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At least 1,747 records · Page 97

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DOE OSTI2017

Optimizing disk registration algorithms for nanobeam electron diffraction strain mapping

Scanning nanobeam electron diffraction strain mapping is a technique by which the positions of diffracted disks sampled at the nanoscale over a crystalline sample can be used to reconstruct a strain map over a large area. However, it is important that the disk positions are measured accurately, as their positions relative to a reference are directly used to calculate strain. Here in this study, we compare several correlation methods using both simulated and experimental data in order to directly probe susceptibility to measurement error due to non-uniform diffracted disk illumination structure. We found that prefiltering the diffraction patterns with a Sobel filter before performing cross correlation or performing a square-root magnitude weighted phase correlation returned the best results when inner disk structure was present. Lastly, we have tested these methods both on simulated datasets, and experimental data from unstrained silicon as well as a twin grain boundary in 304 stainless steel.

36 MATERIALS SCIENCE↗

DOE OSTI2023

High-Precision Calculation of Nanoparticle (Nanocrystal) Potentials of Mean Force and Internal Energies

Thermodynamic stability assessment of nanocrystal systems requires precise free energy calculations. This study highlights the importance of meticulous control over various factors, including the thermostat, time step, potential cutoff, initial configuration, sampling method, and overall simulation duration. Free energy computations in dry (solvent-free) systems are on the order of several hundred $k_BT$ but can be obtained with consistent accuracy. However, calculation of internal energies becomes challenging, as they are typically much larger in magnitude than free energies and exhibit significant noise and reduced reliability. To address this limitation, we propose a new internal energy estimate that drastically reduces the noise. Here, we also present formulas that enable the optimization of the parameters of the harmonic bias potential for optimal convergence. Finally, we discuss the implications of these findings for the computation of free energies in nanocrystal clusters and superlattices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Conformational Equilibria of Multimodal Chromatography Ligands in Water and Bound to Protein Surfaces

Multimodal chromatography uses small ligands with multiple modes of interaction, e.g., charged, hydrophobic or hydrogen bonding, to separate proteins from complex mixtures. The mechanism by which multimodal ligands interact with proteins is expected to be affected by ligand conformations, among other factors. In this report, we determine conformational equilibria of two commercially used multimodal cation exchange ligands, Capto MMC and Nuvia cPrime, in a range of solvents, a Lennard-Jones (LJ) liquid, ethanol, and water, using molecular dynamics (MD) simulations. By mapping ligand conformations onto two key torsion angles, ω and φ, in these solvents and in low and high dielectric media, we quantify the relative importance of intramolecular and solvent-mediated interactions. In a high dielectric medium, Capto MMC preferentially samples three conformations, which are stabilized by a combination of an intramolecular torsion potential (on ω) and LJ interactions. In an LJ liquid, solvent molecules compete with intramolecular interactions while simultaneously providing an osmotic force, stabilizing both closer and farther distances between ligand sites. This has the overall result of “flattening out” the conformational landscape. Interestingly, in ethanol and water, hydrogen bonding among the amide hydrogen and solvent molecules stabilizes two additional conformations of Capto MMC in which ω takes on less favorable cis-like configurations. MD simulations of ligands in free solution with three therapeutic antibody fragments show that ligand conformational equilibria remain effectively unchanged upon binding to proteins. Although, there is 20–30% dehydration of the overall ligand upon binding, the hydrogen-bonding sites are dehydrated to a much smaller extent, particularly in cis-like configurations. Conformational preferences of Nuvia cPrime are similar to that of Capto MMC, except for the effect of symmetry arising from the absence of an alkyl thiol tail. Characterizing the conformational equilibria of these two ligands in free solution and bound to a protein provides a foundation for developing a mechanistic understanding of protein–multimodal ligand interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Effect of Interlayer Co 2+ on Structure and Charge Transfer in NiFe Layered Double Hydroxides

