Search NASA⌕ Search

SEARCH · Search NASA

Results for “atom mapping”

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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Allosteric prediction via convolutional neural networks and protein structural and dynamical features

Allostery is the phenomenon whereby a binding event or covalent modification at one site in a protein modulates function at a distal site, thus changing a protein’s functional state. As such, it is a ubiquitous aspect of protein functional regulation. Computationally predicting allosteric states is important as part of the broader challenge of functional annotation, but it also has practical implications for drug development, as targeting an allosteric site often affords greater specificity compared with targeting an orthosteric site. This study introduces a machine learning approach to predict the allosteric functional state using the small G-protein KRas as the model system, due to its implication in many types of cancer and being well studied as a result with many x-ray crystallographic structures of KRas available with different mutations and ligands bound. Using structural and dynamical features that can be cast as images, namely interatomic distances, contact maps, covariance, and mutual information, supervised learning was performed using convolutional neural networks. Two pretrained convolutional neural network architectures, GoogLeNet and ResNet18, were fine-tuned to classify KRas into active or inactive states based on these features. Across training regimes, atomic contact maps emerged as the most effective structural feature, whereas linearized mutual information outperformed covariance in capturing dynamical correlations relevant to allostery. Models achieved significant validation accuracy, with atomic contact maps yielding up to 90% accuracy. In conclusion, the findings suggest that integrating global structural rearrangements and correlated motion patterns with deep learning can reliably predict protein allosteric states, offering a promising framework for understanding allosteric regulation and developing targeted therapeutics.

Rajeshwar T., Rajitha [Oak Ridge National Laborato↗
DOE OSTI2021

Atomic scale crystal field mapping of polar vortices in oxide superlattices

Polar vortices in oxide superlattices exhibit complex polarization topologies. Using a combination of electron energy loss near-edge structure analysis, crystal field multiplet theory, and first-principles calculations, we probe the electronic structure within such polar vortices in [(PbTiO 3 ) 16 /(SrTiO 3 ) 16 ] superlattices at the atomic scale. The peaks in Ti L-edge spectra shift systematically depending on the position of the Ti 4+ cations within the vortices i.e., the direction and magnitude of the local dipole. First-principles computation of the local projected density of states on the Ti 3d orbitals, together with the simulated crystal field multiplet spectra derived from first principles are in good agreement with the experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Atomic Scale Crystal Field Mapping of Polar Vortices in Oxide Superlattices

Polar vortices in oxide superlattices can be utilized as potential candidates for data storage applications due to their unique polarization topologies. The structure and dipole arrangement in polar vortices has been studied via X-ray scattering techniques, (scanning) transmission electron microscopy ((S)/TEM) and computational calculations. However, the fundamental correlation between the atomic structure and the electronic structure (which is manifested in the chemical bonding) has heretofore not been explored. Further, The hybridization between nominally empty $\textit{d}$ orbitals on the B-site with the occupied O 2$\textit{p}$ orbitals favors the condensation of a polar (ferroelectric) state in $\textit{AB}$O 3 perovskite oxides. The complex, continuously rotating local polarization texture of the vortices, in turn, can result in especially intricate $\textit{d}$- orbital interactions. Soft X-ray spectroscopy can probe these interactions at the transition metal $\textit{L}$-edge, but these techniques do not have the spatial resolution to resolve variations within one vortex (~5 nm region). Electron energy loss spectroscopy (EELS) in the STEM mode uses inelastically scattered electrons to probe the core-shell excitations (empty density of states) of transition metals at atomic resolution.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Nuclear mass measurements map the structure of atomic nuclei and accreting neutron stars

We introduce here mass excesses (ME) of neutron-rich isotopes of Ar through Fe, obtained via time of flight B ρ mass spectrometry at the National Superconducting Cyclotron Laboratory. Our new results have significantly reduced systematic uncertainties relative to a prior analysis, enabling the first determination of ME for Ti 58 , 59 , V 62 , Cr 65 , Mn 67 , 68 , and Fe 69 , 70 . Our results show the N = 34 subshell weaken at Sc and vanish at Ti, along with the absence of an N = 40 subshell at Mn. This further leads to a cooler accreted neutron star crust, highlighting the connection between the structure of nuclei and neutron stars.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Imaging atomic-scale chemistry from fused multi-modal electron microscopy

Efforts to map atomic-scale chemistry at low doses with minimal noise using electron microscopes are fundamentally limited by inelastic interactions. Here, fused multi-modal electron microscopy offers high signal-to-noise ratio (SNR) recovery of material chemistry at nano- and atomic-resolution by coupling correlated information encoded within both elastic scattering (high-angle annular dark-field (HAADF)) and inelastic spectroscopic signals (electron energy loss (EELS) or energy-dispersive x-ray (EDX)). By linking these simultaneously acquired signals, or modalities, the chemical distribution within nanomaterials can be imaged at significantly lower doses with existing detector hardware. In many cases, the dose requirements can be reduced by over one order of magnitude. This high SNR recovery of chemistry is tested against simulated and experimental atomic resolution data of heterogeneous nanomaterials.

