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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

We report the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Abstract Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal ( RCSB.org ) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal ( PDB101.RCSB.org ) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org ; and (v) supports training, outreach, and education via PDB101.RCSB.org . New tools and features at RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Ta Based Damascene Resonators

Transmon qubits have become a leading technology in quantum information science (QIS), with fabrication techniques widely accessible. Historically, devices were predominantly made from aluminum (Al) and niobium (Nb), but state-of-the-art transmons now use tantalum (Ta) achieving coherence times up to and exceeding 0.5 milliseconds [1-3]. The differentiation in performance between Ta and Nb-based devices is attributed to the surface oxidation states affecting Two-Level-System (TLS) noise. One approach to quickly evaluating material and device performance consists of fabricating only the readout resonator of a qubit and evaluating the quality factor which is the strategy employed in this project. Our research focuses on Ta coplanar waveguide (CPW) resonators fabricated using a damascene technique producing pristine metal structures within silicon substrates. This approach increases the dielectric substrate's participation ratio while keeping device edges oxide-free due to entrenchment. This collaborative effort, involving Pacific Northwest National Laboratory (PNNL), NY CREATES/SUNY Poly, and Brookhaven National Laboratory (BNL), has resulted in resonators with Q factors as high as 104 at low power. Ongoing studies aim to further understand and improve device performance by systematic analysis of oxygen trapped between device layers during processing. This research showcases the potential for significant improvements in superconducting qubit performance via the damascene process, heralding new possibilities for the advancement of scalable QIS technology.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Dynamic Nuclear Polarization Enhanced 113 Cd Solid-State Nuclear Magnetic Resonance Spectroscopy Reveals CdSe Nanocrystals with Triangular Two-Dimensional Projections are Terminated by {100} Facets

Surface structure plays an important role in particle growth and determining the chemical and photophysical properties of semiconductor nanocrystals (NCs). Therefore, there is a need for structural tools that can characterize and detect different surface facets. Here, we sought to investigate the structure of {111} CdSe facets by applying dynamic nuclear polarization (DNP) enhanced 113 Cd and 77 Se solid-state nuclear magnetic resonance (SSNMR) spectroscopy to zinc-blende CdSe NCs that exhibit triangular two-dimensional (2D) projections within transmission electron microscope (TEM) images. It was originally hypothesized in the literature that these CdSe NCs were tetrahedral in shape and terminated by facets from the {111} family of lattice planes of the zinc-blende structure. Surprisingly, we observe 113 Cd NMR spectra indicating that the primary facets are from the {100} family of lattice planes. We also obtained DNP-enhanced 113 Cd and 77 Se SSNMR spectra of recently reported right trigonal bipyramidal (rTriBP) CdSe NCs grown by seeded growth. The 113 Cd NMR spectra rTriBP CdSe NCs are consistent with {100} surface facets. TEM images show that rTriBP NCs may also exhibit triangular 2D projections that are similar to the so-called tetrahedral NCs. Based upon these results, we conclude that the so-called tetrahedral NCs are predominantly terminated by {100} surface facets and most likely have the same shape as rTriBP NCs. These results highlight the need for multiple complementary techniques when assigning the shape and surface termination of NCs.

