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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein- DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Helical magnetic order and Fermi surface nesting in noncentrosymmetric ScFeGe

Here, an investigation of the structural, magnetic, thermodynamic, and charge transport properties of noncentrosymmetric hexagonal ScFeGe reveals it to be an anisotropic metal with a transition to a weak itinerant incommensurate helimagnetic state below T N =36 K. Neutron diffraction measurements discovered a temperature and field independent helical wave vector k = (0 0 0.193) with magnetic moments of 0.53 μ B per Fe confined to the ab-plane. Density functional theory calculations are consistent with these measurements and find several bands that cross the Fermi level along the c-axis with a nearly degenerate set of flat bands just above the Fermi energy. The anisotropy found in the electrical transport is reflected in the calculated Fermi surface, which consists of several warped flat sheets along the c-axis with two regions of significant nesting, one of which has a wave vector that closely matches that found in the neutron diffraction. The electronic structure calculations, along with a strong anomaly in the c-axis conductivity at TN, signal a Fermi surface driven magnetic transition, similar to that found in spin density wave materials. Magnetic fields applied in the ab-plane result in a metamagnetic transition with a threshold field of ≈ 6.7 T along with a sharp, strongly temperature dependent discontinuity and a change in sign of the magnetoresistance for in-plane currents. Thus, ScFeGe is an ideal system to investigate the effect of in-plane magnetic fields on a helimagnet with a c-axis propagation vector, where the relative strength of the magnetic interactions and anisotropies determine the topology and magnetic structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Efficient Ab Initio Auxiliary-Field Quantum Monte Carlo Calculations in Gaussian Bases via Low-Rank Tensor Decomposition

We describe an algorithm to reduce the cost of auxiliary-field quantum Monte Carlo (AFQMC) calculations for the electronic structure problem. The technique uses a nested low-rank factorization of the electron repulsion integral (ERI). While the cost of conventional AFQMC calculations in Gaussian bases scales as O(N 4 ), where N is the size of the basis, we show that ground-state energies can be computed through tensor decomposition with reduced memory requirements and subquartic scaling. Here, the algorithm is applied to hydrogen chains and square grids, water clusters, and hexagonal BN. In all cases, we observe significant memory savings and, for larger systems, reduced, subquartic simulation time.

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

Charge Density Waves and Electronic Properties of Superconducting Kagome Metals

We report that kagome metals AV 3 Sb 5 (A = K, Rb, and Cs) exhibit intriguing superconductivity below 0.9 ~ 2.5 K, a charge density wave (CDW) transition around 80 ~ 100 K, and $\mathbb{Z}$ 2 topological surface states. The nature of the CDW phase and its relation to superconductivity remains elusive. In this work, we investigate the electronic and structural properties of CDW by first-principles calculations. We reveal an inverse Star of David deformation as the 2 x 2 x 2 CDW ground state of the kagome lattice. The kagome lattice shows softening breathing-phonon modes, indicating the structural instability. However, electrons play an essential role in the CDW transition via Fermi surface nesting and van Hove singularity. The inverse Star of David structure agrees with recent experiments by scanning tunneling microscopy (STM). The CDW phase inherits the nontrivial $\mathbb{Z}$ 2 -type topological band structure. Further, we find that the electron-phonon coupling is too weak to account for the superconductivity T c in all three materials. It implies the existence of unconventional pairing of these kagome metals. Our results provide essential knowledge toward understanding the superconductivity and topology in kagome metals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Fermi level tuning and double-dome superconductivity in the kagome metal CsV 3 Sb 5 – x Sn x

