Search NASA⌕ Search

SEARCH · Search NASA

Results for “real space”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

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

The DESC stellarator code suite. Part 1. Quick and accurate equilibria computations

Three-dimensional equilibrium codes are vital for stellarator design and operation, and high-accuracy equilibria are also necessary for stability studies. This paper details comparisons of two three-dimensional equilibrium codes: VMEC, which uses a steepest-descent algorithm to reach a minimum-energy plasma state, and DESC, which minimizes the magnetohydrodynamic (MHD) force error in real space directly. Accuracy as measured by satisfaction of MHD force balance is presented for each code, along with the computation time. It is shown that DESC is able to achieve more accurate solutions, especially near axis. The importance of higher-accuracy equilibria is shown in DESC's better agreement of stability metrics with asymptotic formulae. DESC's global Fourier–Zernike basis also yields solutions with analytic derivatives explicitly everywhere in the plasma volume, provides improved accuracy in the radial direction versus conventional finite differences and allows for exponential convergence. Further, DESC can compute a solution with the same accuracy as VMEC in order-of-magnitude less time.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Disentangling Coexisting Structural Order Through Phase Lock-In Analysis of Atomic-Resolution STEM Data

As a real-space technique, atomic-resolution STEM imaging contains both amplitude and geometric phase information about structural order in materials, with the latter encoding important information about local variations and heterogeneities present in crystalline lattices. Such phase information can be extracted using geometric phase analysis (GPA), a method which has generally focused on spatially mapping elastic strain. Here we demonstrate an alternative phase demodulation technique and its application to reveal complex structural phenomena in correlated quantum materials. As with other methods of image phase analysis, the phase lock-in approach can be implemented to extract detailed information about structural order and disorder, including dislocations and compound defects in crystals. Extending the application of this phase analysis to Fourier components that encode periodic modulations of the crystalline lattice, such as superlattice or secondary frequency peaks, we extract the behavior of multiple distinct order parameters within the same image, yielding insights into not only the crystalline heterogeneity but also subtle emergent order parameters such as antipolar displacements. When applied to atomic-resolution images spanning large (~0.5 × 0.5 μm 2 ) fields of view, this approach enables vivid visualizations of the spatial interplay between various structural orders in novel materials.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Analysis of Interpretable Data Representations for 4D-STEM Using Unsupervised Learning

Abstract Understanding the structure of materials is crucial for engineering devices and materials with enhanced performance. Four-dimensional scanning transmission electron microscopy (4D-STEM) is capable of mapping nanometer-scale local crystallographic structure over micron-scale field of views. However, 4D-STEM datasets can contain tens of thousands of images from a wide variety of material structures, making it difficult to automate detection and classification of structures. Traditional automated analysis pipelines for 4D-STEM focus on supervised approaches, which require prior knowledge of the material structure and cannot describe anomalous or deviant structures. In this article, a pipeline for engineering 4D-STEM feature representations for unsupervised clustering using non-negative matrix factorization (NMF) is introduced. Each feature is evaluated using NMF and results are presented for both simulated and experimental data. It is shown that some data representations more reliably identify overlapping grains. Additionally, real space refinement is applied to identify spatially distinct sample regions, allowing for size and shape analysis to be performed. This work lays the foundation for improved analysis of nanoscale structural features in materials that deviate from expected crystallographic arrangement using 4D-STEM.

Bruefach, Alexandra (ORCID:0000000209323477)↗
DOE OSTI2026

Cs X Si 15 P 21 ( X = Sn or Pb): Polar Noncentrosymmetric Si–P Frameworks Stabilized by Covalent X –P Bonding

Metal silicon phosphides composed of earth-abundant Si and P tend to exhibit semiconducting properties and adopt diverse crystal structures with relatively small additions of structure-directing elements. The potential of silicon phosphide materials in nonlinear optical applications has been hindered by the inability to systematically produce noncentrosymmetric structures with such a flexible framework. Here, in this work, two isostructural compounds with a novel noncentrosymmetric structure were made possible by the inclusion of elements with stereochemically active lone pairs (Sn 2+ and Pb 2+ ). The structures were determined through single-crystal and synchrotron powder X-ray diffraction. Analysis of chemical bonding in real space through the electron localization function revealed stereochemically active Pb 2+ and Sn 2+ species in a trigonal pyramidal coordination with {Pb/Sn}–P bonds. Such covalent bonding between Pb and P is quite uncommon in extended solids and has been reported in a few rare instances. Band structure calculations and linear optical measurements confirm the semiconducting nature of Cs X Si 15 P 21 ( X = Sn or Pb). The synthesis was optimized to yield high-purity polycrystalline samples. The nonlinear optical properties show promising second-harmonic generation (SHG) coefficients from the Kurtz–Perry method. First-principles calculations of the nonlinear optical properties support the experimentally determined SHG values and provide moderate values of birefringence, suggesting Cs X Si 15 P 21 could be phase-matchable and practical nonlinear optical materials in the mid-IR region.

