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At least 1,243 records · Page 69
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Conformational spread drives the evolution of the calcium–calmodulin protein kinase II

The calcium calmodulin (Ca 2+ /CaM) dependent protein kinase II (CaMKII) decodes Ca 2+ frequency oscillations. The CaMKIIα isoform is predominantly expressed in the brain and has a central role in learning. I matched residue and organismal evolution with collective motions deduced from the atomic structure of the human CaMKIIα holoenzyme to learn how its ring architecture abets function. Protein dynamic simulations showed its peripheral kinase domains (KDs) are conformationally coupled via lateral spread along the central hub. The underlying β-sheet motions in the hub or association domain (AD) were deconvolved into dynamic couplings based on mutual information. They mapped onto a coevolved residue network to partition the AD into two distinct sectors. A second, energetically stressed sector was added to ancient bacterial enzyme dimers for assembly of the ringed hub. The continued evolution of the holoenzyme after AD–KD fusion targeted the sector’s ring contacts coupled to the KD. Among isoforms, the α isoform emerged last and, it alone, mutated rapidly after the poikilotherm–homeotherm jump to match the evolution of memory. The correlation between dynamics and evolution of the CaMKII AD argues single residue substitutions fine-tune hub conformational spread. The fine-tuning could increase CaMKIIα Ca 2+ frequency response range for complex learning functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Octahedral oxide glass network in ambient pressure neodymium titanate

Abstract Rare-earth titanates form very fragile liquids that can be made into glasses with useful optical properties. We investigate the atomic structure of 83TiO 2 -17Nd 2 O 3 glass using pair distribution function (PDF) analysis of X-ray and neutron diffraction with double isotope substitutions for both Ti and Nd. Six total structure factors are analyzed (5 neutron + 1 X-ray) to obtain complementary sensitivities to O and Ti/Nd scattering, and an empirical potential structure refinement (EPSR) provides a structural model consistent with the experimental measurements. Glass density is estimated as 4.72(13) g cm −3 , consistent with direct measurements. The EPSR model indicates nearest neighbor interactions for Ti-O at $$\overline{r}_{TiO}$$ r ¯ TiO = 1.984(11) Å with coordination of $$n_{TiO}$$ n TiO = 5.72(6) and for Nd-O at $$\overline{r}_{NdO}$$ r ¯ NdO = 2.598(22) Å with coordination of $$n_{NdO}$$ n NdO = 7.70(26), in reasonable agreement with neutron first order difference functions for Ti and Nd. The titanate glass network comprises a mixture of distorted Ti-O 5 and Ti-O 6 polyhedra connected via 71% corner-sharing and 23% edge-sharing. The O-Ti coordination environments include 15% nonbridging O-Ti 1 , 51% bridging O-Ti 2 , and 32% tricluster O-Ti 3 . This structure is highly unusual for oxide glasses melt-quenched at ambient pressure, as it consists of Ti-O x predominantly in octahedral (with nearly no tetrahedral) coordination.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Automatic parameter selection for electron ptychography via Bayesian optimization

Abstract Electron ptychography provides new opportunities to resolve atomic structures with deep sub-angstrom spatial resolution and to study electron-beam sensitive materials with high dose efficiency. In practice, obtaining accurate ptychography images requires simultaneously optimizing multiple parameters that are often selected based on trial-and-error, resulting in low-throughput experiments and preventing wider adoption. Here, we develop an automatic parameter selection framework to circumvent this problem using Bayesian optimization with Gaussian processes. With minimal prior knowledge, the workflow efficiently produces ptychographic reconstructions that are superior to those processed by experienced experts. The method also facilitates better experimental designs by exploring optimized experimental parameters from simulated data.

42 ENGINEERING↗
DOE OSTI2016

Magnetic Ordering in Sr 3 YCo 4 O 10+x

Transition-metal oxides often exhibit complex magnetic behavior due to the strong interplay between atomic-structure, electronic and magnetic degrees of freedom. Cobaltates, especially, exhibit complex behavior because of cobalt’s ability to adopt various valence and spin state configurations. The case of the oxygen-deficient perovskite Sr 3 YCo 4 O 10+x (SYCO) has gained considerable attention because of persisting uncertainties about its structure and the origin of the observed room temperature ferromagnetism. Here we report a combined investigation of SYCO using aberration-corrected scanning transmission electron microscopy and density functional theory calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Unsupervised data mining in nanoscale x-ray spectro-microscopic study of NdFeB magnet