The recently reported AV 3 Sb 5 (A = K , Rb, Cs) family of kagome metals are candidates for unconventional superconductivity and chiral charge density wave (CDW) order; both potentially arise from nested saddle points in their band structures close to the Fermi energy. Here, we use chemical substitution to introduce holes into CsV 3 Sb 5 and unveil an unconventional coupling of the CDW and superconducting states. Specifically, we generate a phase diagram for CsV 3 Sb 5 – x Sn x that illustrates the impact of hole doping the system and lifting the nearest van Hove singularity toward and above E F . Superconductivity exhibits a nonmonotonic evolution with the introduction of holes, resulting in two “domes” peaked at 3.6 and 4.1 K and the rapid suppression of three-dimensional CDW order. Further, the evolution of CDW and superconducting order is compared with the evolution of the electronic band structure of CsV 3 Sb 5 – x Sn x , where the complete suppression of superconductivity seemingly coincides with an electronlike band comprised of Sb p z orbitals pushed above E F .

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. Results Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. Availability and implementation SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Dynamic Copper Site Redispersion through Atom Trapping in Zeolite Defects

Single-site copper-based catalysts have shown remarkable activity and selectivity for a variety of reactions. However, deactivation by sintering in high-temperature reducing environments remains a challenge and often limits their use due to irreversible structural changes to the catalyst. Here, we report zeolite-based copper catalysts in which copper oxide agglomerates formed after reaction can be repeatedly redispersed back to single sites using an oxidative treatment in air at 550 °C. Under different environments, single-site copper in Cu–Zn–Y/deAlBeta undergoes dynamic changes in structure and oxidation state that can be tuned to promote the formation of key active sites while minimizing deactivation through Cu sintering. For example, single-site Cu 2+ reduces to Cu 1+ after catalyst pretreatment (270 °C, 101 kPa H 2 ) and further to Cu0 nanoparticles under reaction conditions (270–350 °C, 7 kPa EtOH, 94 kPa H 2 ) or accelerated aging (400–450 °C, 101 kPa H 2 ). After regeneration at 550 °C in air, agglomerated CuO was dispersed back to single sites in the presence and absence of Zn and Y, which was verified by imaging, in situ spectroscopy, and catalytic rate measurements. Ab initio molecular dynamics simulations show that solvation of CuO monomers by water facilitates their transport through the zeolite pore, and condensation of the CuO monomer with a fully protonated silanol nest entraps copper and reforms the single-site structure. Importantly, the capability of silanol nests to trap and stabilize copper single sites under oxidizing conditions could extend the use of single-site copper catalysts to a wider variety of reactions and allows for a simple regeneration strategy for copper single-site catalysts.

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

The hierarchical energy landscape of screw dislocation motion in refractory high-entropy alloys

High-entropy alloys (HEAs) with concentrated solid solutions are conceived to possess a rugged atomic and energy landscape in which dislocation motion necessarily proceeds to accommodate mechanical deformation. Fundamental questions remain as to how rough the energy landscape is and to what extent it can be influenced by the local ordering of their constituent elements. Here, we construct and report the potential energy landscape (PEL) governing screw dislocation motion in refractory HEAs that reveals a hierarchical and multilevel structure with a collection of small basins nested in large metabasin. This striking feature pertaining to HEAs exerts a trapping force and back stress on saddle point activations, retarding dislocation movement. Further, by introducing chemical short-range order, the energy landscape is smoothed but skewed to different degrees that shifts the rate-liming process from kink-glide to kink-pair nucleation. The chemical disorder-roughened PEL in HEAs, analogous to structural disorder induced in metallic glasses, signifies the role of various barrier-hopping processes underlying the extraordinary mechanical behaviors of the two distinct groups of materials.