crystal structure↗
DOE OSTI2023

Electron Microscopy Studies of Soft Nanomaterials

This review highlights recent efforts on applying electron microscopy (EM) to soft (including biological) nanomaterials. We will show how developments of both the hardware and software of EM have enabled new insights into the formation, assembly, and functioning (e.g., energy conversion and storage, phonon/photon modulation) of these materials by providing shape, size, phase, structural, and chemical information at the nanometer or higher spatial resolution. Specifically, we first discuss standard real-space two-dimensional imaging and analytical techniques which are offered conveniently by microscopes without special holders or advanced beam technology. The discussion is then extended to recent advancements, including visualizing three-dimensional morphology of soft nanomaterials using electron tomography and its variations, identifying local structure and strain by electron diffraction, and recording motions and transformation by in situ EM. On these advancements, we cover state-of-the-art technologies designed for overcoming the technical barriers for EM to characterize soft materials as well as representative application examples. Here, the even more recent integration of machine learning and its impacts on EM are also discussed in detail. With our perspectives of future opportunities offered at the end, we expect this review to inspire and stimulate more efforts in developing and utilizing EM-based characterization methods for soft nanomaterials at the atomic to nanometer length scales in academic research and industrial applications.

Imaging↗
DOE OSTI2026

Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy

Accurate representation of metal ions in macromolecular structures is critical for chemical interpretation, computational modeling, and machine-learning methods that rely on Protein Data Bank (PDB) entries. However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.

Crystallization↗
DOE OSTI2020

Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

Herein, we present a novel method to incorporate structural results from surface-sensitive scattering, such as X-ray or neutron reflectometry, into molecular dynamics simulations. While reflectometry techniques generally provide a means to determine the molecular-scale structures of organized interfacial films, they were recently shown to offer the capability to characterize the structures of protein-membrane complexes supported by a solid substrate. One-dimensional information inherent in the experimental results is used in the form of component volume occupancy (CVO) profiles, which describe the distribution of molecular components within an interfacial architecture, to construct real-space constraints in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown in the re-evaluation of an neutron-reflection-derived structure which was approximated by an independent molecular dynamics simulation in earlier work, and it also leads to faster equilibration of ensemble structures. We further show that time averaging the CVO profile that develops in the simulation while biasing with this approach permits fluctuations about the average that are necessary for conformational exploration of the system. This method is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and may take prohibitively long to equilibrate in simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Accurate Atomic Correlation and Total Energies for Correlation Consistent Effective Core Potentials

Very recently, we introduced a set of correlation consistent effective core potentials (ccECPs) constructed within full many-body approaches. By employing significantly more accurate correlated approaches, we were able to reach a new level of accuracy for the resulting effective core Hamiltonians. We also strived for simplicity of use and easy transferability into a variety of electronic structure methods in quantum chemistry and condensed matter physics. Here, as a reference for future use, we present exact or nearly exact total energy calculations for these ccECPs. The calculations cover H–Kr elements and are based on the state-of-the-art configuration interaction (CI), coupled-cluster (CC), and quantum Monte Carlo (QMC) calculations with systematically eliminated/improved errors. In particular, we carry out full CI/CCSD(T)/CCSDT(Q) calculations with cc-pVnZ with up to n = 6 basis sets and we estimate the complete basis set limits. Using combinations of these approaches, we achieved an accuracy of ≈1–10 mHa for K–Zn atoms and ≈0.1–0.3 mHa for all other elements—within about 1% or better of the ccECP total correlation energies. We also estimate the corresponding kinetic energies within the feasible limit of full CI calculations. In order to provide data for QMC calculations, we include fixed-node diffusion Monte Carlo energies for each element that give quantitative insights into the fixed-node biases for single-reference trial wave functions. The results offer a clear benchmark for future high-accuracy calculations in a broad variety of correlated wave function methods such as CI and CC as well is in stochastic approaches such as real space sampling QMC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car–Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson’s equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. Furthermore, this is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500–1000 atoms (e.g., (H₂O)₂₅₆) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.

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

Monte Carlo MP2-F12 for Noncovalent Interactions: The C 60 Dimer

A scalable stochastic algorithm is presented that can evaluate explicitly correlated (F12) second-order many-body perturbation (MP2) energies of weak, noncovalent, intermolecular interactions. It first transforms the formulas of the MP2 and F12 energy differences into a short sum of high-dimensional integrals of Green’s functions in real space and imaginary time. Furthermore, these integrals are then evaluated by the Monte Carlo method augmented by parallel execution, redundant-walker convergence acceleration, direct-sampling autocorrelation elimination, and control-variate error reduction. By sharing electron-pair walkers across the supermolecule and its subsystems spanned by the joint basis set, the statistical uncertainty is reduced by one to 2 orders of magnitude in the MP2 binding energy corrected for the basis-set incompleteness and superposition errors. The method predicts the MP2-F12/aug-cc-pVDZ binding energy of 19.1 ± 4.0 kcal mol –1 for the C 60 dimer at the center distance of 9.748 Å.

