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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

Abstract Artificial intelligence-based protein structure prediction methods such as AlphaFold have revolutionized structural biology. The accuracies of these predictions vary, however, and they do not take into account ligands, covalent modifications or other environmental factors. Here, we evaluate how well AlphaFold predictions can be expected to describe the structure of a protein by comparing predictions directly with experimental crystallographic maps. In many cases, AlphaFold predictions matched experimental maps remarkably closely. In other cases, even very high-confidence predictions differed from experimental maps on a global scale through distortion and domain orientation, and on a local scale in backbone and side-chain conformation. We suggest considering AlphaFold predictions as exceptionally useful hypotheses. We further suggest that it is important to consider the confidence in prediction when interpreting AlphaFold predictions and to carry out experimental structure determination to verify structural details, particularly those that involve interactions not included in the prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Experimental and theoretical evidence for hydrogen doping in polymer solution-processed indium gallium oxide

The field-effect electron mobility of aqueous solution-processed indium gallium oxide (IGO) thin-film transistors (TFTs) is significantly enhanced by polyvinyl alcohol (PVA) addition to the precursor solution, a >70-fold increase to 7.9 cm 2 /Vs. To understand the origin of this remarkable phenomenon, microstructure, electronic structure, and charge transport of IGO:PVA film are investigated by a battery of experimental and theoretical techniques, including In K-edge and Ga K-edge extended X-ray absorption fine structure (EXAFS); resonant soft X-ray scattering (R-SoXS); ultraviolet photoelectron spectroscopy (UPS); Fourier transform-infrared (FT-IR) spectroscopy; time-of-flight secondary-ion mass spectrometry (ToF-SIMS); composition-/processing-dependent TFT properties; high-resolution solid-state 1 H, 71 Ga, and 115 In NMR spectroscopy; and discrete Fourier transform (DFT) analysis with ab initio molecular dynamics (MD) liquid-quench simulations. The 71 Ga{ 1 H} rotational-echo double-resonance (REDOR) NMR and other data indicate that PVA achieves optimal H doping with a Ga···H distance of ~3.4 Å and conversion from six- to four-coordinate Ga, which together suppress deep trap defect localization. This reduces metal-oxide polyhedral distortion, thereby increasing the electron mobility. Finally, hydroxyl polymer doping thus offers a pathway for efficient H doping in green solvent-processed metal oxide films and the promise of high-performance, ultra-stable metal oxide semiconductor electronics with simple binary compositions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Echo state network for coarsening dynamics of charge density waves

An echo state network (ESN) is a type of reservoir computer that uses a recurrent neural network with a sparsely connected hidden layer. Compared with other recurrent neural networks, one great advantage of ESN is the simplicity of its training process. Yet, despite the seemingly restricted learnable parameters, ESN has been shown to successfully capture the spatial-temporal dynamics of complex patterns. Here we build an ESN to model the coarsening dynamics of charge-density waves (CDWs) in a semiclassical Holstein model, which exhibits a checkerboard electron density modulation at half-filling stabilized by a commensurate lattice distortion. The inputs to the ESN are local CDW order parameters in a finite neighborhood centered around a given site, while the output is the predicted CDW order of the center site at the next time step. Special care is taken in the design of couplings between hidden layer and input nodes to ensure lattice symmetries are properly incorporated into the ESN model. Since the model predictions depend only on CDW configurations of a finite domain, the ESN is scalable and transferrable in the sense that a model trained on dataset from a small system can be directly applied to dynamical simulations on larger lattices. Furthermore, our work opens avenues for efficient dynamical modeling of pattern formations in functional electron materials.

2-dimensional systems↗
DOE OSTI2024

Single-crystal X-ray diffraction on the structure of (Al,Fe)-bearing bridgmanite in the lower mantle