36 MATERIALS SCIENCE↗
DOE OSTI2019

High-Resolution Simulation of Snowfall over the Korean Eastern Coastal Region Using WRF Model: Sensitivity to Domain Nesting-Down Strategy

The eastern coastal area of the Korean Peninsula, Yeongdong region, often experiences severe snowfall during the winter season. We studied here the development mechanism of a snowfall case occurred in February 2014 using the Weather Research and Forecasting (WRF) model at the convection-permitting resolution of 1 km. The model reasonably captured the observed snowfall, and three factors were discovered as important contributors to this snowfall case: a temperature contrast between land and ocean, a high-pressure system over the northeastern part of the Korean Peninsula, and the mountainous terrain. Cold and dry air blown from the high-pressure system gains heat and moisture when it passes over the East Sea enhancing the low-level instability. When the air mass reaches the coastline, updraft is generated by the density difference with the continental atmosphere and by the mountain slope. Further sensitivity experiments were conducted by adjusting strategies of nesting down (offline and online). Sensitivity experiments consist of three offline nesting experiments with different boundary condition update frequencies in 6, 3 and 1 h and one online nesting experiment that updates the boundary condition every integration time step. The major snowfall along the mountain range located in the middle of domain does not change significantly regardless of the nesting frequency. The offline nesting causes unphysical discontinuities of precipitation along the north and east sides of lateral boundary where wind blows in, which are caused by the absence of condensed hydrometeor variables in the lateral boundary condition. The domain nesting strategy tested in this study has dramatically impacted on the upper troposphere structure in the model: artificial fluctuations at the upper troposphere in the offline nesting simulations were significantly alleviated in the online nesting simulation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Self-assembled Ag(111) nanostructures induced by Fermi surface nesting

Scanning tunneling microscopy measurements on Ag(111)/MoS 2 reveal atomically flat preferred, or “magic,” heights occurring at 6, 10, and 14 atomic layers. We note these results are consistent with Ag growth on a variety of semiconducting substrates and correlate with electronic energy savings in electronic structure calculations of freestanding Ag(111) films. Thus, under certain conditions, Ag will spontaneously form quantized structures independent of the substrate. To explain this, we have found Fermi surface nesting vectors in the bulk Ag band structure which account for these results and the fact Ag that is gapped along the surface normal. This model extends to a range of metallic systems which exhibit electronic confinement, epitaxial growth, and minimal strain. As with Au/MoS 2 , the Ag/MoS 2 system exhibits this behavior at unusually high temperatures so that these principles might be used for control over device features at the nanometer scale under standard fabrication conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Disentangling the role of bond lengths and orbital symmetries in controlling $T_c$ of optimally doped YBa 2 Cu 3 O 7

Optimally doped YBa 2 Cu 3 O 7 (YBCO) has a high critical temperature, at 92 K. It is largely believed that Cooper pairs form in YBCO and other cuprates because of spin fluctuations, but the issue and the detailed mechanism are far from settled. In the present work, we employ a state-of-the-art first-principles ability to compute both the low- and high-energy spin fluctuations in optimally doped YBCO. We benchmark our results against recent inelastic neutron scattering and resonant inelastic x-ray scattering measurements. Further, we use strain as an external parameter to modulate the spin fluctuations and superconductivity. We disentangle the roles of barium-apical oxygen hybridization, interlayer coupling, and orbital symmetries by applying an idealized strain, and also a strain with a fully relaxed structure. We show that shortening the distance between Cu layers is conducive to enhanced Fermi surface nesting, which increases spin fluctuations and drives up $T_c$. However, when the structure is fully relaxed, electrons flow to the $d_{z^2}$ orbital as a consequence of a shortened Ba-O bond, which is detrimental for superconductivity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Evaluation of the Performance of the SAVY Container Subjected to Various Impact Events using Finite Element Methods

The SAVY container is a Safety Class Design Feature utilized both inside engineered features and outside engineered features (e.g. gloveboxes) at TA-55 Plutonium Facility Building 4. These containers were certified as low damage ratio containers by demonstrating their ability to retain material after exposure to impacts and elevated temperatures resulting from a design basis seismic event. Original testing of the SAVY did not evaluate the effects of various facility specific insults to the SAVY while within a DOT Type A Container, caused either by design basis accident or an operational mishap. These insults include: 1. Impact of a structural I-beam (drum upright & drum on side); 2. Impact of a section of Positive Pressure Chilled Water Pipe (PPCWS); 3. Forklift fork tine impact; 4. Fuel truck impact. Abaqus Explicit Dynamics Finite Element Analysis was performed on a nested SAVY/DOT Type 7A container configuration to assess the structural integrity of the SAVY under the accident conditions listed.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2019

