocation substructures that evolve in pure metals from low (10 –2 s –1 ) to very high indentation strain rates (10 4 s –1 ), using face-centered cubic aluminum and body-centered cubic molybdenum as model materials. The results help to establish the conditions under which micro- and macro-scale tests can be compared with validity and also provide a promising pathway that could lead to accelerated high-strain-rate testing at substantially reduced costs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Main bearing response in a waked 15-MW floating wind turbine in below-rated conditions

Increased wind turbine size raises unknowns related to structural flexibility. Moreover, moving to deeper waters, component reliability becomes more critical. This work investigates main bearing response dependence on drivetrain flexibility and wake impingement in a two-turbine wind farm. A 15-MW floating direct-drive turbine is considered. Large eddy simulations (LES) are employed to model neutral, stable and unstable atmospheric conditions at below-rated mean wind speed, while the engineering codes OpenFAST and FAST.Farm simulate turbine and wake behavior. Results indicate significant sensitivities in fatigue estimates to lateral distance between the upstream and downstream turbine. The trends are most substantial in stable conditions, where the waked downwind main bearing sees twice the fatigue damage estimates of the upstream turbine for one position and 50% for another. Main bearing fatigue sensitivity to drivetrain flexibility is minor, while properly including generator rotor inertia loads is important for the axial forces of the locating (axially fixed) bearing, especially in stable conditions.

17 WIND ENERGY↗
DOE OSTI2023

Decay rates of almost strong modes in Floquet spin chains beyond Fermi's Golden Rule

The stability and dynamics of almost strong zero and π modes in weakly nonintegrable Floquet spin chains are investigated. Such modes can also be viewed as localized Majorana modes at the edge of a topological superconductor. Perturbation theory in the strength of integrability breaking interaction J z is employed to estimate the decay rates of these modes, and compared to decay rates obtained from exact diagonalization. Here, the structure of the perturbation theory and thus the lifetime of the modes is governed by the conservation of quasienergy modulo 2π/T, where T is the period of the Floquet system. If there are 4n – 1 bulk excitations whose quasienergies add up to zero (or π/T for a π mode), one obtains a decay channel of the Majorana mode with a decay rate proportional to $J$$^{2n}_{z}$. Thus the lifetime is sensitively controlled by the width of the single-particle Floquet bands. For regimes where the decay rates are quadratic in J z , an analytic expression for the decay rate in terms of an infinite temperature autocorrelation function of the integrable model is derived, and shown to agree well with exact diagonalization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Association of Cl with C 2 H 2 by unified variable-reaction-coordinate and reaction-path variational transition-state theory

Significance A key issue in chemical kinetics is advancing the theoretical framework to handle reactions beyond the domain of textbook transition-state theory by including––for example––anharmonicity, barrierless transition states, transition states in series, and the effect of conformational flexibility on equilibrium constants. Other key issues are validating affordable electronic structure methods for direct dynamics and the direct calculation of high-pressure limiting rate constants, which are often obtainable experimentally only by extrapolation. The present article addresses all these issues for a prototype radical–molecule association reaction and thereby demonstrates how to combine improved theoretical methods to provide rate constants in cases where experimental data are uncertain or missing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Study of Key 57 Ni ⁢(𝑝,𝛾)⁢ 58 Cu Resonances to Understand 44 Ti Nucleosynthesis in Supernovae

An important validation of nucleosynthesis models of core-collapse supernovae is the comparison of radioisotope predictions to abundances inferred from observations of 𝛾 rays emitted in remnants. One such isotope, 44 Ti, is especially sensitive to the 57 Ni ⁢(𝑝,𝛾)⁢ 58 Cu reaction rate. Despite this importance, no experimentally constrained rate exists for this reaction. It is thus crucial to determine this rate. GRETINA ORRUBA: Dual Detectors for Experimental Structure Studies (GODDESS) was used along with the first use of the Enge split-pole spectrograph at Notre Dame to measure structure properties of 58 Cu via the 58 Ni ⁢( 3 He,𝑡)⁢ 58 Cu reaction. Here, the combined analysis of these complementary data sets allows for precise determination of 58 Cu level energies, and spins are constrained from analysis of the 𝛾-ray decay. 44 Ti yields were found to change by over 25% compared to previous estimates in model calculations using the new experimentally constrained reaction rate.