Santhiran, Anuluxan [Ames Laboratory (AMES), Ames,↗
DOE OSTI2024

Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis

Methyl-coenzyme M reductase (MCR) is the key enzyme in the biological formation and anaerobic oxidation of methane (AOM). Methane is a potent greenhouse gas and the major component of natural gas. Given the abundance of natural gas reserves in remote areas, there is great current interest in a scalable bio-based process for the conversion of methane to liquid fuel or other high-value commodity chemicals. MCR holds much promise for use in such a methane bioconversion strategy. However, MCR cannot currently be produced in an active form in a heterologous host, due in large part to the lack of genetic and biochemical information about the production of holo MCR. In an effort to overcome this deficiency, our laboratory elucidated the biosynthetic pathway of the unique nickel-containing coenzyme of MCR, F430. The key step in coenzyme F430 biosynthesis (Cfb) was found to involve an unprecedented reductive cyclization reaction that converts Ni-sirohydrochlorin a , c -diamide to 15,17 3 -seco-F430-17 3 -acid. This remarkable transformation, which involves a 6-electron reduction of the isobacteriochlorin ring system, cyclization of the c -acetamide side chain to form a γ-lactam ring, and the formation of 7 stereocenters, is catalyzed by a primitive homolog of nitrogenase (CfbCD). Nitrogenase is a two-component metalloenzyme that catalyzes the ATP-dependent reduction of dinitrogen to ammonia (nitrogen fixation). Homologs of nitrogenase are also involved in the biosynthesis of the photosynthetic pigments chlorophyll and bacteriochlorophyll. Phylogenetic analysis of the CfbCD complex suggests that it is representative of a more ancient lineage of the nitrogenase superfamily, and a thorough investigation of its structure and function is likely to shed light on the mechanisms and evolution of these important metalloenzymes that catalyze multi-electron redox reactions. Moreover, a detailed understanding of the mechanism of the CfbCD complex may aid in the development of specific inhibitors to help reduce natural greenhouse gas emissions and can be exploited for the heterologous production of MCR for methane bioconversion. Towards these goals, the following Specific Aims will be pursued to determine the: 1) Identity of the CfbCD reaction product. The exact reaction catalyzed by CfbCD, including the number of electrons transferred and whether it involves enzymatic cyclization, is unclear. Several approaches, including reaction stoichiometry measurements, spectroelectrochemistry, and magnetic resonance spectroscopy will be applied to elucidate the structure of the reaction product and establish whether CfbCD is a reductase or reductive cyclase. 2) Structure, conformational dynamics, and oligomerization state changes of CfbCD. Significant insight into the mechanism and allosteric regulation of CfbCD can be obtained by assessing changes in the structure and dynamics of the complex during the catalytic cycle. To accomplish this, a combination of size-exclusion chromatography, hydrogen-deuterium exchange mass spectrometry, molecular dynamics simulations, and high-resolution structural methods will be employed. 3) Source, order, and stereochemistry of proton additions during CfbCD catalysis. Details regarding the order and stereochemistry of proton additions during the CfbCD reaction will be uncovered using a combined spectroscopic and computational approach. Complementary mechanistic studies employing site-directed mutagenesis and substrate analogs will establish the identity of active site acid residues and the possible involvement of substrate-assisted catalysis during the CfbCD reaction.

09 BIOMASS FUELS↗
DOE OSTI2024

Quasiparticle Poisoning of Superconducting Qubits from Resonant Absorption of Pair-Breaking Photons

The ideal superconductor provides a pristine environment for the delicate states of a quantum computer: because there is an energy gap to excitations, there are no spurious modes with which the qubits can interact, causing irreversible decay of the quantum state. As a practical matter, however, there exists a high density of excitations out of the superconducting ground state even at ultralow temperature; these are known as quasiparticles. Observed quasiparticle densities are of order 1 μ m - 3 , tens of orders of magnitude greater than the equilibrium density expected from theory. Nonequilibrium quasiparticles extract energy from the qubit mode and can induce dephasing. Here we show that a dominant mechanism for quasiparticle poisoning is direct absorption of high-energy photons at the qubit junction. We use a Josephson junction-based photon source to controllably dose qubit circuits with millimeter-wave radiation, and we use an interferometric quantum gate sequence to reconstruct the charge parity of the qubit. We find that the structure of the qubit itself acts as a resonant antenna for millimeter-wave radiation, providing an efficient path for photons to generate quasiparticles. A deep understanding of this physics will pave the way to realization of next-generation superconducting qubits that are robust against quasiparticle poisoning.