Abstract Here we have performed single-crystal X-ray diffraction (SCXRD) experiments on two high-quality crystal platelets of (Al,Fe)-bearing bridgmanite (Mg0.88Fe0.0653+Fe0.0352+Al0.03)(Al0.11Si0.90)O3 (Fe10-Al14-Bgm) up to 64.6(6) GPa at room temperature in a Boehler-Almax type diamond-anvil cell. Refinements on the collected SCXRD patterns reveal reliable structural information of single-crystal Fe10-Al14-Bgm, including unit-cell parameters, atomic coordinates, and anisotropic displacement parameters. Together with Mössbauer and electron microprobe analyses, our best single-crystal refinement model indicates that the sample contains ~6.5 mol% Fe3+, 3.5 mol% Fe2+, and 3 mol% Al3+ in the large pseudo-dodecahedral site (A site), and ~11 mol% Al3+ in the small octahedral site (B site). This may indicate that Al3+ in bridgmanite preferentially occupies the B site. Our results show that the compression of Fe10-Al14-Bgm with pressure causes monotonical decreases in the volumes of AO12 pseudo-dodecahedron and BO6 octahedron (VA and VB, respectively) as well as the associated A-O and B-O bond lengths. The interatomic angles of B-O1-B and B-O2-B decrease from 145.2–145.8° at 4.2(1) GPa to 143.3–143.5° at 64.6(6) GPa. Quantitative calculations of octahedral tilting angles (Ф) show that Ф increases smoothly with pressure. We found a linear relationship between the polyhedral volume ratio and the Ф in the bridgmanite with different compositions: VA/VB = –0.049Φ + 5.549. Our results indicate an increased distortion of the Fe10-Al14-Bgm structure with pressure, which might be related to the distortion of A-site Fe2+. The local environmental changes of A-site Fe2+ in bridgmanite could explain previous results on the hyperfine parameters, abnormal lattice thermal conductivity, mean force constant of iron bonds and other physical properties, which in turn provide insights into our understanding on the geophysics and geochemistry of the planet.

Geochemistry & Geophysics↗
NASA NTRS1989

Distortion effects in spacecraft observations of MHD toroidal standing waves - Theory and observations

This paper considers the distortion effect of the simultaneous occurrence of locally resonant toroidal pulsations over a range of L shells on the interpretation of spacecraft observations of these waves. A theoretical model is developed which yields quantitative predictions of the phase shear effect that causes a shift from the true pulsation frequency measured from a spacecraft moving radially across L shells. Calculations with this model indicate that, due to this effect, the AMPTE/CCE satellite should observe 8-30 percent lower frequencies on outbound passes than on inbound passes. A comparison of fundamental mode frequency measurements made on 10 inbound and 9 outbound passes of the AMPTE/CCE satellite in the morning sector confirms the predictions of the model.

Anderson, B. J.↗
NASA NTRS1994

Design and operation of a supersonic annular flow facility

Supersonic annular flow passages exist in propulsion applications that include dual combustion ramjet engines where a supersonic annular flow (the outer flow) mixes with a sonic (or supersonic) gas generator flow (the inner flow) in the shock expansion zone downstream of the gas generator nozzle exit. Other engine designs include components in the form of annular ducts whose cross-sectional area varies in the streamwise flow direction. In some of these configurations, it is necessary to support the outer shroud (cowl) by means of struts positioned between the cowl and centerbody. To investigate the distorting influence of these struts on the local flow structure, it is first necessary to ensure that the intrinsic flow without struts is free of wave reflections and the effects of upstream disturbances. It is also necessary to demonstrate that the intrinsic flow exhibits the characteristics of a well-defined turbulent boundary layer flow, so that changes in the local flow structure induced by the presence of struts can be interpreted properly. The purpose of this Note is to demonstrate that a supersonic flow facility that meets these objectives has been developed.

Williams, K. E.↗
NASA NTRS1996

Optimal 3D Viewing with Adaptive Stereo Displays for Advanced Telemanipulation

A method of optimal 3D viewing based on adaptive displays of stereo images is presented for advanced telemanipulation. The method provides the viewer with the capability of accurately observing a virtual 3D object or local scene of his/her choice with minimum distortion.

3D viewing advanced telemanipulation telemanipulat↗
DOE OSTI2020

Evidence for pseudo–Jahn-Teller distortions in the charge density wave phase of 1$\textit{T}-\text{TiSe}_2$

Here, the charge density wave (CDW) instability in 1$\textit{T}-\text{TiSe}_2$ is revisited to investigate its electronic and structural origins using angle resolved photoemission spectroscopy (ARPES), neutron diffraction, and density functional theory (DFT) calculations. The evidence for Jahn-Teller (JT)-like distortions in the CDW state is provided from the local structure analysis that shows splitting of the Ti-Se bonds into short and long. The magnitude of the split is inconsistent with the commonly accepted Di Salvo model for the structural distortions in the CDW phase. From the APRES data, it is deduced that a nontrivial temperature-dependent energy shift of the Se $4\textit{p}$ valence bands occurs, but is absent for the Ti $3\textit{d}$ conduction bands. Collectively, these observations suggest that a JT-like mechanism is most likely central to the CDW instability in 1$\textit{T}-\text{TiSe}_2$.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Higher-order topological corner and bond-localized modes in magnonic insulators