energy levels↗
DOE OSTI2023

Graphic contrastive learning analyses of discontinuous molecular dynamics simulations: Study of protein folding upon adsorption

A comprehensive understanding of the interfacial behaviors of biomolecules holds great significance in the development of biomaterials and biosensing technologies. In this work, we used discontinuous molecular dynamics (DMD) simulations and graphic contrastive learning analysis to study the adsorption of ubiquitin protein on a graphene surface. Our high-throughput DMD simulations can explore the whole protein adsorption process including the protein structural evolution with sufficient accuracy. Contrastive learning was employed to train a protein contact map feature extractor aiming at generating contact map feature vectors. Subsequently, these features were grouped using the k-means clustering algorithm to identify the protein structural transition stages throughout the adsorption process. The machine learning analysis can illustrate the dynamics of protein structural changes, including the pathway and the rate-limiting step. Our study indicated that the protein–graphene surface hydrophobic interactions and the π–π stacking were crucial to the seven-stage adsorption process. Upon adsorption, the secondary structure and tertiary structure of ubiquitin disintegrated. The unfolding stages obtained by contrastive learning-based algorithm were not only consistent with the detailed analyses of protein structures but also provided more hidden information about the transition states and pathway of protein adsorption process and structural dynamics. Our combination of efficient DMD simulations and machine learning analysis could be a valuable approach to studying the interfacial behaviors of biomolecules.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Using advanced data structures to enable responsive security monitoring

Write-optimized data structures (WODS), offer the potential to keep up with cyberstream event rates and give sub-second query response for key items like IP addresses. These data structures organize logs as the events are observed. To work in a real-world environment and not fill up the disk, WODS must efficiently expire older events. As the basis for our research into organizing security monitoring data, we implemented a tool, called Diventi, to index IP addresses in connection logs using RocksDB (a write-optimized LSM tree). In this work, we extended Diventi to automatically expire data as part of the data structures’ normal operations. We guarantee that Diventi always tracks the N most recent events and tracks no more than N + k events for a parameter k < N, while ensuring the index is opportunistically pruned. To test Diventi at scale in a controlled environment, we used anonymized traces of IP communications collected at SuperComputing 2019. We synthetically extended the 2.4 billion connection events to 100 billion events. We tested Diventi vs. Elasticsearch, a common log indexing tool. In our test environment, Elasticsearch saw an ingestion rate of at best 37,000 events/s while Diventi sustained ingestion rates greater than 171,000 events/s. Our query response times were as much as 100 times faster, typically answering queries in under 80 ms. Furthermore, we saw no noticeable degradation in Diventi from expiration. We have deployed Diventi for many months where it has performed well and supported new security analysis capabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Fracture-based shape optimization built upon the topological derivative

In Silva et al. (2011) and Alidoost et al. (2020), the authors developed an approximation of the energy release rate field associated with a small edge or surface crack at any boundary location and with any orientation using the topological derivative. The approximation is computationally attractive because it requires only a single analysis on the non-cracked domain in contrast with conventional boundary-element and finite-element-based methods, which require a separate and costlier analysis for each crack length-location-orientation combination. Here, a shape optimization scheme for fracture-resistant structures is developed using the energy release rate approximation. In the gradient-based optimization scheme, the domain and its boundary are defined implicitly using level-set functions. The level-set functions of arbitrary geometries are constructed using Boolean operations from the level-set functions of simple primitives. This geometrical representation has the dual advantage of (i) allowing shapes to intersect and/or separate during the optimization and (ii) simplifying the computation of the shape sensitivities.