Novel developments in X-ray based spectro-microscopic characterization techniques have increased the rate of acquisition of spatially resolved spectroscopic data by several orders of magnitude over what was possible a few years ago. This accelerated data acquisition, with high spatial resolution at nanoscale and sensitivity to subtle differences in chemistry and atomic structure, provides a unique opportunity to investigate hierarchically complex and structurally heterogeneous systems found in functional devices and materials systems. However, handling and analyzing the large volume data generated poses significant challenges. Here we apply an unsupervised data-mining algorithm known as DBSCAN to study a rare-earth element based permanent magnet material, Nd 2 Fe 14 B. We are able to reduce a large spectro-microscopic dataset of over 300,000 spectra to 3, preserving much of the underlying information. Scientists can easily and quickly analyze in detail three characteristic spectra. Our approach can rapidly provide a concise representation of a large and complex dataset to materials scientists and chemists. For instance, it shows that the surface of common Nd 2 Fe 14 B magnet is chemically and structurally very different from the bulk, suggesting a possible surface alteration effect possibly due to the corrosion, which could affect the material’s overall properties.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Precision controlled atomic resolution scanning transmission electron microscopy using spiral scan pathways

Atomic-resolution imaging in an aberration-corrected scanning transmission electron microscope (STEM) can enable direct correlation between atomic structure and materials functionality. The fast and precise control of the STEM probe is, however, challenging because the true beam location deviates from the assigned location depending on the properties of the deflectors. To reduce these deviations, i.e. image distortions, we use spiral scanning paths, allowing precise control of a sub-Å sized electron probe within an aberration-corrected STEM. Although spiral scanning avoids the sudden changes in the beam location (fly-back distortion) present in conventional raster scans, it is not distortion-free. “Archimedean” spirals, with a constant angular frequency within each scan, are used to determine the characteristic response at different frequencies. We then show that such characteristic functions can be used to correct image distortions present in more complicated constant linear velocity spirals, where the frequency varies within each scan. Through the combined application of constant linear velocity scanning and beam path corrections, spiral scan images are shown to exhibit less scan distortion than conventional raster scan images. The methodology presented here will be useful for in situ STEM imaging at higher temporal resolution and for imaging beam sensitive materials.

47 OTHER INSTRUMENTATION↗
DOE OSTI2017

Towards identifying the active sites on RuO 2 (110) in catalyzing oxygen evolution

While the surface atomic structure of RuO 2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO 2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) were used to determine the surface structural changes on single-crystal RuO2(110) as a function of potential in acidic electrolyte. The redox peaks at 0.7, 1.1 and 1.4 V vs. reversible hydrogen electrode (RHE) could be attributed to surface transitions associated with the successive deprotonation of –H 2 O on the coordinatively unsaturated Ru sites (CUS) and hydrogen adsorbed to the bridging oxygen sites. At potentials relevant to the oxygen evolution reaction (OER), an –OO species on the Ru CUS sites was detected, which was stabilized by a neighboring –OH group on the Ru CUS or bridge site. Combining potential-dependent surface structures with their energetics from DFT led to a new OER pathway, where the deprotonation of the –OH group used to stabilize –OO was found to be rate-limiting.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Valence-to-core X-ray emission spectroscopy of vanadium oxide and lithiated vanadyl phosphate materials

In this work, we report valence-to-core (VTC) X-ray emission spectroscopy (XES) measurements and theoretical calculations of the electrochemical sequence ε-VOPO 4 , ε-LiVOPO 4 , ε-Li 2 VOPO 4 and the reference oxides V 2 O 3 , VO 2 , and V 2 O 5 . In our analysis of these results, we establish a framework for interrogating chemical bonding that is generally applicable to a wide range of systems, including complex, extended inorganic compounds. While this latter regime has garnered less focused application than, e.g. , metalloenzymes in many excellent catalysis studies, we show that the technique provides high utility in materials-focused energy storage research. Here, sensitivities to the local atomic structure and hybridization schemes are discussed in detail. Similarly, the effect of lithiation on oxidation, delocalization, and shifts in ligand valence energy levels are all readily apparent in the analyzed results. Finally, the TDDFT projections clearly reveal the directional dependencies of the valence band at each of the vanadium sites. Our results demonstrate laboratory-based X-ray spectroscopy instrumentation is a viable route for attaining well-resolved VTC-XES features for inorganic compounds of 3d transition metals, even for samples of limited quantity or suffering from sensitivity to the atmosphere. The experimental results are in good agreement with results produced by real-space Green's function and time-dependent density functional theory (TDDFT) methods, respectively. Hence, we propose that VTC-XES, when equipped with appropriate theoretical support, can be a valuable complement to X-ray absorption pre-edge features for more detailed characterization of a compound's electronic structure. We expect similar analyses will find application in a broad range of materials chemistry research and provide both fundamental and applied insights.