36 MATERIALS SCIENCE↗
DOE OSTI2026

The Squeezed Bispectrum from CHIME H I Emission and Planck Cosmic Microwave Background Lensing: Current Sensitivity and Forecasts

Line intensity mapping using atomic hydrogen (H I) has the potential to efficiently map large volumes of the Universe if the signal can be successfully separated from overwhelmingly bright radio foreground emission. This motivates cross correlations, to ascertain the cosmological nature of measured H I fluctuations, and to study their connections with galaxies and the underlying matter density field. However, these same foregrounds render the cross correlation with projected fields such as the lensing of the cosmic microwave background (CMB) difficult. Indeed, the correlated Fourier modes vary slowly along the line of sight and are thus most contaminated by the smooth-spectrum radio continuum foregrounds. In this paper, we implement a method that avoids this issue by attempting to measure the nonlinear gravitational coupling of the small-scale 21 cm power from the Canadian Hydrogen Intensity Mapping Experiment (CHIME) with large-scale Planck CMB lensing. This measurement is a position-dependent power spectrum, i.e., a squeezed integrated bispectrum. Using 94 nights of CHIME data between 1.0 < z < 1.3 and aggressive foreground filtering, we find that the expected signal is 5 times smaller than the current noise. We forecast that incorporating the additional nights of CHIME data already collected would enable a signal-to-noise ratio of 3, without any further improvements in filtering for foreground cleaning.

21cm↗
DOE OSTI2020

Measurement of atom resolvability in cryo-EM maps with Q-scores

Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Here, assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Atomic far-IR fine-structure line mapping of L1630, M17, and W3: Comparison of (O I) and (C II) distributions

We mapped the distribution of atomic far-IR line emission from (O I) and (C II) over parsec scales in the Galactic star-forming regions L1630, M17, and W3 using the MPE Far-Infrared Fabry-Perot Imaging spectrometer (FIFI) on board the NASA Kuiper Airborne Observatory. The lines mapped include (O I) 63 microns, (O I) 146 microns, and (C II) 158 microns. Comparison of the intensities and ratios of these lines with models of photodissociation regions (e.g., Tielens & Hollenbach 1985, ApJ, 344, 770) allows us to derive temperatures and densities of the primarily neutral atomic gas layers lying on the surfaces of UV-illuminated molecular gas. In general, the (C II) line arises ubiquitously throughout the molecular clouds while the (O I) lines are mainly confined to warm, dense gas (T is greater than 100 K, n is greater than 10(exp 4)/cu cm) near the sites of O and B stars. The distribution of (C II) in the star-forming clouds implies that the (C II) emission arises on the surfaces of molecular clumps throughout the clouds, rather than only at the boundary layer between molecular gas and H II regions.

Howe, J. E.↗
DOE OSTI2025

Atom Identification in Bilayer Moiré Materials with Gomb-Net

Moiré patterns in van der Waals bilayer materials complicate the analysis of atomic-resolution images, hindering the atomic-scale insight typically attainable with scanning transmission electron microscopy. Here, we report a method to detect the positions and identities of atoms in each of the individual layers that compose twisted bilayer heterostructures. We developed a deep learning model, Gomb-Net, which identifies the coordinates and atomic species in each layer, deconvoluting the moiré pattern. This enables layer-specific mapping of atomic positions and dopant distributions, unlike other commonly used segmentation models which struggle with moiré-induced complexity. Using this approach, we explored the Se atom substitutional site distribution in a twisted fractional Janus WS 2 -WS 2(1–x) Se 2x heterostructure and found that layer-specific implantation sites are unaffected by the moiré pattern’s local energetic or electronic modulation. In conclusion, this advancement enables atom identification within material regimes where it was not possible before, opening new insights into previously inaccessible material physics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