42 ENGINEERING↗
DOE OSTI2020

Discovery of Marburg virus neutralizing antibodies from virus-naïve human antibody repertoires using large-scale structural predictions

Marburg virus (MARV) disease is lethal, with fatality rates up to 90%. Neutralizing antibodies (Abs) are promising drug candidates to prevent or treat the disease. Current efforts are focused in part on vaccine development to induce such MARV-neutralizing Abs. We analyzed the antibody repertoire from healthy unexposed and previously MARV-infected individuals to assess if naïve repertoires contain suitable precursor antibodies that could become neutralizing with a limited set of somatic mutations. Here, we computationally searched the human Ab variable gene repertoire for predicted structural homologs of the neutralizing Ab MR78 that is specific to the receptor binding site (RBS) of MARV glycoprotein (GP). Eight Ab heavy-chain complementarity determining region 3 (HCDR3) loops from MARV-naïve individuals and one from a previously MARV-infected individual were selected for testing as HCDR3 loop chimeras on the MR78 Ab framework. Three of these chimerized antibodies bound to MARV GP. We then tested a full-length native Ab heavy chain encoding the same 17-residue-long HCDR3 loop that bound to the MARV GP the best among the chimeric Abs tested. Despite only 57% amino acid sequence identity, the Ab from a MARV-naïve donor recognized MARV GP and possessed neutralizing activity against the virus. Crystallization of both chimeric and full-length native heavy chain-containing Abs provided structural insights into the mechanism of binding for these types of Abs. Our work suggests that the MARV GP RBS is a promising candidate for epitope-focused vaccine design to induce neutralizing Abs against MARV.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Initiator-dependent kinetics of lyotropic liquid crystal-templated thermal polymerization

In this study, we examine the polymerization kinetics with different thermal initiators in lamellar and hexagonal lyotropic liquid crystal (LLC) structures directed by Pluronic L64. Ammonium persulfate is used to initiate the polymerization from the water phase, whereas azobisisobutyronitrile and benzoyl peroxide are employed to commence the reaction through the monomer phase. While the mesophase structure remains intact for all the initiation systems, the kinetics of polymerization and conversion vary significantly. The obtained differential scanning calorimetry (DSC) results reveal that, under same conditions, initiation from water (IFW) system results in enhanced reaction rates as well as higher monomer conversions compared to initiation from oil (IFO) one. Higher termination rate in LLC nanoconfinements induces lower reaction rates in IFO system. Moreover, our work on different LLC structures show that the effect of nanoconfinement on polymerization rate can be minimized through IFW. Chemorheology not only confirms the results obtained from DSC, but also shows that, in similar monomer conversions, the polymers obtained from IFW system exhibit an improved mechanical properties over the samples produced though IFO process.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Orientational Pair Correlations and Local Structure of Benzonitrile from Molecular Dynamics Simulations with Comparisons to Experiments [plus supplemental information]

Here, we present an experimentally parametrized molecular dynamics study of single-molecule and collective orientational relaxation in neat benzonitrile through the analysis of the reorientational anisotropy and polarizability anisotropy time-correlation function (PA-TCF). The simulations show that the PA-TCF is dominated by collective reorientation after 20 ps. Collective reorientation is found to be slower than single-molecule reorientation by a factor of 1.67, consistent with recent experiments. The simulations provide direct evidence of local antiparallel benzonitrile configurations. These structures, which have been the center of some debate, are responsible for the slower rate of collective vs. single-molecule reorientation in the liquid. Further structural analysis indicates that significant Coulombic interactions between the nitrile group and hydrogen atoms on adjacent molecules play a role in the formation of the antiparallel structures. The single-molecule dynamics reflected in the anisotropy are complex and consist of a ballistic regime, restricted angular diffusion, and spatially anisotropic free diffusion. The principal components of the rotational diffusion tensor are independently obtained and shown to reproduce the free diffusion regime of the anisotropy for each principal axis according to the predictions of a previous theory.

