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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA

The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T–G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Dataset of 3D Structural and Simulated Transport Properties of Complex Porous Media

Physical processes that occur within porous materials have wide-ranging applications including - but not limited to - carbon sequestration, battery technology, membranes, oil and gas, geothermal energy, nuclear waste disposal, water resource management. The equations that describe these physical processes have been studied extensively; however, approximating them numerically requires immense computational resources due to the complex behavior that arises from the geometrically-intricate solid boundary conditions in porous materials. Here, we introduce a new dataset of unprecedented scale and breadth, DRP-372: a catalog of 3D geometries, simulation results, and structural properties of samples hosted on the Digital Rocks Portal. The dataset includes 1736 flow and electrical simulation results on 217 samples, which required more than 500 core years of computation. This data can be used for many purposes, such as constructing empirical models, validating new simulation codes, and developing machine learning algorithms that closely match the extensive purely-physical simulation. This article offers a detailed description of the contents of the dataset including the data collection, simulation schemes, and data validation.

3D images↗
DOE OSTI2023

Newly reconstructed Arctic surface air temperatures for 1979–2021 with deep learning method

A precise Arctic surface air temperature (SAT) dataset, that is regularly updated, has more complete spatial and temporal coverage, and is based on instrumental observations, is critically important for timely monitoring and improving understanding of the rapid change in the Arctic climate. In this study, a new monthly gridded Arctic SAT dataset dated back to 1979 was reconstructed with a deep learning method by combining surface air temperatures from multiple data sources. The source data include the observations from land station of GHCN (Global Historical Climatology Network), ICOADS (International Comprehensive Ocean-Atmosphere Data Set) over the oceans, drifting ice station of Russian NP (North Pole), and buoys of IABP (International Arctic Buoy Programme). The last two are crucial for improving the representation of the in-situ observed temperatures within the Arctic. The newly reconstructed dataset includes monthly Arctic SAT beginning in 1979 and daily Arctic SAT beginning in 2011. This dataset would represent a new improvement in developing observational temperature datasets and can be used for a variety of applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Universal scaling of weak localization in graphene due to bias-induced dispersion decoherence

The differential conductance of graphene is shown to exhibit a zero-bias anomaly at low temperatures, arising from a suppression of the quantum corrections due to weak localization and electron interactions. A simple rescaling of these data, free of any adjustable parameters, shows that this anomaly exhibits a universal, temperature- (T) independent form. According to this, the differential conductance is approximately constant at small voltages (V < kBT/e), while at larger voltages it increases logarithmically with the applied bias. For theoretical insight into the origins of this behaviour, which is inconsistent with electron heating, we formulate a model for weak-localization in the presence of nonequilibrium transport. According to this model, the applied voltage causes unavoidable dispersion decoherence, which arises as diffusing electron partial waves, with a spread of energies defined by the value of the applied voltage, gradually decohere with one another as they diffuse through the system. The decoherence yields a universal scaling of the conductance as a function of eV/kBT, with a logarithmic variation for eV/kBT > 1, variations in accordance with the results of experiment. Our theoretical description of nonequilibrium transport in the presence of this source of decoherence exhibits strong similarities with the results of experiment, including the aforementioned rescaling of the conductance and its logarithmic variation as a function of the applied voltage.

42 ENGINEERING↗
DOE OSTI2022

Spin-polarized imaging of the antiferromagnetic structure and field-tunable bound states in kagome magnet FeSn

Abstract Kagome metals are an exciting playground for the explorations of novel phenomena at the intersection of topology, electron correlations and magnetism. The family of FeSn-based kagome magnets in particular attracted a lot of attention for simplicity of the layered crystal structure and tunable topological electronic band structure. Despite a significant progress in understanding their bulk properties, surface electronic and magnetic structures are yet to be fully explored in many of these systems. In this work, we focus on a prototypical kagome metal FeSn. Using a combination of spin-averaged and spin-polarized scanning tunneling microscopy, we provide the first atomic-scale visualization of the layered antiferromagnetic structure at the surface of FeSn. In contrast to the field-tunable electronic structure of cousin material Fe 3 Sn 2 that is a ferromagnet, we find that electronic density-of-states of FeSn is robust to the application of external magnetic field. Interestingly, despite the field insensitive electronic band structure, FeSn exhibits bound states tied to specific impurities with large effective moments that strongly couple to the magnetic field. Our experiments provide microscopic insights necessary for theoretical modeling of FeSn and serve as a spring board for spin-polarized measurements of topological magnets in general.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Domain-wall magnetoelectric coupling in multiferroic hexagonal YbFeO 3 films

Electrical modulation of magnetic states in single-phase multiferroic materials, using domain-wall magnetoelectric (ME) coupling, can be enhanced substantially by controlling the population density of the ferroelectric (FE) domain walls during polarization switching. In this work, we investigate the domain-wall ME coupling in multiferroic h-YbFeO 3 thin films, in which the FE domain walls induce clamped antiferromagnetic (AFM) domain walls with reduced magnetization magnitude. Simulation according to the phenomenological theory indicates that the domain-wall ME effect is dramatically enhanced when the separation between the FE domain walls shrinks below the characteristic width of the clamped AFM domain walls during the ferroelectric switching. Experimentally, we show that while the magnetization magnitude remains same for both the positive and the negative saturation polarization states, there is evidence of magnetization reduction at the coercive voltages. These results suggest that the domain-wall ME effect is viable for electrical control of magnetization.