The 158 micron (CII) mapping of galaxies: Probing the atomic medium

Using the MPE/UCB Far-infrared Imaging Fabry-Perot Interferometer (FIFI) on the Kuiper Airborne Observatory (KAO), we have made large scale maps of (CII) in the spiral galaxies NGC 6946, NGC 891, M83 and the peculiar elliptical Cen A, thus allowing for the first time, detailed studies of the spatial distribution of the FIR line emission in external galaxies. We find that the (CII) emission comes from a mixture of components of interstellar gas. The brightest emission is associated with the nuclear regions, a second component traces the spiral arms as seen in the nearly face on spiral galaxies NGC 6946 and M83 and the largest star forming/H2 regions contained within them, and another extended component of low brightness can be detected in all of the galaxies far from the nucleus, beyond the extent of CO emission.

Madden, S. C.↗
DOE OSTI2024

Small, solubilized platinum nanocrystals consist of an ordered core surrounded by mobile surface atoms

In situ structures of Platinum (Pt) nanoparticles (NPs) can be determined with graphene liquid cell transmission electron microscopy. Atomic-scale three-dimensional structural information about their physiochemical properties in solution is critical for understanding their chemical function. We here analyze eight atomic-resolution maps of small (<3 nm) colloidal Pt NPs. Their structures are composed of an ordered crystalline core surrounded by surface atoms with comparatively high mobility. 3D reconstructions calculated from cumulative doses of 8500 and 17,000 electrons/pixel, respectively, are characterized in terms of loss of atomic densities and atomic displacements. Less than 5% of the total number of atoms are lost due to dissolution or knock-on damage in five of the structures analyzed, whereas 10–16% are lost in the remaining three. Less than 5% of the atomic positions are displaced due to the increased electron irradiation in all structures. The surface dynamics will play a critical role in the diverse catalytic function of Pt NPs and must be considered in efforts to model Pt NP function computationally.

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

Effect of Stoichiometry on the Structure and Polarization of BaTiO 3

Barium titanate (BaTiO 3 ) is a material of interest for photonic device applications due to its strong optical non-linearity. However, BaTiO 3 -based devices have not found widespread adoption, in part due to the challenges associated with synthesizing high quality thin-films. Here, high-resolution scanning transmission electron microscope (STEM) imaging is used to investigate the atomic structure of both on- and off-stoichiometric BaTiO 3 synthesized by molecular beam epitaxy (MBE). Here, this investigation reveals an asymmetry in the way the BaTiO 3 atomic lattice accommodates off-stoichiometry growth and unveils features beyond what is expected from diffraction or surface characterization techniques. Excess titanium incorporates into the BaTiO 3 lattice to form pervasive defects despite titanium-rich films having a low surface roughness and high-quality appearance in diffraction. Excess barium forms a rough, water-soluble surface layer but does not significantly impact the quality of the BaTiO 3 lattice. STEM is used to map titanium atom displacement in real-space. The average displacement distance is 30–60 pm in the strained thin-films, higher than the <20 pm displacement in bulk BaTiO 3 . Additionally, the titanium atom displacement direction deviates from the c-axis of the unit cell, which may have implications for the material's electro-optic tensor and thus for electro-optic device design.

Cavanagh, Ashley E. [Harvard Univ., Cambridge, MA ↗
DOE OSTI2021

Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics

Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a “ring polymer” whose spread is related to the quantum mechanical uncertainty in the particle’s position, i.e., its thermal wavelength. A number of metrics have previously been used to investigate and characterize this spread and explain effects arising from quantum delocalization, zero-point energy, and tunneling. Many of these shape metrics consider just the instantaneous structure of the ring polymers. However, given the significant interest in methods such as centroid molecular dynamics and ring polymer molecular dynamics that link the molecular dynamics of these ring polymers to real time properties, there exists significant opportunity to exploit metrics that also allow for the study of the fluctuations of the atom delocalization in time. Here we consider the ring polymer delocalization from the perspective of computational topology, specifically persistent homology, which describes the 3-dimensional arrangement of point cloud data, (i.e. atomic positions). We employ the Betti sequence probability distribution to define the ensemble of shapes adopted by the ring polymer. The Wasserstein distances of Betti sequences adjacent in time are used to characterize fluctuations in shape, where the Fourier transform and associated principal components provides added information differentiating atoms with different NQEs based on their dynamic properties. We demonstrate this methodology on two representative systems, a glassy system consisting of two atom types with dramatically different de Broglie thermal wavelengths, and ab initio molecular dynamics simulation of an aqueous 4 M HCl solution where the H-atoms are differentiated based on their participation in proton transfer reactions.