We theoretically investigate a two-dimensional decorated honeycomb lattice framework to realize a second-order topological magnon insulator (SOTMI) phase featuring distinct corner-localized modes. Here, our study emphasizes the pivotal role of spin-magnon mapping in characterizing bosonic topological properties, which exhibit differences from their fermionic counterparts. We employ a symmetry indicator topological invariant to identify and characterize this SOTMI phase, particularly for systems respecting time-reversal and rotational symmetry. Using a spin model defined on a honeycomb lattice geometry, we demonstrate that introducing “kekulé” type distortions yields a topological phase. In contrast, “antikekulé” distortions result in a nontopological magnonic phase. The presence of kekulé distortions manifests in two distinct topologically protected bosonic corner modes—an intrinsic and a pseudo, based on the specific edge terminations. On the other hand, antikekulé distortions give rise to Tamm/Shockley type bond-localized boundary modes, which are nontopological and reliant on particular edge termination. We further investigate the effects of random out-of-plane exchange anisotropy disorder on the robustness of these bosonic corner modes. The distinction between SOTMIs and their fermionic counterparts arises due to the system-specific magnonic onsite energies, a crucial feature often overlooked in prior literature. Our study unveils exciting prospects for engineering higher-order topological phases in magnon systems and enhances our understanding of their unique behavior within decorated honeycomb lattices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRSDate not supplied

Stability Analysis of the Flow Over a Swept Forward-Facing Step Using PIV Base Flows

Step excrescences are a type of surface imperfection encountered on swept wings of commercial aircraft, commonly because accessibility requirements prevent creating the wing’s surface from a single panel. If the step height is too large, super-critical, the flow can undergo an early transition to turbulence, which can be highly detrimental for the performance of the wing. In the case of a forward-facing step on a swept wing in a low-disturbance environment, stationary crossflow vortices can develop a significant amplitude upstream of the step and hence dominate the structure of the boundary-layer flow over the step. The main goal of the present investigation is to illuminate the path to transition supported by the fascinatingly complex flow field in the direct downstream vicinity of a step with a super critical height. The high-resolution, stereographic Particle Image Velocimetry (PIV) measurement dataset presently available for this flow field provides a complete description of the laminar flow for the execution of BiGlobal stability analysis in a plane parallel to the step. Although the notorious sensitivity of stability results to the description of the base flow demands a very careful uncertainty analysis of those results, it is argued that this very fact can be leveraged to produce new insight into the supported perturbation dynamics. In performing the analysis, several unsteady mode families are discovered that display the explosive perturbation expected for early transition to be induced. In considering domain widths equal to an integer-multiple of the incident crossflow-vortex wavelength and analyzing an extent of 5 crossflow-vortex wavelengths parallel to the step, it is found that the stability results converge while increasing the domain width. It is demonstrated, moreover, that the results for the wider domains can be approximated by appropriately averaging the results on neighboring single-crossflow-vortex-wavelength domains covering the same region. Besides being useful for computational purposes, this observed property suggests interpreting the instability mechanism as a distorted primary mechanism rather than a “proper” secondary mechanism. This follows in the context of the secondary in-stability analysis of three-dimensional boundary layers, because the secondary mechanism is usually characterized by being localized in a pocket of strong shear, while the distorted primary mechanism typically has an infinite support in the direction parallel to the step. Even though the growth rates are found to be sensitive to the interrogation-window size inherent to the PIV post-processing procedure, the spatial structure of the eigenfunctions is found to be relatively insensitive. Lastly, the spatial structure of the eigenfunctions corresponding to all velocity components are matched with the shape functions determined by computing the Spectral Proper Orthogonal Decomposition (SPOD) of a time-resolved measurement of the perturbation content.

forward-facing step↗
NASA NTRS2004

Generalization of Equivalent Crystal Theory to Include Angular Dependence

In the original Equivalent Crystal Theory, each atomic site in the real crystal is assigned an equivalent lattice constant, in general different from the ground state one. This parameter corresponds to a local compression or expansion of the lattice. The basic method considers these volumetric transformations and, in addition, introduces the possibility that the reference lattice is anisotropically distorted. These distortions however, were introduced ad-hoc. In this work, we generalize the original Equivalent Crystal Theory by systematically introducing site-dependent directional distortions of the lattice, whose corresponding distortions account for the dependence of the energy on anisotropic local density variations. This is done in the spirit of the original framework, but including a gradient term in the density. This approach is introduced to correct a deficiency in the original Equivalent Crystal Theory and other semiempirical methods in quantitatively obtaining the correct ratios of the surface energies of low index planes of cubic metals (100), (110), and (111). We develop here the basic framework, and apply it to the calculation of Fe (110) and Fe (111) surface energy formation. The results, compared with first principles calculations, show an improvement over previous semiempirical approaches.