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

Nanopore facilitated monohydrocalcitic amorphous calcium carbonate precipitation

Predicting the precipitation of solids is important in both natural systems and subsurface energy applications. The factors controlling reaction mechanisms, phase selection and conversion between phases are particularly important. In this contribution the precipitation and growth of an amorphous calcium carbonate species from flowing aqueous solution in a nanoporous controlled pore glass is followed in situ with differential X-ray pair distribution function analysis. It is discovered that the local atomic structure of this phase indicates monohydrocalcite-like pair–pair correlations, yet is functionally amorphous because it lacks long-range structure. The unexpected occurrence of synthetic proto-monohydrocalcite amorphous calcium carbonate, precipitated from a solution undersaturated with respect to published solubilities, suggests that nanopore confinement facilitates formation of an amorphous phase at the expense of more favorable crystalline ones. Finally, this result illustrates that confinement and interface effects are physical factors exerting control on mineral nucleation behavior in natural and geological systems.

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

Determination of the vacancy distribution over Al cation sites in γ-Al 2 O 3

Although gamma-alumina (γ-Al 2 O 3 ) is an extensively used material with wide-ranging applications due to its inherently high surface area and acidity, its atomic structure is still not fully understood. γ-Al 2 O 3 is described as having a spinel-like structure, where the O sublattice has a face-centered cubic (FCC) arrangement and Al cations are placed in the spinel tetrahedral and octahedral interstitial sites. Achieving the correct stoichiometry of Al 2 O 3 , however, requires the introduction of Al vacancies into some of the interstitial sites. Despite the importance of accurately describing the structure of γ-Al 2 O 3 , the distribution of vacancies between tetrahedral and octahedral sites remains unclear, in part because of the usually poor crystalline quality of γ-Al 2 O 3 that has often been used in previous studies. To determine the actual cation distribution in γ-Al 2 O 3 , single-crystalline γ-Al 2 O 3 was investigated using a correlative approach of experimental and simulated selected-area electron diffraction (SAED) and high-resolution electron energy-loss spectroscopy (EELS). Comparison of the reflection intensities in single-crystal SAED to simulated SAED from models with varied vacancy distributions revealed that vacancies exist primarily on tetrahedral sites, contrary to the placement of vacancies on octahedral sites proposed in several common models. Comparison of EELS spectra—acquired with the highest energy resolution reported so far for γ-Al 2 O 3 —with ab initio multiple scattering EELS simulations confirmed the distribution of vacancies on tetrahedral sites. These results enable more accurate modeling of γ-Al 2 O 3 to better predict its properties in existing and future applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Reinforcement learning-based design of shape-changing metamaterials

During the last decade, artificially architected materials have been designed to obtain properties unreachable by naturally occurring materials, whose properties are determined by their atomic structure and chemical composition. In this work, we implement a new reinforcement learning (RL) method able to rationally design unique metamaterial structures at the nano-, micro-, and macroscale, which change shape during operational conditions. As an example, we apply this method to design nanostructured silicon anodes for Li-ion batteries (LIBs). The RL model is designed to apply different actions and predict change during operational conditions. The multi-component reward function comprises an increase in the total storage capacity of the resulting battery electrode and structural parameters, such as the minimum distance between the individual components of the nanostructure. Upon experimental validation using a polymer-based 3D printing technique, we expect that the newly discovered structures improve the current Si-based LIB anodes state-of-the-art by almost three times and almost ten times the current commercial LIB based on a graphitic anode. Furthermore, this RL-based optimization method opens up vast design space for other responsive metamaterials with tailored properties and pre-programmed structural transformation.

25 ENERGY STORAGE↗
DOE OSTI2012

Agglomeration defects on irradiated carbon nanotubes

Aligned carbon nanotubes (CNT) were irradiated in the longitudinal and perpendicular directions, with low energy carbon and helium ions in order to observe the formation of defects in the atomic structure. Analysis through Raman spectroscopy and scanning electron microscopy indicated bundle rupture and ion track formation on nanotube bundles. Aligned CNT presented a kind of defect comprising ravine formation and tube agglomeration on top of the substrate. The latter structure is possibly caused by static charge accumulation induced by the incoming ions. Fluence plays a role on the short range order. Higher fluence irradiation transforms CNT into amorphous carbon nanowires.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Plasma screening effects on the energies of hydrogen atom