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

Spatial Signatures of Electron Correlation in Least-Squares Tensor Hypercontraction

Least Squares Tensor Hypercontraction (LS-THC) has received some attention in recent years as an approach to reduce the significant computational costs of wavefunc- tion based methods in quantum chemistry. However, previous work has demonstrated that the LS-THC factorization performs disproportionately worse in the description of wavefunction components (e.g. cluster amplitudes T 2 ) than Hamiltonian compo- nents (e.g. electron repulsion integrals (pq|rs)). This work develops novel theoretical methods to study the source of these errors in the context of the real-space T 2 kernel, and reports, for the first time, the existence of a “correlation feature” in the errors of the LS-THC representation of the “exchange-like” correlation energy EX and T 2 that is remarkably consistent across ten molecular species, three correlated wavefunctions, and four basis sets. This correlation feature portends the existence of a “pair-point kernel” missing in the usual LS-THC representation of the wavefunction, which critically depends upon pairs of grid points situated close to atoms and with inter-pair distances between one and two Bohr radii. These findings point the way for future LS-THC developments to address these shortcomings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

X‑ray Coherent Diffractive Imaging of Large Helium Nanodroplets Doped with Small Molecules

We report the first X-ray coherent diffractive imaging experiment on molecule-doped helium nanodroplets. It complements previous work, where we reported single-shot X-ray coherent diffractive imaging studies of Xe dopant clusters formed in 4He and 3He droplets. These noble gas clusters were used to visualize the impact of rotational excitation of the droplets on the spatial distribution of atomic dopants within the droplets, and to study the differences and connections between quantum and classical droplet rotational motion. Here, we expand our studies to the molecular dopants CF4, CHF3, CH3CN, and SF6, imaged with 1.5 keV photons. We find multiple Bragg spots in the diffraction patterns of molecule-doped droplets with radii of approximately 600 nm, which provide evidence that molecules form elongated clusters with preferential alignment along the angular momentum axis of the 4He droplets, in agreement with our previous results on the aggregation of Xe clusters on quantum vortices. Real-space reconstructions of molecular dopant cluster density profiles are obtained for droplets with smaller radii of approximately 300 nm. The diffuse images suggest the formation of low-density, potentially porous, molecular clusters upon aggregation at T = 0.4 K in 4He droplets. In the normal fluid 3He droplets, molecules aggregate into loose clusters on the droplets' equator, similar to previous observations for Xe atoms. Time-of-flight mass spectra reveal that the doped helium nanodroplet moieties fragment extensively into constituent atomic ions, producing only a small fraction of molecular fragment ions. The findings are discussed in the context of previously proposed schemes to use He droplets as potential tamper materials for ultrafast X-ray imaging experiments.

Feinberg, AlexandraJ↗
DOE OSTI2024

Medium-Range Structural Order as the Driver of Activated Dynamics and Complexity Reduction in Glass-Forming Liquids

Here, we analyze in depth the Elastically Collective Nonlinear Langevin Equation theory of activated dynamics in metastable liquids to establish that the predicted inter-relationships between the alpha relaxation time, local cage and collective elastic barriers, dynamic localization length, and shear modulus are causally related within the theory to the medium range order (MRO) static correlation length. The latter grows exponentially with density for metastable hard sphere fluids and as a nonuniversal inverse power law with temperature for supercooled liquids under isobaric conditions. The physical origin of predicted connections between the alpha time and other metrics of cage order and the thermodynamic inverse dimensionless compressibility is fully established. It is discovered that although kinetic constraints from the real space first coordination shell are important for the alpha time, they are of secondary importance compared to the consequences of the more universal MRO correlations in both the modestly and deeply metastable regimes. This understanding sheds new light on the theoretical basis for, and prior successes of, the predictive mapping of chemically complex thermal liquids to effective hard sphere fluids based on matching their dimensionless compressibilities, a scheme we call “complexity reduction”. In essence, the latter is equivalent to the physical requirement that the thermal liquid MRO correlation equals that of its effective hard sphere analog. The mapping alone is shown to provide a remarkable level of quantitative predictive power for the glass transition temperature T g of 21 molecular and polymer liquids. Predictions for the chemically specific absolute magnitude and growth with cooling of the MRO correlation length are obtained and lie in the window of 2–6 nm at T g . Dynamic heterogeneity, elastic facilitation, and beyond pair structure issues are briefly discussed. Future opportunities to theoretically analyze the equilibrated deep glass regime are outlined.

