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DOE OSTI2021

CERES : a cryo-EM re-refinement system for continuous improvement of deposited models

The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System ( CERES ) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1999

Energetic Neutral Atom Imaging with the POLAR CEPPAD/ IPS Instrument : Initial Forward Modeling Results

Although the primary function of the CEPPAD/IPS instrument on Polar is the measurement of energetic ions in-situ, it has also proven to be a very capable Energetic Neutral Atom (ENA) imager. Raw ENA images are currently being constructed on a routine basis with a temporal resolution of minutes during both active and quiet times. However, while analyses of these images by themselves provide much information on the spatial distribution and dynamics of the energetic ion population in the ring current. detailed modeling is required to extract the actual ion distributions. In this paper. we present the initial results of forward modeling an IPS ENA image obtained during a small geo-magnetic storm on June 9, 1997. The equatorial ion distribution inferred with this technique reproduces the expected large noon/midnight and dawn/dusk asymmetries. The limitations of the model are discussed and a number of modifications to the basic forward modeling technique are proposed which should significantly improve its performance in future studies.

Henderson, M. G.↗

NASA NTRS2008

Methods and apparatus of spatially resolved electroluminescence of operating organic light-emitting diodes using conductive atomic force microscopy

A conductive atomic force microscopy (cAFM) technique which can concurrently monitor topography, charge transport, and electroluminescence with nanometer spatial resolution. This cAFM approach is particularly well suited for probing the electroluminescent response characteristics of operating organic light-emitting diodes (OLEDs) over short length scales.

Hersam, Mark C.↗

NASA NTRS2021

DSN Radio Astronomy Spectrometer

The Deep Space Network (DSN) enables NASA to communicate with its deep space spacecraft. By virtue of its large antennas, the DSN can be used as a powerful instrument for radio astronomy. In particular, Deep Space Station (DSS) 43, the 70 m antenna at the Canberra Deep Space Communications Complex (CDSCC) has a K-band radio astronomy system covering a 10 GHz bandwidth at 17 to 27 GHz. This spectral range covers a number of atomic and molecular lines, produced in a rich variety of interstellar gas conditions. A new high-resolution spectrometer was deployed at CDSCC in November 2019 and connected to the K-band downconverter. The system has two different firmware modes: 1) Using a 65k-pt FFT to provide 32,768 spectral channels at ~30.5 kHz (0.45 km/s velocity resolution) and 2) Using a 16k-pt polyphase filterbank (PFB) to provide 8,192 spectral channels with ~122 kHz resolution (1.8 km/s velocity resolution). Previous work extensively described the spectrometer system. In this paper we present added functionality and updates to the commissioned spectrometer. The changes include developments in system timing, metadata, firmware and data products.

Bradford, Brian↗

NASA NTRS2022

Ultraviolet Spectropolarimetry with Polstar: Interstellar Medium Science

Continuum polarization over the UV-to-microwave range is due to dichroic extinction (or emission) by asymmetric, aligned dust grains. Scattering can also be an important source of polarization, especially at short wavelengths. Because of both grain alignment and scattering physics, the wavelength dependence of the polarization, generally, traces the size of the aligned grains. Similarly because of the differing wavelength dependencies of dichroic extinction and scattering polarization, the two can generally be reliably separated. Ultraviolet (UV) polarimetry therefore provides a unique probe of the smallest dust grains (diameter<0.09 μm ), their mineralogy and interaction with the environment. However, the current observational status of interstellar UV polarization is very poor with less than 30 lines of sight probed. With the modern, quantitative and well-tested, theory of interstellar grain alignment now available, we have the opportunity to advance the understanding of the interstellar medium (ISM) by executing a systematic study of the UV polarization in the ISM of the Milky Way and near-by galaxies. The Polstar mission will provide the sensitivity and observing time needed to carry out such a program (probing hundreds of stars in the Milky Way and dozens of stars in the LMC/SMC), addressing questions of dust composition as a function of size and location, radiation- and magnetic-field characteristics as well as unveiling the carrier of the 2175 Å extinction feature. In addition, using high-resolution UV line spectroscopy Polstar will search for and probe the alignment of, and polarization from, aligned atoms and ions - so called “Ground State Alignment”, a potentially powerful new probe of magnetic fields in the diffuse ISM.