42 ENGINEERING↗
DOE OSTI2024

Structural basis of divergent substrate recognition and inhibition of human neurolysin

A zinc metallopeptidase neurolysin (Nln) processes diverse bioactive peptides to regulate signaling in the mammalian nervous system. To understand how Nln interacts with various peptides with dissimilar sequences, we determined crystal structures of Nln in complex with diverse peptides including dynorphins, angiotensin, neurotensin, and bradykinin. The structures show that Nln binds these peptides in a large dumbbell-shaped interior cavity constricted at the active site, making minimal structural changes to accommodate different peptide sequences. The structures also show that Nln readily binds similar peptides with distinct registers, which can determine whether the peptide serves as a substrate or a competitive inhibitor. We analyzed the activities and binding of Nln toward various forms of dynorphin A peptides, which highlights the promiscuous nature of peptide binding and shows how dynorphin A (1–13) potently inhibits the Nln activity while dynorphin A (1–8) is efficiently cleaved. Our work provides insights into the broad substrate specificity of Nln and may aid in the future design of small molecule modulators for Nln.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Significant contributions of trimethylamine to sulfuric acid nucleation in polluted environments

Abstract As one of the least understood aerosol processes, nucleation can be a dominant source of atmospheric aerosols. Sulfuric acid (SA)-amine binary nucleation with dimethylamine (DMA) has been recognized as a governing mechanism in the polluted continental boundary layer. Here we demonstrate the importance of trimethylamine (TMA) for nucleation in the complex atmosphere and propose a molecular-level SA-DMA-TMA ternary nucleation mechanism as an improvement upon the conventional binary mechanism. Using the proposed mechanism, we could connect the gaseous amines to the SA-amine cluster signals measured in the atmosphere of urban Beijing. Results show that TMA can accelerate the SA-DMA-based new particle formation in Beijing by 50–100%. Considering the global abundance of TMA and DMA, our findings imply comparable importance of TMA and DMA to nucleation in the polluted continental boundary layer, with probably higher contributions from TMA in polluted rural environments and future urban environments with controlled DMA emissions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Sustainable layered cathode with suppressed phase transition for long-life sodium-ion batteries

Sodium-ion batteries are among the most promising alternatives to lithium-based technologies for grid and other energy storage applications due to their cost benefits and sustainable resource supply. For the cathode—the component that largely determines the energy density of a sodium-ion battery cell—one major category of materials is P2-type layered oxides. Unfortunately, at high state-of-charge, such materials tend to undergo a phase transition with a very large volume change and consequent structural degradation during long-term cycling. Here we address this issue by introducing vacancies into the transition metal layer of P2-Na$_{0.7}$Fe$_{0.1}$Mn$_{0.75\square}$$_{0.15}$O2 (‘$_{\square}$’ represents a vacancy). The transition metal vacancy serves to suppress migration of neighbouring Na ions and therefore maintain structural and thermal stability in Na-depleted states. Moreover, the specific Na-O-$_{\square}$ configuration triggers a reversible anionic redox reaction and boosts the energy density. As a result, the cathode design here enables pouch cells with energy densities of 170 Wh kg -1 and 120 Wh kg -1 that can operate for over 600 and 1,000 cycles, respectively. In conclusion, our work not only suggests a feasible strategy for cathode design but also confirms the possibility of developing a battery chemistry that features a reduced need for critical raw materials.

25 ENERGY STORAGE↗
DOE OSTI2022

Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production

Abstract Despite advances in understanding the metabolism of Pseudomonas putida KT2440, a promising bacterial host for producing valuable chemicals from plant-derived feedstocks, a strain capable of producing free fatty acid-derived chemicals has not been developed. Guided by functional genomics, we engineered P. putida to produce medium- and long-chain free fatty acids (FFAs) to titers of up to 670 mg/L. Additionally, by taking advantage of the varying substrate preferences of paralogous native fatty acyl-CoA ligases, we employed a strategy to control FFA chain length that resulted in a P. putida strain specialized in producing medium-chain FFAs. Finally, we demonstrate the production of oleochemicals in these strains by synthesizing medium-chain fatty acid methyl esters, compounds useful as biodiesel blending agents, in various media including sorghum hydrolysate at titers greater than 300 mg/L. This work paves the road to produce high-value oleochemicals and biofuels from cheap feedstocks, such as plant biomass, using this host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Low-temperature magnetic crossover in the topological kagome magnet TbMn 6 Sn 6