Liu, Chuan-Hong↗
NASA NTRS2012

Development and Validation of an Interactive Liner Design and Impedance Modeling Tool

The Interactive Liner Impedance Analysis and Design (ILIAD) tool is a LabVIEW-based software package used to design the composite surface impedance of a series of small-diameter quarter-wavelength resonators incorporating variable depth and sharp bends. Such structures are useful for packaging broadband acoustic liners into constrained spaces for turbofan engine noise control applications. ILIAD s graphical user interface allows the acoustic channel geometry to be drawn in the liner volume while the surface impedance and absorption coefficient calculations are updated in real-time. A one-dimensional transmission line model serves as the basis for the impedance calculation and can be applied to many liner configurations. Experimentally, tonal and broadband acoustic data were acquired in the NASA Langley Normal Incidence Tube over the frequency range of 500 to 3000 Hz at 120 and 140 dB SPL. Normalized impedance spectra were measured using the Two-Microphone Method for the various combinations of channel configurations. Comparisons between the computed and measured impedances show excellent agreement for broadband liners comprised of multiple, variable-depth channels. The software can be used to design arrays of resonators that can be packaged into complex geometries heretofore unsuitable for effective acoustic treatment.

Howerton, Brian M.↗
NASA NTRS1972

Production cross sections for Lee-Wick massive electromagnetic bosons and for spin-zero and spin-one W bosons at high energies.

Production cross sections for three types of hypothetical particles are calculated in the presented paper. Several (Z, Z') cases were studied corresponding to elastic scattering off protons and neutrons (either free or embedded within a Fermi sea), coherent scattering off a nucleus, and inelastic scattering off a proton (in which case Z' denotes a nucleon resonance or hadronic system in the continuum). Detailed structure-function data are used to improve the accuracy of the inelastic scattering calculation. Results of calculations are given for beam energies between 50 and 10,000 GeV, and masses between 5 and 40 GeV for the massive Lee-Wick spin-1 boson. Cross sections were computed for resonant and semiweak processes. The production cross section of spin-zero weak intermediate bosons was found to be at least one order of magnitude smaller than for spin-1 weak bosons in nearly all regions of interest. The production cross section of spin-zero weak intermediate bosons for inelastic scattering off protons compares with that for elastic scattering in the regions of interest. In the case of massive spin-1 bosons and spin-1 weak intermediates, the main contribution to total production cross section off protons is elastic.

Linsker, R.↗
NASA NTRS2007

Simplified Generation of High-Angular-Momentum Light Beams

A simplified method of generating a beam of light having a relatively high value of angular momentum (see figure) involves the use of a compact apparatus consisting mainly of a laser, a whispering- gallery-mode (WGM) resonator, and optical fibers. The method also can be used to generate a Bessel beam. ( Bessel beam denotes a member of a class of non-diffracting beams, so named because their amplitudes are proportional to Bessel functions of the radii from their central axes. High-order Bessel beams can have high values of angular momentum.) High-angular-momentum light beams are used in some applications in biology and nanotechnology, wherein they are known for their ability to apply torque to make microscopic objects rotate. High-angular-momentum light beams could also be used to increase bandwidths of fiber-optic communication systems. The present simplified method of generating a high-angular-momentum light beam was conceived as an alternative to prior such methods, which are complicated and require optical setups that include, variously, holograms, modulating Fabry-Perot cavities, or special microstructures. The present simplified method exploits a combination of the complex structure of the electromagnetic field inside a WGM resonator, total internal reflection in the WGM resonator, and the electromagnetic modes supported by an optical fiber. The optical fiber used to extract light from the WGM resonator is made of fused quartz. The output end of this fiber is polished flat and perpendicular to the fiber axis. The input end of this fiber is cut on a slant and placed very close to the WGM resonator at an appropriate position and orientation. To excite the resonant whispering- gallery modes, light is introduced into the WGM resonator via another optical fiber that is part of a pigtailed fiber-optic coupler. Light extracted from the WGM resonator is transformed into a high-angular- momentum beam inside the extraction optical fiber and this beam is emitted from the polished flat output end. By adjusting the geometry of this apparatus, it is possible to generate a variety of optical beams characterized by a wide range of parameters. These beams generally have high angular momenta and can be of either Bessel or Bessel-related types.