B-G Andersson↗

DOE OSTI2021

Integrated transmission electron microscope

An integrated transmission electron microscope comprising multiple electron sources for tuned beams of ultrafast, scanning probe, and parallel illumination in varied beam energies can be alternated within sub-microseconds onto a sample with dynamic ‘transient state’ processes to acquire atomic-scale structural/chemical data with site specificity. The various electron sources and condenser optics enable high-resolution imaging, high-temporal resolution imaging, and chemical imaging, using fast-switching magnets to direct the different electron beams onto a single maneuverable objective pole piece where the sample resides. Such multimodal in situ characterization tools housed in a single microscope have the potential to revolutionize materials science.

Jungjohann, Katherine L.↗

NASA NTRS2004

Remote Sensing of Icy Galilean Moon Surface and Atmospheric Composition Using Low Energy (1 eV-4 keV) Neutral Atom Imaging

We describe a low energy neutral atom imager suitable for composition measurements Europa and other icy Galilean moons in the Jovian magnetosphere. This instrument employs conversion surface technology and is sensitive to either neutrals converted to negative ions, neutrals converted to positive ions and the positive ions themselves depending on the power supply. On a mission such as the Jupiter Icy Moons Orbiter (JIMO), two back-to-back sensors would be flown with separate power supplies fitted to the neutral atom and iodneutral atom sides. This will allow both remote imaging of 1 eV < E < 4 keV neutrals from icy moon surfaces and atmospheres, and in situ measurements of ions at similar energies in the moon ionospheres and Jovian magnetospheric plasma. The instrument provides composition measurements of the neutrals and ions that enter the spectrometer with a mass resolution dependent on the time-of-flight subsystem and capable of resolving molecules. The lower energy neutrals, up to tens of eV, arise from atoms and molecules sputtered off the moon surfaces and out of the moon atmospheres by impacts of more energetic (keV to MeV) ions from the magnetosphere. Direct Simulation Monte Carlo (DSMC) models are used to convert measured neutral abundances to compositional distributions of primary and trace species in the sputtered surfaces and atmospheres. The escaping neutrals can also be detected as ions after photo- or plasma-ionization and pickup. Higher energy, keV neutrals come from charge exchange of magnetospheric ions in the moon atmospheres and provide information on atmospheric structure. At the jovicentric orbits of the icy moons the presence of toroidal gas clouds, as detected at Europa's orbit, provide M e r opportunities to analyze both the composition of neutrals and ions originating from the moon surfaces, and the characteristics of magnetospheric ions interacting with neutral cloud material. Charge exchange of low energy ions near the moons, and directional distributions of the resultant neutrals, allow indirect global mapping of magnetic field structures around the moons. Temporal variation of the magnetic structures can be linked to induced magnetic fields associated with subsurface oceans.

Collier, M. R.↗

DOE OSTI2021

Generation of Bright Soft X-ray Laser Beams (Final Report)