Magnetic topological phases of quantum matter are an emerging frontier in physics and materials science, of which kagome magnets appear as a highly promising platform. Here, we explore magnetic correlations in the recently identified topological kagome system TbMn6 S n 6 using muon spin rotation, combined with local field analysis and neutron diffraction. Our studies identify an out-of-plane ferrimagnetic structure with slow magnetic fluctuations which exhibit a critical slowing down below $T^{*}_{C1}$ ≃ 120 K and finally freeze into static patches with ideal out-of-plane order below T C1 ≃ 20 K. We further show that hydrostatic pressure of 2.1 GPa stabilises the static out-of-plane topological ferrimagnetic ground state in the whole volume of the sample. Therefore the exciting perspective arises of a magnetically-induced topological system whose magnetism can be controlled through external parameters. The present results will stimulate theoretical investigations to obtain a microscopic understanding of the relation between the low-temperature volume-wise magnetic evolution of the static c-axis ferrimagnetic patches and the topological electronic properties in TbMn 6 Sn 6 .

36 MATERIALS SCIENCE↗
DOE OSTI2024

Discovery of charge order above room-temperature in the prototypical kagome superconductor La(Ru1−xFex)3Si2

Abstract The kagome lattice is an intriguing and rich platform for discovering, tuning and understanding the diverse phases of quantum matter, crucial for advancing modern and future electronics. Despite considerable efforts, accessing correlated phases at room temperature has been challenging. Using single-crystal X-ray diffraction, we discovered charge order above room temperature in La(Ru 1−x Fe x ) 3 Si 2 (x= 0, 0.01, 0.05), where charge order related to out-of-plane Ru atom displacements appears belowT CO,I ≃ 400 K. The secondary charge ordered phase emerges belowT CO,II ≃ 80–170 K. Furthermore, first principles calculations reveal both the kagome flat band and the van Hove point near the Fermi energy in LaRu 3 Si 2 , driven by Ru-dz 2 orbitals. Our results identify LaRu 3 Si 2 as the kagome superconductor with the highest known charge ordering temperature, offering a promising avenue for researching room temperature quantum phases and developing related technologies.

Physics↗
DOE OSTI2021

Probing topological quantum matter with scanning tunnelling microscopy

The search for topological phases of matter is evolving towards strongly interacting systems, including magnets and superconductors, where exotic effects emerge from the quantum-level interplay between geometry, correlation and topology. Over the past decade or so, scanning tunnelling microscopy has become a powerful tool to probe and discover emergent topological matter, because of its unprecedented spatial resolution, high-precision electronic detection and magnetic tunability. Scanning tunnelling microscopy can be used to probe various topological phenomena, as well as complement results from other techniques. We discuss some of these proof-of-principle methodologies applied to probe topology, with particular attention to studies performed under a tunable vector magnetic field, which is a relatively new direction of recent focus. Finally, we then project the future possibilities for atomic-resolution tunnelling methods in providing new insights into topological matter.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

AtomAI framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy

Over the past several decades, electron and scanning probe microscopes have become critical components of condensed matter physics, materials science and chemistry research. At the same time, the infrastructure for establishing a connection between microscopy observations and materials behaviour over a broader parameter space is lacking. In this work, we introduce AtomAI, an open-source software package bridging instrument-specific Python libraries, deep learning and simulation tools into a single ecosystem. AtomAI allows direct applications of deep neural networks for atomic and mesoscopic image segmentation converting image and spectroscopy data into class-based local descriptors for downstream tasks such as statistical and graph analysis. For atomically resolved imaging data, the output is types and positions of atomic species, with an option for subsequent refinement. AtomAI further allows the implementation of a broad range of image and spectrum analysis functions, including invariant variational autoencoders for disentangling structural factors of variation and im2spec type of encoder–decoder models for mapping structure–property relationships. Finally, our framework allows seamless connection to the first principles modelling with a Python interface on the inferred atomic positions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Imaging real-space flat band localization in kagome magnet FeSn

Kagome lattices host flat bands due to their frustrated lattice geometry, which leads to destructive quantum interference of electron wave functions. Here, we report imaging of the kagome flat band localization in real-space using scanning tunneling microscopy. We identify both the Fe 3 Sn kagome lattice layer and the Sn 2 honeycomb layer with atomic resolution in kagome antiferromagnet FeSn. On the Fe 3 Sn lattice, at the flat band energy determined by the angle resolved photoemission spectroscopy, tunneling spectroscopy detects an unusual state localized uniquely at the Fe kagome lattice network. We further show that the vectorial in-plane magnetic field manipulates the spatial anisotropy of the localization state within each kagome unit cell. Our results are consistent with the real-space flat band localization in the magnetic kagome lattice. We further discuss the magnetic tuning of flat band localization under the spin–orbit coupled magnetic kagome lattice model.

36 MATERIALS SCIENCE↗