Savchenkov, Anatoliy↗
DOE OSTI2021

Understanding the microstructural evolution of hypersaline cemented paste backfill with low-field NMR relaxation

Highlights: • Microstructural evolution of CPB, prepared with tap and hypersaline water, is monitored using low-field NMR relaxometry. • T{sub 1} and T{sub 2} NMR relaxation measurements compared with mechanical strength via UCS tests • Hypersaline mixing water results in slower structural evolution and lower mechanical strength. Cemented paste backfill (CPB) comprising mineral tailings, binders and mixing water is an important potential support material in the mining industry. As the mechanical properties of CPB are significantly influenced by its microstructural characteristics the development of measurement tools to better understand its pore structure evolution is important for its increased utilisation. This study reports the application of low-field nuclear magnetic resonance (NMR) relaxation time measurements to characterise the microstructural evolution of CPB materials over 56 days of hydration, contrasting common tap water and hypersaline water (~22 wt% salt) as mixing water. Distinct NMR relaxation time populations were evidenced within each CPB sample, revealing the presence of both capillary (T{sub 1,2} ≈ 10 ms) and gel pore water (T{sub 1,2} ≈ 300–500 μs), with time-dependent relaxation measurements facilitating characterisation of capillary pore structure evolution over the hydration period assessed. Hypersaline samples demonstrated a time-lag in this measured capillary pore evolution, relative to those hydrated with tap water, while pore structure evolution rates were observed to increase with increased CPB binder content. Further, both T{sub 1} and T{sub 2} NMR relaxation times were found to correlate with the uniaxial compressive strength of the CPB materials investigated, facilitating the formulation of a predictive correlation function between NMR relaxation characteristics and mechanical properties.

36 MATERIALS SCIENCE↗
NASA NTRS2026

Polarized Resonant Soft X-ray Scattering (P-RSoXS) as a New Technique for Characterizing Amorphous Astromaterials

In the coming years, samples will be returned from several asteroids, the lunar surface, and the first material returned directly from the Martian surface. Previous in-situ and remote studies indicate these samples will contain abundant amorphous or weakly crystalline materials. However, detailed characterization and quantification of these amorphous materials remains challenging. Conventional techniques, including electron microscopy and X-ray diffraction, provide important information on material structure, but are generally limited to crystalline materials. Polarized resonant soft X-ray scattering (P-RSoXS) is a synchrotron-based X-ray scattering technique that has been used to characterize and quantify weakly crystalline systems, including soft materials. This research aims to translate this technique to geologic and extraterrestrial materials, building off the knowledge of using P-RSoXS to interrogate soft materials. P-RSoXS is well-suited to interrogate geologic materials, which are often multiphase, heterogeneous systems with crystalline and amorphous components, and domain sizes on the order of tens of nanometers. It is anticipated that future work will help reveal new chemical and structural information in geologic materials. Maturation of this preliminary work to develop P-RSoXS to characterize astromaterial-relevant samples will provide new understanding of the secondary processes responsible for the development of amorphous astromaterials and further elucidate our knowledge of the geologic history and past alteration processes.

Joshua H Litofsky↗
NASA NTRS1992

Dynamics and control of coherent structure in turbulent jets

Current understanding of coherent structure dynamics in incompressible turbulent jets as explained by the nonlinear stability theory is reviewed, focusing on nonswirling turbulent jets. Topics addressed include hydrodynamic stability theory and coherent structures; dynamics of energy transfers among different scales of motion; nonlinear development of amplitude; development of single-frequency coherent mode; fundamental-subharmonic interaction and vortex pairing; and reversal of Reynolds stresses. Attention is also given to the effect of initial phase-difference angle between fundamental and subharmonic, conditions for resonance interaction, modulation of spreading rate by controlling coherent structure, turbulence enhancement or suppression due to excitation, 3D effects, jet noise, and swirling jets.