The project goal was to demonstrate new compact soft x-ray lasers emitting high energy ultrashort pulses at shorter wavelengths and increased repetition rates by amplification in atomic transitions in high density laser-created plasmas. To demonstrate these lasers we developed new high power solid state lasers. The project succeeded in demonstrating the shortest wavelength compact soft x-ray laser to date, 6.85 nm wavelength, and the highest repetition rate table-top soft x-ray laser, 400 Hz. We also applied these compact soft x-ray laser sources to determine the composition of materials with nanoscale resolution using a new technique that combines soft x-ray laser ablation with mass spectrometry, and we demonstrated that these lasers are capable of acquiring nanoscale resolution holograms with picosecond time resolution. The combination of an increased pumping efficiency with increased repetition rates can yield soft x-ray laser beams with an unprecedented average power on a table-top for applications demanding a high photon flux. We have demonstrated that the efficiency of plasma-based laser-pumped soft x-ray lasers can be significantly increased by detailed pulse shaping of the pump laser using a new pulse synthesizer. Results include the demonstration of 18.9 nm wavelength laser operation at a record 400 Hz repetition rate, and the extension of repetitive gain-saturated plasma-based table-top x-ray lasers to the shortest wavelength to date, 6.85 nm. Laser amplification was also observed at wavelengths as short at 5.8 nm by isolectronic scaling in Ni-like lanthanide ions. We have also conducted simulations to explore the possibility of demonstrating gain saturated atomic x-ray lasers near the carbon K-edge, in the “carbon window” for the first time. The work conducted under this program also includes the use of compact soft x-ray lasers in applications to problems of chemical interest, such as isotopic composition mapping of micron-size uranium particles with nanoscale resolution, and nanoscale resolution depth profiling analysis of CoNCN-coated electrodes for water oxidation catalysis. We also demonstrated single-shot high resolution soft x-ray Fourier transform holography over a broad 7 µm diameter field of view with ~ 5 ps temporal resolution.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Orientational analysis of atomic pair correlations in nanocrystalline indium oxide thin films

The application of grazing-incidence total X-ray scattering (GITXS) for pair distribution function (PDF) analysis using >50 keV X-rays from synchrotron light sources has created new opportunities for structural characterization of supported thin films with high resolution. Compared with grazing-incidence wide-angle X-ray scattering, which is only useful for highly ordered materials, GITXS/PDFs expand such analysis to largely disordered or nanostructured materials by examining the atomic pair correlations dependent on the direction relative to the surface of the supporting substrate. A characterization of nanocrystalline In 2 O 3 -derived thin films is presented here with in-plane-isotropic and out-of-plane-anisotropic orientational ordering of the atomic structure, each synthesized using different techniques. The atomic orientations of such films are known to vary based on the synthetic conditions. Here, an azimuthal orientational analysis of these films using GITXS with a single incident angle is shown to resolve the markedly different orientations of the atomic structures with respect to the planar support and the different degrees of long-range order, and hence, the terminal surface chemistries. It is anticipated that orientational analysis of GITXS/PDF data will offer opportunities to extend structural analyses of thin films by providing a means to qualitatively determine the major atomic orientation within nanocrystalline and, eventually, non-crystalline films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Refined Telluric Absorption Correction for Low-resolution Ground-based Spectroscopy: Resolution and Radial Velocity Effects in the O{sub 2}A-band for Exoplanets and K i Emission Lines

Telluric correction of spectroscopic observations is either performed via standard stars that are observed close in time and airmass along with the science target, or recently growing in importance, by theoretical telluric absorption modeling. Both approaches work fine when the telluric lines are resolved, i.e., at a spectral resolving power larger than about 10,000, and it is sufficient to facilitate the detection of spectral features at lower resolution. However, a meaningful quantitative analysis also requires the reliable recovery of line strengths. Here, we show for the Fraunhofer A-band of molecular O{sub 2} that the standard telluric correction approach fails in this at lower spectral resolutions, as an example for the general problem. Doppler-shift-dependent errors of the restored flux may arise, which can amount to more than 50% in extreme cases, depending on the line shapes of the target spectral features. Two applications are discussed: the recovery of the O{sub 2} band in the reflected light of an Earth analog atmosphere, as facilitated potentially in the future using an orbiting starshade and a ground-based extremely large telescope; and the recovery of the intrinsic ratio of the K i lines in the post-nova V4332 Sgr tracing the optical depth of the emitting region, to exemplify the relevance using present-day instrumentation. We show how one should derive correction functions for the compensation of the error in dependence of radial velocity shift, spectral resolution, and target line-profile function by use of high-resolution atmospheric transmission modeling, which has to be solved for the individual case.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Nature of native atomic defects in ZrTe 5 and their impact on the low-energy electronic structure