cancer↗
DOE OSTI2020

Spatially Resolved Mapping of Three-Dimensional Molecular Orientations with ~2 nm Spatial Resolution through Tip-Enhanced Raman Scattering

We record local optical field images of silver nanocubes (75 nm) using tip-enhanced Raman (TER) spectral imaging. The images that we observe are consistent with several recent reports from our group, but here, we demonstrate sub-2 nm spatial resolution in local optical field nanoimaging under ambient laboratory conditions. This is achieved by scanning the substrate (nanocube on Si) relative to a 4-thiobenzonitrile (TBN)-functionalized Ag-coated TER probe. The spatial resolution that we obtain necessitates that only a few molecules govern the recorded optical response; molecular orientation becomes an important consideration in such measurements. We model the orientation through geometry optimization of a TBN molecule chemisorbed onto an Ag79 cluster (sphere with a ~1 nm diameter). Using the computed orientation of the cluster-bound molecule, we then model the optical response using formalism that accounts for the orientation of the molecule relative to vector components of the local optical fields. We find optimal agreement between experiment and theory. In effect, this work reveals the parallels between single-molecule Raman scattering and high-spatial-resolution TER spectroscopy, even when the images themselves cannot be used to visualize a single molecule in real space.

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

Local Lattice Deformation of Tellurene Grain Boundaries by Four-Dimensional Electron Microscopy

Two-dimensional (2D) tellurene is a promising competitor for the fabrication of ultrathin optoelectronic devices belonging to a new family of monoelemental 2D materials. Furthermore, the precise fabrication and characterization of tellurene and its lattice defects is of utmost importance to determine device reliability and predict functionality, yet it remains experimentally challenging. The rapid growth of the four-dimensional scanning transmission electron microscopy (4D-STEM) technique as well as postprocessing tools now allows for structural analysis with nanometer-scale resolution over a broad range of length scales. Here, we use 4D-STEM to reveal the three-dimensional (3D) atomic structure of the characteristic grain boundary in 2D tellurium formed through a new microwave-enabled chemical self-assembly. Strain and lattice parameter maps permit the reconstruction of the roughness of the grain boundary and suggest that its formation is promoted by a wedge of helical atomic chains along the [0001] crystallographic direction. The observation of wrinkles at the grain boundary is found to be the dominant relaxation mechanism. Insights into the formation mechanism are elucidated by mapping the lattice parameters as the first demonstration of local in-plane and out-of-plane unit cell variation in a nanometer-by-nanometer real-space array.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Ab-Initio Investigation of Finite Size Effects in Rutile Titania Nanoparticles with Semilocal and Nonlocal Density Functionals

In this work, we employ hybrid and generalized gradient approximation (GGA) level density functional theory (DFT) calculations to investigate the convergence of surface properties and electronic gap of rutile titania nanoparticles with particle size. The surface energies and electronic gaps are calculated for cuboidal particles with minimum dimension ranging from 3.7 Angstrom (24 atoms) to 10.3 Angstrom (384 atoms) using a highly-parallel real-space DFT code to enable hybrid level DFT calculations of larger nanoparticles than are typically practical. We deconvolute the geometric and electronic finite size effects in surface energy, and evaluate the influence of defects on electronic gap and density of states (DOS). The electronic finite size effects in surface energy vanish when the minimum length scale of the nanoparticles becomes greater than 10 Angstrom. We show that this length scale is consistent with a computationally efficient numerical analysis of the characteristic length scale of electronic interactions. The surface energy of nanoparticles having minimum dimension beyond this characteristic length can be approximated using slab calculations that account for the geometric defects. In contrast, the finite size effects on the electronic gap and DOS is highly dependent on the shape and size of these particles. Furthermore, the DOS for cuboidal particles and more realistic particles constructed using the Wulff algorithm reveal that defect states within the electronic gap play a key role in determining the eigen value distribution of nanoparticles and the electronic gap does not converge to the bulk limit for the particle sizes investigated.

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

A Closer Look at Tip-Enhanced Raman Chemical Reaction Nanoimages

Tip-enhanced Raman spectroscopy (TERS) is a powerful technique that enables ultrahigh spatial resolution and ultrasensitive chemical imaging. This technique’s ability to track plasmon-induced/enhanced chemical reactions in real space has gained increasing popularity in recent years. Here, in this study, we expose inherent difficulties associated with assigning TERS signatures that accompany chemical transformations. Namely, distinct selection rules as well as the possibility of multiple physical processes/chemical reaction pathways complicate spectral assignments and necessitate caution in assigning the experimental observables. We illustrate the latter using 4,4'-dimercaptostilbene-functionalized plasmonic silver nanocubes, wherein we identify the TERS signatures of product formation, molecular charging, multipolar Raman scattering, and preferred molecular orientations that all lead to distinct and assignable spectral patterns.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