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

X‐ray characterization of three possible edible oleogelators: Experiment and theory

Abstract Three oleogelator molecules (Triacontane (TC), Stearic acid (SA), and Behenyl Lignocerate (BL)) were studied individually, in pairs, or all together to make an oleogel using triolein as the oil. WAXS, SAXS and USAXS were used to elucidate the solid structures from angstroms to a few micrometers. A two‐dimensional mapping of atomic positions for each molecule was carried out to understand the crystalline multilayer structures formed. We assumed that the molecules were rigidly extended and that they underwent no significant (hindered) rotations so that the free energy is determined by the Lennard‐Jones interactions of closely packed multilayers. TC molecules were predicted to form a tilt angle of , yielding a SAXS line at Å ─1 , in acceptable agreement with the measured . For SA crystals (predicted) yielding a SAXS line at compared to (observed). No mixed crystals were observed for any pair of molecules or when all three were used. USAXS data showed that SA forms large nanocrystals compared to TC and BL. All three combinations of molecular pairs showed basic scatterers smaller or similar to those of individual molecules. The theory presented here, together with the experimental results, showed why no mixed crystals are formed from two or all three molecules. Data from the USAXS region suggested that, when using all three molecules, a more compact fractal structure was obtained, compared with those if one or two of the molecules were used.

Chemistry↗
DOE OSTI2025

Mapping Thermal Conductivity at the Atomic Scale: A Step toward the Thermal Design of Materials

We describe a spatial decomposition of the thermal conductivity, termed site-projected thermal conductivity, which quantifies the thermal conduction activity at each atomic site—a critical parameter for the thermal design of materials. The method is based on the Green–Kubo formula and the harmonic approximation and requires the force-constant and dynamical matrices, as well as a relaxed structural model. Throughout the study, it uses high quality models previously tested and compared to many experiments. It discusses the method and underlying approximations for amorphous silicon, carries the detailed analysis for amorphous silicon, and then examines an amorphous-crystal silicon interface and representative carbon materials. This study identifies the sites and local structures that reduce heat transport, and quantify these (estimate the spatial range) over which these “thermal defects” are effective. It identifies filamentary structures in the amorphous silicon network which impact heat transport and electronic structure (the Urbach edge) and electronic transport.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Protecting groups in insertion chemistry: Site-selective positioning of lithium ions in intercalation hosts

The expanding toolbox of functionalization chemistries for selectively installing moieties on specific sites of a substrate underpins almost all modern organic and biochemical syntheses. Likewise, the installation of mobile guest ions in specific interstitial sites and their transport along specific diffusion pathways forms the basis of modern lithium (Li)-ion battery electrodes. Many insertion hosts afford a diverse range of accessible interstitial sites. However, site-selective positioning of cations with atomic precision remains almost entirely unexplored. Here, we show that by deciphering site preferences of co/pre-intercalated cations, we can position Li ions in four distinct sites within a 1D ζ-V 2 O 5 insertion host. The use of topochemistry to effect single-crystal-to-single-crystal transformations enables atomic-resolution mapping of the selective positioning of Li ions through single-crystal X-ray diffraction. Here we image interstitial sites that are occupied at high depths of discharge, thereby obtaining unprecedented structural insight into “fully stuffed” frameworks critical for the realization of high-energy-density intercalation electrodes.

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

Atomic-Scale View of Redox Induced Changes for Monolayer MoO x on α-TiO 2 (110) with Chemical-State Sensitivity

Supported molybdenum oxide (MoO x ) plays an important role in catalytic transformations from alcohol dehydrogenation to transesterification. During these reactions, Mo and oxygen surface species undergo structural and chemical changes. A detailed, chemical-state specific, atomic-scale structural analysis of the catalyst under redox conditions is important for improving catalytic properties. In this study, monolayer of MoO x grown on α-TiO 2 (110) by atomic-layer deposition is analyzed by X-ray standing wave (XSW) excited X-ray photoelectron spectroscopy (XPS). The chemical shifts for Mo 2p 3/2 and O 1s peaks are used to distinguish Mo 6+ from Mo 4+ and surface O from bulk O. Excitation of XPS by XSW allows pin-pointing the location of these surface species relative to the underlying substrate lattice. Finally, measured 3D composite atomic density maps for the oxidized and reduced interfaces compare well with our density functional theory models, and collectively create a unique view of the redoxdriven dynamics for this complex catalytic structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