Over the past decades, investigations of the anomalous low-energy electronic properties of ZrTe 5 have reached a wide array of conclusions. An open question is the growth method's impact on the stoichiometry of ZrTe 5 samples, especially given the very small density of states near its chemical potential. In this work, we report on high-resolution scanning tunneling microscopy and spectroscopy measurements performed on samples grown via different methods. Using density functional theory calculations, we identify the most prevalent types of atomic defects on the surface of ZrTe 5 , namely, Te vacancies and intercalated Zr atoms. Finally, we precisely quantify their density and outline their role as ionized defects in the anomalous resistivity of this material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Spin Squeezing as a Probe of Emergent Quantum Orders

Nuclear magnetic resonance (NMR) experiments can reveal local properties in materials, but are often limited by the low signal-to-noise ratio. Spin squeezed states have an improved resolution below the Heisenberg limit in one of the spin components, and have been extensively used to improve the sensitivity of atomic clocks, for example [1]. Interacting and entangled spin ensembles with non-linear coupling are a natural candidate for implementing squeezing. Furthermore, we propose measurement of the spin-squeezing parameter that itself can act as a local probe of emergent orders in quantum materials. In particular, we demonstrate how to investigate an anisotropic electric field gradient via its coupling to the nuclear quadrupole moment. While squeezed spin states are pure, the squeezing parameter can be estimated for both pure and mixed states. We evaluate the range of fields and temperatures for which a thermal-equilibrium state is sufficient to improve the resolution in an NMR experiment and probe relevant parameters of the quadrupole Hamiltonian, including its anisotropy.

36 MATERIALS SCIENCE↗

DOE OSTI2021

The Third Data Release of the KODIAQ Survey

We present and make publicly available the third data release (DR3) of the Keck Observatory Database of Ionized Absorption toward Quasars (KODIAQ) survey. KODIAQ DR3 consists of a fully reduced sample of 727 quasars at 0.1 < z {sub em} < 6.4 observed with the Echellette Sepctrograph and Imager at moderate resolution (4000 ≤ R ≤ 10,000). DR3 contains 872 spectra available in flux calibrated form, representing a sum total exposure time of ∼2.8 megaseconds. These coadded spectra arise from a total of 2753 individual exposures of quasars taken from the Keck Observatory Archive (KOA) in raw form and uniformly processed using a data reduction package made available through the XIDL distribution. DR3 is publicly available to the community, housed as a higher level science product at the KOA and in the igmspec database.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Nanomechanical sampling of material for nanoscale mass spectrometry chemical analysis

The ability to spatially resolve the chemical distribution of compounds on a surface is important in many applications ranging from biological to material science. To this extent, we have recently introduced a hybrid atomic force microscopy (AFM)-mass spectrometry (MS) system for direct thermal desorption and pyrolysis of material with nanoscale chemical resolution. However, spatially resolved direct surface heating using local thermal desorption becomes challenging on material surfaces with low melting points, because the material will undergo a melting phase transition due to heat dissipation prior to onset of thermal desorption. Therefore, here we developed an approach using mechanical sampling and collection of surface materials on an AFM cantilever probe tip for real-time analysis directly from the AFM tip. This approach allows for material to be concentrated directly onto the probe for subsequent MS analysis. We evaluate the performance metrics of the technique and demonstrate localized MS sampling from a candelilla wax matrix containing UV stabilizers avobenzone and oxinoxate from areas down to 250 nm × 250 nm. Overall, this approach removes heat dissipation into the bulk material allowing for a faster desorption and concentration of the gas phase analyte from a single heating pulse enabling higher signal levels from a given amount of material in a single sampling spot.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Quantum-amplified global-phase spectroscopy on an optical clock transition