We present that the intercalation of Co in Ni/Fe layered double hydroxides (LDH) significantly improves the electrocatalytic performance of the LDH for the oxygen evolution reaction. The mechanism behind the improvement and the structure of the Co-intercalated LDHs, however, is not precisely known. We use classical molecular dynamics (CMD) to study the impact of intercalated Co on the structure of Ni/Fe LDH and the electron transfer process. CMD studies find that the Co ions form small clusters, pushing apart the surrounding hydroxide sheets to form small “pockets” around these clusters, disrupting the planar nature of the sheets in the absence of intercalated Co clusters. The structure of the “pockets” is a strong function of force field parameters and the accuracy of the LDH bulk modulus. Lastly, we use umbrella sampling to study electron transfer and show that the clusters of Co in the interlayer are important for electron transfer, such that solvent molecules have greater freedom to reorient with a change in charge state, thereby reducing the barrier to electron transfer.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Interactions of Oxide Surfaces with Water Revealed with Solid-State NMR Spectroscopy

Hydrous materials are ubiquitous in the natural environment and efforts have previously been made to investigate the structures and dynamics of hydrated surfaces for their key roles in various chemical and physical applications, with the help of theoretical modeling and microscopy techniques. However, an overall atomic-scale understanding of the water–solid interface, including the effect of water on surface ions, is still lacking. Herein, we employ ceria nanorods with different amounts of water as an example and demonstrate a new approach to explore the water–surface interactions by using solid-state NMR in combination with density functional theory. NMR shifts and relaxation time analysis provide detailed information on the local structure of oxygen ions and the nature of water motion on the surface: the amount of molecularly adsorbed water decreases rapidly with increasing temperature (from room temperature to 150 °C), whereas hydroxyl groups are stable up to 150 °C, and dynamic water molecules are found to instantaneously coordinate to the surface oxygen ions. Additionally, the applicability of dynamic nuclear polarization for selective detection of surface oxygen species is also compared to conventional NMR with surface selective isotopic-labeling: the optimal method depends on the feasibility of enrichment and the concentration of protons in the sample. These results provide new insight into the interfacial structure of hydrated oxide nanostructures, which is important to improve performance for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Spin-current probe for phase transition in an insulator

Spin fluctuation and transition have always been one of the central topics of magnetism and condensed matter science. Experimentally, the spin fluctuation is found transcribed onto scattering intensity in the neutron-scattering process, which is represented by dynamical magnetic susceptibility and maximized at phase transitions. Importantly, a neutron carries spin without electric charge, and therefore it can bring spin into a sample without being disturbed by electric energy. However, large facilities such as a nuclear reactor are necessary. Here we present that spin pumping, frequently used in nanoscale spintronic devices, provides a desktop microprobe for spin transition; spin current is a flux of spin without an electric charge and its transport reflects spin excitation. Additionally, we demonstrate detection of antiferromagnetic transition in ultra-thin CoO films via frequency-dependent spin-current transmission measurements, which provides a versatile probe for phase transition in an electric manner in minute devices.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Radial structure and formation of the Milky Way disc

The formation of the Galactic disc is an enthusiastically debated issue. Numerous studies and models seek to identify the dominant physical process(es) that shaped its observed properties; for example, satellite accretion, starburst, quenching, gas infall, and stellar radial migration. Taking advantage of the improved coverage of the inner Milky Way provided by the SDSS DR16 APOGEE catalogue and of the ages published in the APOGEE-AstroNN Value Added Catalogue (VAC), we examined the radial evolution of the chemical and age properties of the Galactic stellar disc with the aim of better constraining its formation. Using a sample of 199 307 giant stars with precise APOGEE abundances and APOGEE-AstroNN ages, selected in a ±2 kpc layer around the galactic plane, we assessed the dependency as a function of guiding radius of (i) the median metallicity, (ii) the ridge lines of the [Fe/H] – [Mg/Fe] and age–[Mg/Fe] distributions, and (iii) the age distribution function (ADF). The giant star sample allows us to probe the radial behaviour of the Galactic disc from R g = 0 to 14–16 kpc. The thick disc [Fe/H] – [Mg/Fe] ridge lines follow closely grouped parallel paths, supporting the idea that the thick disc did form from a well-mixed medium. However, the ridge lines present a small drift in [Mg/Fe], which decreases with increasing guiding radius. At sub-solar metallicity, the intermediate and outer thin disc [Fe/H] – [Mg/Fe] ridge lines follow parallel sequences shifted to lower metallicity as the guiding radius increases. We interpret this pattern as the signature of a dilution of the interstellar medium from R g ~ 6 kpc to the outskirts of the disc, which occurred before the onset of the thin disc formation. The APOGEE-AstroNN VAC provides stellar ages for statistically significant samples of thin disc stars from the Galactic centre up to R g ~ 14 kpc. An important result provided by this dataset is that the thin disc presents evidence of an inside-out formation up to R g ~ 10 – 12 kpc. Moreover, about ~7 Gyr ago, the [Mg/Fe] ratio in the outer thin disc (R g > 10 kpc) was higher by about ~0.03–0.05 dex than in the more internal regions of the thin disc. This could be the fossil record of a pollution of the outer disc gas reservoir by the thick disc during its starburst phase.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2014