Ferrante, John↗
DOE OSTI2024

Magnetic structure and properties of the compositionally complex perovskite (Y 0.2 La 0.2 Pr 0.2 Nd 0.2 Tb 0.2 )MnO 3

Large configurational disorder in compositionally complex ceramics can lead to unique functional properties that deviate from traditional rules of alloy mixing. In recent years, compositionally complex oxides (CCOs) have shown intriguing magnetic behavior including long-range order, enhanced magnetic exchange couplings, and mixed phase magnetic structures. This work focuses on how large local spin disorder affects magnetic ordering in a CCO. Specifically, we investigated the A-site alloyed perovskite, (Y 0.2 La 0.2 Pr 0.2 Nd 0.2 Tb 0.2 )MnO 3 , or (5A)MnO 3 , using a combination of bulk magnetometry, synchrotron X-ray diffraction, and temperature-dependent neutron diffraction. The five A-site ions have an average spin and ionic radius nearly equal to that of Nd 3+ ions, which minimizes structural distortions and allows for an understanding of the local spin disorder effects through a direct comparison with NdMnO 3 . Our magnetometry data show that (5A)MnO 3 exhibits two distinct phase transitions associated with the A-site and B-site sublattices, as seen in NdMnO 3 , as well as the presence of domain pinning and exchange bias at low temperature, suggesting a mixed phase magnetic ground state, as seen in other magnetic CCOs. Neutron powder diffraction shows clear long-range antiferromagnetic ordering below 67 K and refines to a Pn'ma' magnetic structure at low temperature, in excellent agreement with the well-studied behavior of NdMnO 3 . The two most notable differences in (5A)MnO 3 magnetism apparent from our data are a slight suppression of the B-site ordering temperature, which is explained by a smaller Mn–O–Mn bond angle in (5A)MnO 3 than NdMnO 3 , and the presence of a magnetic susceptibility transition above the B-site ordering, which could indicate the formation of a cluster glass but requires further study. Finally, this work demonstrates a general method of isolated investigation of size and spin disorder in CCOs and motivates future work using local structure probes to better understand the effects of nanoscale clustering and local spin disorder in magnetic CCOs.

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

Spectral distortion anisotropy from inflation for primordial black holes

Single-field inflationary models that seek to greatly enhance small-scale power in order to form primordial black holes predict both a squeezed bispectrum that is enhanced by this small-scale power and a potentially detectable enhancement of cosmic microwave background (CMB) spectral distortions. Despite this combination, spectral distortion anisotropy on CMB scales remains small since the squeezed bispectrum represents an unobservable modulation of the scale rather than local amplitude for the short-wavelength acoustic power that dissipates and forms the μ spectral distortion. Furthermore, the leading-order amplitude effect comes from the local modulation of acoustic dissipation at the beginning of the μ epoch at the end of thermalization by a long-wavelength mode that is correlated with CMB anisotropy itself. Compensating factors from the suppression by the square of the ratio the comoving horizon at thermalization to the smallest detectable primary CMB scales (~0.0005) and maximal allowed enhancement of μ (~5000) leaves a signal in the μT cross spectrum that is still well beyond the capabilities of PIXIE or LiteBIRD space missions due to sensitivity and resolution while remaining much larger than in single-field slow-roll inflation and potentially observable.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Intricacies of frustrated magnetism in the Kondo metal YbAgGe

The combination of localized magnetic moments, their frustration and interaction with itinerant electrons is a key challenge of condensed matter physics. Frustrated magnetic interactions promote degenerate ground states with enhanced fluctuations, a topic that is predominantly studied in magnetic insulators. The coupling between itinerant and localized electrons in metals add complexity to the problem, and is presently formulated only for extreme cases in which the itinerant electrons mediate exchange between localized spins (RKKY interaction) or suppress the formation of magnetic moments (Kondo screening). Here, we report an in-depth experimental study of the distorted Kagome metal YbAgGe, unravelling the open questions of how frustration, localized magnetism and itinerant electrons are intertwined in frustrated Kondo metals. We find that coupled itinerant and localized electrons give rise to dynamic magnetic correlations below T* ≈ 20 K. At lower temperature, frustrated magnetic interactions establish anisotropic magnetic short-range correlations that culminate into antiferromagnetic long-range order below T N = 0.68 K with a significantly reduced modulated magnetic moment. We show that local moment Hamiltonians can yield limited understanding of the microscopic behaviour in frustrated metals, and prompt the extension of more sophisticated model Hamiltonians incorporating itinerant effects.