A more general exponential cosine screened Coulomb potential is used for the first time to investigate the screening effects on the hydrogen atom in plasmas. This potential is examined for four different cases that correspond to four different type potentials when the different parameters are used in the potential within the framework of the well-known asymptotic iteration method. By solving the corresponding the radial Schroedinger equation with the screened and exponential cosine screened Coulomb potentials and comparing the obtained energy eigenvalues with the results of other studies, the applicability of the method to this kind of plasma physics problem is shown. The energy values of more general exponential cosine screened Coulomb potential are presented for various parameters in the potential. One of the advantages of the present potential is that it exhibits stronger screening effect than that of the exponential cosine screened Coulomb potential and it is also reduced to screened Coulomb and exponential cosine screened Coulomb as well as Coulomb potentials for special values of parameters. The parameters in the potential would be useful to model screening effects which cause an increase or decrease in the energy values of hydrogen atom in both Debye and quantum plasmas and in this manner this potential would be useful for the investigations of the atomic structure and collisions in plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Incoherent twin boundary migration induced by ion irradiation in Cu

Grain boundaries can act as sinks for radiation-induced point defects. The sink capability is dependent on the atomic structures and varies with the type of point defects. Using high-resolution transmission electron microscopy, we observed that {Sigma}3{l_brace}112{r_brace} incoherent twin boundary (ITB) in Cu films migrates under Cu{sup 3+} ion irradiation. Using atomistic modeling, we found that {Sigma}3{l_brace}112{r_brace} ITB has the preferred sites for adsorbing interstitials and the preferential diffusion channels along the Shockley partial dislocations. Coupling with the high mobility of grain boundary Shockley dislocations within {Sigma}3{l_brace}112{r_brace} ITB, we infer that {Sigma}3{l_brace}112{r_brace} ITB migrates through the collective glide of grain boundary Shockley dislocations, driven by a concurrent reduction in the density of radiation-induced defects, which is demonstrated by the distribution of nearby radiation-induced defects.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Domain formation due to surface steps in topological insulator Bi{sub 2}Te{sub 3} thin films grown on Si (111) by molecular beam epitaxy

The atomic structure of topological insulators Bi{sub 2}Te{sub 3} thin films on Si (111) substrates grown in van der Waals mode by molecular beam epitaxy has been investigated by in situ scanning tunneling microscopy and scanning transmission electron microscopy. Besides single and multiple quintuple layer (QL) steps, which are typical for the step-flow mode of growth, a number of 0.4 QL steps is observed. We determine that these steps originate from single steps at the substrate surface causing domain boundaries in the Bi{sub 2}Te{sub 3} film. Due to the peculiar structure of these domain boundaries the domains are stable and penetrate throughout the entire film.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Laser wakefield generated X-ray probe for femtosecond time-resolved measurements of ionization states of warm dense aluminum

We have developed a laser wakefield generated X-ray probe to directly measure the temporal evolution of the ionization states in warm dense aluminum by means of absorption spectroscopy. As a promising alternative to the free electron excited X-ray sources, Betatron X-ray radiation, with femtosecond pulse duration, provides a new technique to diagnose femtosecond to picosecond transitions in the atomic structure. The X-ray probe system consists of an adjustable Kirkpatrick-Baez (KB) microscope for focusing the Betatron emission to a small probe spot on the sample being measured, and a flat Potassium Acid Phthalate Bragg crystal spectrometer to measure the transmitted X-ray spectrum in the region of the aluminum K-edge absorption lines. An X-ray focal spot size of around 50 μm was achieved after reflection from the platinum-coated 10-cm-long KB microscope mirrors. Shot to shot positioning stability of the Betatron radiation was measured resulting in an rms shot to shot variation in spatial pointing on the sample of 16 μm. The entire probe setup had a spectral resolution of ∼1.5 eV, a detection bandwidth of ∼24 eV, and an overall photon throughput efficiency of the order of 10{sup −5}. Approximately 10 photons were detected by the X-ray CCD per laser shot within the spectrally resolved detection band. Thus, it is expected that hundreds of shots will be required per absorption spectrum to clearly observe the K-shell absorption features expected from the ionization states of the warm dense aluminum.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Monte Carlo study for optimal conditions in single-shot imaging with femtosecond x-ray laser pulses

Intense x-ray pulses from x-ray free electron lasers (XFELs) enable the unveiling of atomic structure in material and biological specimens via ultrafast single-shot exposures. As the radiation is intense enough to destroy the sample, a new sample must be provided for each x-ray pulse. These single-particle delivery schemes require careful optimization, though systematic study to find such optimal conditions is still lacking. We have investigated two major single-particle delivery methods: particle injection as flying objects and membrane-mount as fixed targets. The optimal experimental parameters were searched for via Monte Carlo simulations to discover that the maximum single-particle hit rate achievable is close to 40%.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