The panchromatic Hubble Andromeda Treasury. VI. The reliability of far-ultraviolet flux as a star formation tracer on subkiloparsec scales

We have used optical observations of resolved stars from the Panchromatic Hubble Andromeda Treasury to measure the recent (<500 Myr) star formation histories (SFHs) of 33 far-UV (FUV)-bright regions in M31. The region areas ranged from ∼10{sup 4} to 10{sup 6} pc{sup 2}, which allowed us to test the reliability of FUV flux as a tracer of recent star formation on subkiloparsec scales. The star formation rates (SFRs) derived from the extinction-corrected observed FUV fluxes were, on average, consistent with the 100 Myr mean SFRs of the SFHs to within the 1σ scatter. Overall, the scatter was larger than the uncertainties in the SFRs and particularly evident among the smallest regions. The scatter was consistent with an even combination of discrete sampling of the initial mass function and high variability in the SFHs. This result demonstrates the importance of satisfying both the full-IMF and the constant-SFR assumptions for obtaining precise SFR estimates from FUV flux. Assuming a robust FUV extinction correction, we estimate that a factor of 2.5 uncertainty can be expected in FUV-based SFRs for regions smaller than 10{sup 5} pc{sup 2} or a few hundred parsecs. We also examined ages and masses derived from UV flux under the common assumption that the regions are simple stellar populations (SSPs). The SFHs showed that most of the regions are not SSPs, and the age and mass estimates were correspondingly discrepant from the SFHs. For those regions with SSP-like SFHs, we found mean discrepancies of 10 Myr in age and a factor of 3-4 in mass. It was not possible to distinguish the SSP-like regions from the others based on integrated FUV flux.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

Imaging of Vanadium in Microfossils: A New Potential Biosignature

Being able to distinguish unambiguously the biogenicity of microfossil-like structures in the ancient rock record is a fundamental predicament facing Archean paleobiologists and astrobiologists. Therefore, novel methods for discriminating biological from non-biological chemistries of microfossil-like structures are of the utmost importance in the search for evidence of early life on Earth. This too, is important for the search for life on Mars; either by in situ analyses via rovers, or sample return missions for future analysis here on Earth. Here, we report the application of synchrotron X-ray fluorescence imaging of vanadium, within thermally altered organic-walled microfossils of bona fide biological origin. From our data, we demonstrate that vanadium is present within microfossils of undisputable biological origin. It is well known in the organic geochemistry literature, that elements such as vanadium are enriched and contained within crude oils, asphalts, and black shales that have been formed by diagensis of biological organic material. It has been demonstrated that the origin of vanadium is due to the diagenetic alteration of precursor chlorophyll and heme porphyrin pigment compounds from living organisms. Here, we propose that taken together, microfossil-like morphology, carbonaceous composition, and the presence of vanadium could be used in tandem as a biosignature to ascertain the biogenecity of putative microfossil-like structures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Mars Extant Life: What's Next? Conference Report