Mazzone, Daniel G. [PSI Center for Neutron and Muo↗
NASA NTRS1977

Electron-impact excitation of carbon and silicon in the distorted-wave approximation

The 3P to 1D electron-impact excitation cross section within the ground configuration of both neutral carbon and silicon is calculated in the distorted-wave approximation of the two-state Hartree-Fock coupled equations. An essential element of the present treatment is that orthogonality to core orbitals is not assumed in deriving equations for the scattering orbitals. A local adiabatic polarization potential is also added to the distorted-wave equations. Both elements are necessary in getting good agreement with close-coupling results for carbon to low impacting energies. The agreement is sufficiently good that predictions for silicon should be accurate to within a factor of 2.

Pindzola, M. S.↗
DOE OSTI2022

Persona of Transition Metal Ions in Solids: A Statistical Learning on Local Structures of Transition Metal Oxides

Abstract The local structure of a transition metal (TM) ion is a function of cation elements and valence states. More than that, in this work, by employing a trove of first‐principles data of TM oxides, the local structures of TM cations are statistically analyzed to extract detailed information about cation site preference, bond length, site structural distortion, and cation magnetization. It is found that cation radius alone poorly describes the local structure of a transition metal oxide, while the statistics of coordination number as well as the TMO bond length distribution, especially that of the 3d TMs, can provide comprehensive knowledge for understanding the behavior of TM elements. Based on these statistics, the interplay of site distortion due to the Jahn–Teller effect, cation site similarity, and a new set of ionic radii are all obtained to chart the “persona” of transition metal ions in solids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Local atomic and magnetic structure of multiferroic (Sr,Ba)⁢(Mn,Ti)⁢O 3

Here, we present a detailed study of the local atomic and magnetic structure of the type-I multiferroic perovskite system (Sr,Ba)(Mn,Ti)O 3 using x-ray and neutron pair distribution function (PDF) analysis, polarized neutron scattering, and muon spin relaxation (μSR) techniques. The atomic PDF analysis reveals widespread nanoscale tetragonal distortions of the crystal structure even in the paraelectric phase with average cubic symmetry, corresponding to incipient ferroelectricity in the local structure. Magnetic PDF analysis, polarized neutron scattering, and μSR likewise confirm the presence of short-range antiferromagnetic correlations in the paramagnetic state, which grow in magnitude as the temperature approaches the magnetic transition. We show that these short-range magnetic correlations coincide with a reduction of the tetragonal (i.e., ferroelectric) distortion in the average structure, suggesting that short-range magnetism can play an important role in magnetoelectric and/or magnetostructural phenomena even without genuine long-range magnetic order. The reduction of the tetragonal distortion scales linearly with the local magnetic order parameter, pointing to spontaneous linear magnetoelectric coupling in this system. These findings provide greater insight into the multiferroic properties of (Sr,Ba)(Mn,Ti)O 3 and demonstrate the importance of investigating the local atomic and magnetic structure to gain a deeper understanding of the intertwined degrees of freedom in multiferroics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

The Dynamical Role of Optical Phonons and Sublattice Screening in a Solid-State Ion Conductor

Solid-state electrolytes (SSEs) require ionic conductivities that are competitive with liquid electrolytes to realize applications in all-solid-state batteries. Although candidate SSEs have been discovered, the underlying mechanisms enabling superionic conduction (>1 mS cm –1 ) remain elusive. In particular, the role of ultrafast lattice dynamics in mediating ion migration, which involves couplings between ions, phonons, and electrons, is rarely explored experimentally at their corresponding time scales. To investigate the complex contributions of coupled lattice dynamics on ion migration, we modulate the charge density occupations within the crystal framework and then measure the time-resolved change in impedance on picosecond time scales for a candidate SSE, Li 0.5 La 0.5 TiO 3 (LLTO). Upon perturbation, we observe enhanced ion migration at ultrafast time scales. The respective transients match the time scales of optical and acoustic phonon vibrations, suggesting their involvement in ion migration. We further computationally evaluate the effect of a charge transfer from the O 2p to the Ti 3d band on the electronic and physical structure of LLTO. We hypothesize that the charge-transfer excitation distorts the TiO 6 polyhedra by altering the local charge density occupancy of the hopping site at the migration pathway saddle point, thereby causing a reduction in the migration barrier for the Li + hop. We rule out the contribution of photogenerated electron carriers and laser heating. Overall, our investigation introduces a new spectroscopic tool to probe fundamental ion hopping mechanisms transiently at ultrafast time scales, which has previously only been achieved in a time-averaged manner or solely via computational methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