Optical lattice clocks are at the forefront of precision metrology, operating near a standard quantum limit set by quantum noise. Harnessing quantum entanglement offers a promising route to surpass this limit; however, there are practical difficulties in terms of scalability and measurement resolution requirements. Here we adapt the holonomic quantum gate concept to develop a new Rabi-type ‘global-phase spectroscopy’ that uses the detuning-sensitive global Aharonov–Anandan phase19. With this approach, we can demonstrate quantum-amplified time-reversal spectroscopy on an optical clock transition that achieves directly measured 2.4(7) dB metrological gain and 4.0(8) dB improvement in laser noise sensitivity beyond the standard quantum limit. To this end, we introduce rotary echo to protect the dynamics from inhomogeneities in light–atom coupling and implement a laser-noise-cancelling differential measurement through symmetric phase encoding in two nuclear spin states. Our technique is not limited by measurement resolution, scales easily because of the global nature of entangling interaction and exhibits high resilience to typical experimental imperfections. As a result, we expect it to be broadly applicable to next-generation atomic clocks and other quantum sensors approaching the fundamental quantum precision limits.

Zaporski, Leon [Massachusetts Institute of Technol↗

DOE OSTI2025

Detection of Br and I as atomic anions using liquid sampling – atmospheric pressure glow discharge/Orbitrap mass spectrometry

The quantification and determination of halogen isotope composition is essential in many fields including geochemistry and nuclear forensics. Detection of the halogen elements is commonly attempted with inductively coupled plasma mass spectrometry (ICP-MS) however, there are multiple challenges faced. Most significantly this includes very poor ionization efficiency and the potential for isobaric interferences from either matrix or plasma species. Thus, sensitivity and accuracy are often limiting issues. Here a liquid sampling-atmospheric pressure glow discharge (LS-APGD) ionization source is coupled with an ultrahigh resolution Orbitrap MS to perform halogen detection of bromine and iodine as initial analytes. This facilitates simple and sensitive detection of these elements as atomic anions from simple aqueous salt solutions. Collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD) energies were optimized to produce the maximum response of Br − and I − . The LS-APGD conditions were optimized using a design of experiments (DOE) approach for Br − and I − concurrently. Response curves for Br − and I − solutions determined limit of detection (LOD) values of 50 pg and 5 pg, respectively, in 20 μL aliquots. The curves indicated response factors of 0.67 for 79 Br − and 0.90 for 127 I − . Br isotope ratios were determined with precision between 0.7 and 7.3% RSD, with the isotope ratios determined with precision 0.8% RSD at concentrations above the limit of quantification. Preliminary tests were conducted to evaluate the effect of different cations (Na + , K + , and Mg 2+ ) on Br − responses, with no discernible impacts observed on the halogen signal responses. This study demonstrates the potential use of the LS-APGD-Orbitrap-MS for the detection of multiple halogens while avoiding interferences, minimizing sample preparation, and overcoming ionization barriers.

Lang, Dehlia A. [Clemson University, SC (United St↗

DOE OSTI2021

Correlating Nanoscale Secondary Ion Mass Spectrometry and Atom Probe Tomography Analysis of Uranium Enrichment in Metallic Nuclear Fuel

Distribution and enrichment of 235U within nuclear fuels are essential to material performance and reactor safety. With the development of metallic U fuels, understanding 235U homogeneity has become increasingly important, however, it is difficult to map with high spatial, and mass resolution to analyze both matrix and secondary phase precipitates. Here, we analyze 235U enrichment in matrix and carbide phases in LEU-Mo via two chemical imaging modalities: nanoscale secondary ion mass spectrometry (nanoSIMS) and atom probe tomography (APT). NanoSIMS and APT provided consistent results, with no statistically significant difference between measured and nominal enrichment (19.75 % 235U).

U-10Mo, atom probe tomography, nanoscale secondary↗

DOE OSTI2026

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Han, Zhenyu [Department of Chemistry, Northwestern↗