Defect‐Mediated Ordering of Condensed Water Structures in Microporous Zeolites

Abstract Ab‐initio molecular dynamics simulations and transmission infrared spectroscopy are employed to characterize the structure of water networks in defect‐functionalized microporous zeolites. Thermodynamically stable phases of clustered water molecules are localized at some of the defects in zeolite Beta, which include catalytic sites such as framework Lewis acidic Sn atoms in closed and hydrolyzed‐open forms, as well as silanol nests. These water clusters compete with ideal gas‐like structures at low water densities and pore‐filling phases at higher water densities, with the equilibrium phase determined by the water chemical potential. The physical characteristics of these phases are determined by the defect identity, with the local binding and orientation of hydroxyl moieties around the defects playing a central role. The results suggest general principles for how the structure of polar solvents in microporous solid acids is influenced by local defect functionalization, and the thermodynamic stability of the condensed phases surrounding such sites, in turn, implies that the catalysis of Lewis acids will be influenced by local water ordering.

Bukowski, Brandon C.↗
DOE OSTI2019

Defect‐Mediated Ordering of Condensed Water Structures in Microporous Zeolites

Abstract Ab‐initio molecular dynamics simulations and transmission infrared spectroscopy are employed to characterize the structure of water networks in defect‐functionalized microporous zeolites. Thermodynamically stable phases of clustered water molecules are localized at some of the defects in zeolite Beta, which include catalytic sites such as framework Lewis acidic Sn atoms in closed and hydrolyzed‐open forms, as well as silanol nests. These water clusters compete with ideal gas‐like structures at low water densities and pore‐filling phases at higher water densities, with the equilibrium phase determined by the water chemical potential. The physical characteristics of these phases are determined by the defect identity, with the local binding and orientation of hydroxyl moieties around the defects playing a central role. The results suggest general principles for how the structure of polar solvents in microporous solid acids is influenced by local defect functionalization, and the thermodynamic stability of the condensed phases surrounding such sites, in turn, implies that the catalysis of Lewis acids will be influenced by local water ordering.

Bukowski, Brandon C.↗
DOE OSTI2024

Topological Characterization and Uncertainty Visualization of Atmospheric Rivers

Atmospheric rivers (ARs) are long, narrow regions of water vapor in the Earth's atmosphere that transport heat and moisture from the tropics to the mid-latitudes. ARs are often associated with extreme weather events in North America and contribute significantly to water supply and flood risk. However, characterizing ARs has been a major challenge due to the lack of a universal definition and their structural variations. Existing AR detection tools (ARDTs) produce distinct AR boundaries for the same event, making the risk assessment of ARs a difficult task. Understanding these uncertainties is crucial to improving the predictability of AR impacts, including their landfall areas and associated precipitation, which could cause catastrophic flooding and landslides over the coastal regions. In this work, we develop an uncertainty visualization framework that captures boundary and interior uncertainties, i.e., structural variations, of an ensemble of ARs that arise from a set of ARDTs. We first provide a statistical overview of the AR boundaries using the contour boxplots of Whitaker et al. that highlight the structural variations of AR boundaries based on their nesting relationships. We then introduce the topological skeletons of ARs based on Morse complexes that characterize the interior variation of an ensemble of ARs. We propose an uncertainty visualization of these topological skeletons, inspired by MetroSets of Jacobson et al. that emphasizes the agreements and disagreements across the ensemble members. Through case studies and expert feedback, we demonstrate that the two approaches complement each other, and together they could facilitate an effective comparative analysis process and provide a more confident outlook on an AR's shape, area, and onshore impact.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Perturbation theory for the logarithm of a positive operator