On November 5–8, 2019, the ‘‘Mars Extant Life: What’s Next?’’ conference was convened in Carlsbad, New Mexico. The conference gathered a community of actively publishing experts in disciplines related to habitability and astrobiology. Primary conclusions are as follows: A significant subset of conference attendees concluded that there is a realistic possibility that Mars hosts indigenous microbial life. A powerful theme that permeated the conference is that the key to the search for martian extant life lies in identifying and exploring refugia (‘‘oases’’), where conditions are either permanently or episodically significantly more hospitable than average. Based on our existing knowledge of Mars, conference participants highlighted four potential martian refugium (not listed in priority order): Caves, Deep Subsurface, Ices, and Salts. The conference group did not attempt to reach a consensus prioritization of these candidate environments, but instead felt that a defensible prioritization would require a future competitive process. Within the context of these candidate environments, we identified a variety of geological search strategies that could narrow the search space. Additionally, we summarized a number of measurement techniques that could be used to detect evidence of extant life (if present). Again, it was not within the scope of the conference to prioritize these measurement techniques—that is best left for the competitive process. We specifically note that the number and sensitivity of detection methods that could be implemented if samples were returned to Earth greatly exceed the methodologies that could be used at Mars. Finally, important lessons to guide extant life search processes can be derived both from experiments carried out in terrestrial laboratories and analog field sites and from theoretical modeling.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Frequency shifts in the electron paramagnetic resonance spectrum of 39 K due to spin-exchange collisions with polarized 3 He and precise 3 He polarimetry

The Zeeman splittings and electron paramagnetic resonance frequencies of alkali-metal atoms are shifted in the presence of a polarized noble gas. For a spherical geometry, the shift is enhanced over what is expected classically by a dimensionless atomic parameter 𝜅 0 that is unique to each alkali-metal-atom–noble-gas pair. Here, we present a precise measurement of 𝜅 0 for the 39 K − 3 He system with a relative accuracy of better than 1%. A critical component of achieving subpercent accuracy involved characterizing the shape of our samples using both MRI and CT medical-imaging techniques. The parameter 𝜅 0 plays an important role in establishing the absolute polarization of 3 He in a variety of contexts, including polarized targets for electron-scattering experiments and MRI of the gas space of the lungs. Our measurement more than doubles the accuracy possible when using 𝜅 0 for polarimetry purposes. Just as important, the work presented here represents a direct measurement of 𝜅 0 for the 39 K − 3 He system; previous values for 𝜅 0 in the 39 K − 3 He system relied on a chain of measurements that were benchmarked by previous measurements of 𝜅 0 in the Rb- 3 He system.

Zeeman effect↗

DOE OSTI2016

Revisiting the ground state of CoAl 2 O 4 : Comparison to the conventional antiferromagnet MnAl 2 O 4

The A-site spinel material CoAl 2 O 4 is a physical realization of the frustrated diamond-lattice antiferromagnet, a model in which unique incommensurate or “spin-spiral-liquid” ground states are predicted. Our previous single-crystal neutron scattering study instead classified it as a “kinetically inhibited” antiferromagnet, where the long-ranged correlations of a collinear Néel ground state are blocked by the freezing of domain-wall motion below a first-order phase transition at T*=6.5 K. This study provides new data sets from a number of experiments, which support and expand this work in several important ways. We show that the phenomenology leading to the kinetically inhibited order is unaffected by sample measured and instrument resolution, while new low-temperature measurements reveal spin correlations are unchanging between T=2 K and 250 mK, consistent with a frozen state. Polarized diffuse neutron measurements show several interesting magnetic features, which can be entirely explained by the existence of short-ranged Néel order. Finally, and crucially, this paper presents some neutron scattering studies of single crystalline MnAl 2 O 4 , which acts as an unfrustrated analog to CoAl 2 O 4 and shows all the hallmarks of a classical antiferromagnet with a continuous phase transition to Néel order at T N =39 K. Direct comparison between the two compounds indicates that CoAl 2 O 4 is unique, not in the nature of high-temperature diffuse correlations, but rather in the nature of the frozen state below T*. Finally, the higher level of cation inversion in the MnAl 2 O 4 sample indicates that this behavior is primarily an effect of greater next-nearest-neighbor exchange.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Atomic structure of different surface terminations of polycrystalline ZnPd

The intermetallic compound ZnPd has been found to have desirable characteristics as a catalyst for the steam reforming of methanol. The understanding of the surface structure of ZnPd is important to optimize its catalytic behavior. However, due to the lack of bulk single-crystal samples and the complexity of characterizing surface properties in the available polycrystalline samples using common experimental techniques, all previous surface science studies of this compound have been performed on surface alloy samples formed through thin-film deposition. In this study, we present findings on the chemical and atomic structure of the surfaces of bulk polycrystalline ZnPd studied by a variety of complementary experimental techniques, including scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy (XPS), low energy electron microscopy (LEEM), photoemission electron microscopy (PEEM), and microspot low-energy electron diffraction ( μ -LEED). These experimental techniques, combined with density functional theory (DFT)-based thermodynamic calculations of surface free energy and detachment kinetics at the step edges, confirm that surfaces terminated by atomic layers composed of both Zn and Pd atoms are more stable than those terminated by only Zn or Pd layers. DFT calculations also demonstrate that the primary contribution to the tunneling current arises from Pd atoms, in agreement with the STM results. The formation of intermetallics at surfaces may contribute to the superior catalyst properties of ZnPd over Zn or Pd elemental counterparts. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗

DOE OSTI2016

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca 2+ -calmodulin

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+ -CaM, but no assignment of these features has been made. In addition, Ca 2+ -CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+ -CaM. Density-modified electron-density maps enabled the accurate assignment of Ca 2+ -CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+ -CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+ -CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+ -CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.

Lin, Jiusheng↗

DOE OSTI2019

ResStock™ [SWR-19-15 and SWR-20-07]

The ResStock™ analysis tool is helping states, municipalities, utilities, and manufacturers identify which home improvements save the most energy and money.With support from the U.S. Department of Energy (DOE), researchers at NREL developed ResStock. It's a versatile tool that takes a new approach to large-scale residential energy analysis by combining: - Large public and private data sources - Statistical sampling - Detailed subhourly building simulations - High-performance computing. - This combination achieves unprecedented granularity and most importantly—accuracy—in modeling the diversity of the single-family housing stock.

Horowitz, Scott↗

DOE OSTI2015

Modification of Helicobacter pylori peptidoglycan enhances NOD1 activation and promotes cancer of the stomach

Helicobacter pylori is the strongest known risk factor for gastric carcinogenesis. One cancer-linked locus is the cag pathogenicity island, which translocates components of peptidoglycan (PGN) into host cells. NOD1 is an intracellular immune receptor that senses PGN from Gram-negative bacteria and responds by inducing autophagy and activating NF-κB, leading to inflammation-mediated bacterial clearance; however chronic pathogens can evade NOD1-mediated clearance by altering PGN structure. We previously demonstrated that the H. pylori cag + strain 7.13 rapidly induces gastric cancer in Mongolian gerbils. Using 2D-DIGE and mass spectrometry, we identified a novel mutation within the gene encoding the peptidoglycan deacetylase PgdA; therefore, we sought to define the role of H. pylori PgdA in NOD1-dependent activation of NF-κB, inflammation, and cancer. Co-culture of H. pylori strain 7.13 or its pgdA $-$ isogenic mutant with AGS gastric epithelial cells or HEK293 epithelial cells expressing a NF-κB reporter revealed that pgdA inactivation significantly decreased NOD1-dependent NF-κB activation and autophagy. Infection of Mongolian gerbils with an H. pylori pgdA $-$ mutant strain led to significantly decreased levels of inflammation and malignant lesions in the stomach; however, pre-activation of NOD1 prior to bacterial challenge reciprocally suppressed inflammation and cancer in response to wild-type H. pylori . Expression of NOD1 differs in human gastric cancer specimens compared to non-cancer samples harvested from the same patients. In conclusion, these results indicate that PGN deacetylation plays an important role in modulating host inflammatory responses to H. pylori , allowing the bacteria to persist and induce carcinogenic consequences in the gastric niche.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data

High-dimensional mixed-effects models are an increasingly important form of regression in which the number of covariates rivals or exceeds the number of samples, which are collected in groups or clusters. The penalized likelihood approach to fitting these models relies on a coordinate descent algorithm that lacks guarantees of convergence to a global optimum. Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. Our simulations provide new insights into the algorithm’s behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. To empower researchers in biology and other fields to fit models with the SCAD penalty, we implement the algorithm in a Julia package, HighDimMixedModels.jl .

Gorstein, Evan↗

DOE OSTI2022

Modeling O and N Alloying in Nb for SRF Applications

N and O-alloyed superconducting radio frequency cavities exhibit extraordinary quality factors. Developing diffusion models that describe interstitial N and O in Nb is important for optimizing alloyed cavity quality factors and accelerating gradients. N and O-alloyed Nb samples are examined with SEM AND SIMS and their diffusion profiles modeled.

Lechner, Eric↗