14 SOLAR ENERGY↗
DOE OSTI2022

Fatigue-crack propagation behavior in a high-carbon chromium SUJ2 bearing steel: Role of microstructure

High-carbon chromium martensite steels are commonly selected for bearing components in the power generation, automotive and aerospace industries where fatigue failure is a major concern. Accordingly, it is of importance to elucidate the structure-property relationships governing the fatigue properties of such bearing steels. Here, the role of microstructure in influencing the fatigue-crack propagation behavior of a high-carbon chromium SUJ2 bearing steel is examined with emphasis on three martensitic structures: (i) a fine-grained (~10 μm) structure with intragranular (but no intergranular) carbides, (ii) a coarser-grained (~25 μm) structure with discontinuous grain-boundary carbides primarily near triple junctions, and (iii) a coarse-grained (~31 μm) structure with continuous grain-boundary carbides. Although growth rates were fairly similar above ~10 -8 m/cycle, significant differences in behavior were observed at lower, near-threshold growth rates; specifically at a load ratio of 0.1, the ΔKth fatigue threshold was increased from 3.8 MPa m ½ in the fine-grained structure to 5.9 to 6.3 MPa m ½ in the two coarser-grained structures. The dominant factor governing such near-threshold behavior was found to be crack-tip shielding from roughness-induced crack closure, which was most pronounced in the coarser-grained structures; additionally, shielding from crack deflection and branching was apparent in these structures as the crack propagated through the network of intersecting martensite lamellae within the coarse grains. Compared to high-strength stainless steels and low-strength carbon steels, the fine-grained SUJ2 steel displays an exceptional combination of high strength and fatigue-crack growth resistance and is considered to be a superior structural alloy for bearing applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Solder Bond Fatigue is Insensitive to Module Size

In this article, we explore the influence of module size on the rate of interconnecting solder bond thermomechanical fatigue (TMF) damage. Structural mechanics models of crystalline silicon PV models are created to solve with the finite-element method. Results conclusively demonstrate that the rate of solder bond TMF damage is independent of module size, interconnect location across the cell and cell location across the module.

14 SOLAR ENERGY↗
DOE OSTI2021

Grain boundary formation through particle detachment during coarsening of nanoporous metals

Significance Nanoporous metals are prototypical bicontinuous structures that have a large surface area and many applications. We demonstrate that an in-grain orientation spread develops during coarsening in nanoporous metals, leading to the formation of a nanocrystalline–nanoporous structure. The process of particles detaching and reattaching as the structure coarsens is identified as a mechanism of grain boundary formation. Coarsening the structure results in significant particle detachment with detachment rates that vary drastically with changes in the volume fraction and volume fraction inhomogeneities in the nanostructure. These results demonstrate that particle detachment must be understood to have full control of the nanocrystalline–nanoporous structure and improve material properties.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Patchy particle model of hydrated amorphous silica

Glasses corroded in static aqueous conditions typically reach a slow, residual rate of dissolution as a result of the complex interplay between multiple processes. While intrinsically suited to address this problem, Monte Carlo (MC) models developed to date have relied on lattices to describe the amorphous structure of glass and are thus unable to reproduce the residual rate of glass corrosion. A recently developed MC approach based on amorphous structures derived from molecular dynamics simulations offers a solution [Kerisit and Du J. Non-Cryst. Solids 522 (2019) 119601], but it requires a simple model that can rapidly relax the glass-water interface upon each dissolution/condensation event to retain the ability of MC simulations to reach large spatial and temporal scales. To this end, a patchy particle model of hydrated amorphous silica was developed and evaluated against atomistic simulations in this work. Models of water and amorphous silica were first developed separately, and cross terms were then defined to enable simulations of hydrated amorphous silica structures with varying water content. While the nature of its interaction potential prevents the patchy particle model from reproducing simultaneously the structure and dynamics of the systems of interest with a single set of parameters, it described well the connectivity of hydrated amorphous silica structures and the local coordination geometry of individual species. Therefore, this model opens the door to MC simulations of the residual rate of glass corrosion and offers an alternative to atomistic models to investigate the evolution of silica gels over large spatial and temporal scales.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