In various contexts in mathematical physics, such as out-of-equilibrium physics and the asymptotic information theory of many-body quantum systems, one needs to compute the logarithm of a positive unbounded operator. Examples include the von Neumann entropy of a density matrix and the flow of operators with the modular Hamiltonian in the Tomita-Takesaki theory. Often, one encounters the situation where the operator under consideration, which we denote by ∆, can be related by a perturbative series to another operator ∆ 0 , whose logarithm is known. We set up a perturbation theory for the logarithm log ∆. It turns out that the terms in the series possess a remarkable algebraic structure, which enables us to write them in the form of nested commutators plus some “contact terms”.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Incorporating geological structure into sensitivity analysis of subsurface contaminant transport

Simulating subsurface contaminant transport at the kilometer-scale often entails modeling reactive flow and transport within and through complex geologic structures. These structures are typically meshed by hand and as a result geologic structure is usually represented by one or a few deterministically generated geological models for uncertainty studies of flow and transport in the subsurface. Uncertainty in geologic structure can have a significant impact on contaminant transport. In this study, the impact of geologic structure on contaminant tracer transport in a shale formation is investigated for a simplified generic deep geologic repository for permanent disposal of spent nuclear fuel. An open-source modeling framework is used to perform a sensitivity analysis study on transport of two tracers from a generic spent nuclear fuel repository with uncertain location of the interfaces between the stratum of the geologic structure. The automated workflow uses sampled realizations of the geological structural model in addition to uncertain flow parameters in a nested sensitivity analysis. Concentration of the tracers at observation points within, in line with, and downstream of the repository are used as the quantities of interest for determining model sensitivity to input parameters and geological realization. Finally, the results of the study indicate that the location of strata interfaces in the geological structure has a first-order impact on tracer transport in the example shale formation, and that this impact may be greater than that of the uncertain flow parameters.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Efficacy of the Cell Perturbation Method in Large-Eddy Simulations of Boundary Layer Flow over Complex Terrain

A challenge to simulating turbulent flow in multiscale atmospheric applications is the efficient generation of resolved turbulence motions over an area of interest. One approach is to apply small perturbations to flow variables near the inflow planes of turbulence-resolving simulation domains nested within larger mesoscale domains. While this approach has been examined in numerous idealized and simple terrain cases, its efficacy in complex terrain environments has not yet been fully explored. Here, we examine the benefits of the stochastic cell perturbation method (CPM) over real complex terrain using data from the 2017 Perdigão field campaign, conducted in an approximately 2-km wide valley situated between two nearly parallel ridges. Following a typical configuration for multiscale simulation using nested domains within the Weather Research and Forecasting (WRF) model to downscale from the mesoscale to a large-eddy simulation (LES), we apply the CPM on a domain with horizontal grid spacing of 150 m. At this resolution, spurious coherent structures are often observed under unstable atmospheric conditions with moderate mean wind speeds. Results from such an intermediate resolution grid are often nested down for finer, more detailed LES, where these spurious structures adversely affect the development of turbulence on the subsequent finer grid nest. We therefore examine the impacts of the CPM on the representation of turbulence within the nested LES domain under moderate mean flow conditions in three different stability regimes: weakly convective, strongly convective, and weakly stable. In addition, two different resolutions of the underlying terrain are used to explore the role of the complex topography itself in generating turbulent structures. We demonstrate that the CPM improves the representation of turbulence within the LES domain, relative to the use of high-resolution complex terrain alone. During the convective conditions, the CPM improves the rate at which smaller-scales of turbulence form, while also accelerating the attenuation of the spurious numerically generated roll structures near the inflow boundary. During stable conditions, the coarse mesh spacing of the intermediate LES domain used herein was insufficient to maintain resolved turbulence using CPM as the flow develops downstream, highlighting the need for yet higher resolution under even weakly stable conditions, and the importance of accurate representation of flow on intermediate LES grids.

17 WIND ENERGY↗