Mankbadi, Reda R.↗
DOE OSTI2022

Zoology of Multiple- Q Spin Textures in a Centrosymmetric Tetragonal Magnet with Itinerant Electrons

Magnetic skyrmion is a topologically stable particle-like swirling spin texture potentially suitable for high-density information bit, which was first observed in noncentrosymmetric magnets with Dzyaloshinskii–Moriya interaction. Recently, nanometric skyrmion has also been discovered in centrosymmetric rare-earth compounds, and the identification of their skyrmion formation mechanism and further search of nontrivial spin textures are highly demanded. Here, magnetic structures in a prototypical skyrmion-hosting centrosymmetric tetragonal magnet GdRu2Si2 is exhaustively studied by performing the resonant X-ray scattering experiments. A rich variety of double-Q magnetic structures, including the antiferroic order of meron(half-skyrmion)/anti-meron-like textures with fractional local topological charges are identified. The observed intricate magnetic phase diagram is successfully reproduced by the theoretical framework considering the four-spin interaction mediated by itinerant electrons and magnetic anisotropy. The present results will contribute to the better understanding of the novel skyrmion formation mechanism in this centrosymmetric rare-earth compound, and suggest that itinerant electrons can ubiquitously host a variety of unique multiple-Q spin orders in a simple crystal lattice system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Generalizable, tunable control of divalent cation solvation structure via mixed anion contact ion pair formation

Multivalent batteries are a promising new technology for energy storage, but they face challenges to developing suitable electrolytes that can support reversible deposition/dissolution at the metal anode and enable compatibility with high voltage oxide cathode materials. Here, in this work, we investigate the solvation behavior of Zn 2+ , Mg 2+ , Ca 2+ and Cu 2+ in mixed anion electrolytes containing TFSI - and Cl - . Raman and nuclear magnetic resonance spectroscopies are utilized to probe the bulk solvation structure of these electrolytes and demonstrate that mixed anion contact ion pairs (CIPs) are formed in all four systems, indicating this behavior is likely general to divalent cations. Furthermore, the relative population of mixed anion CIPs can be tuned by controlling the relative ratio of TFSI : Cl, with significant CIP populations observed even at low relative fractions of Cl - . These findings imply that modifying the anion chemistry can easily adjust the solvation structure of bulk cations, which has important implications for the development of next-generation electrolytes. By understanding the factors that influence the formation of mixed anion CIPs, we can design systems that promote the formation of electrochemically-active solvation structures that can enable multivalent batteries with improved performance and lifetimes.

25 ENERGY STORAGE↗
DOE OSTI2022

Status Update on the Development of Transducers and Bonding Techniques for Enabling Acoustic Measurements of Damage in Microreactor Components

This report provides an overview of potential sensors and sensor-bonding techniques to enable the online acoustic interrogation of microreactor components and enhance structural health monitoring capabilities. The report focuses primarily on optical fiber–based acoustic sensors and describes initial experimental progress toward the deployment of these sensors for microreactor applications. The general approach is to monitor the resonant frequencies of microreactor components and search for evidence of structural defects that could indicate imminent failure. If properly identified, then the components could be repaired during the next reactor outage to prevent costly unplanned shutdowns. The ability to monitor the structural health of components could also reduce the need for time-consuming visual inspections and reduce staffing to improve microreactor economic viability. Increased sensor density is also one of the first steps to moving toward eventual semiautonomous operation. The expected microreactor conditions in which acoustic sensors must survive are characterized, including temperatures, neutron fluences, thermomechanical strains, and vibrational frequencies. Optical fiber–based acoustic sensors are identified as an attractive candidate for acoustic monitoring because of their high accuracy, immunity to electromagnetic interference, and resiliency in high-temperature, high-radiation environments. Optical fiber–based intrinsic sensors, such as type-II fiber-Bragg gratings and Fabry-Pérot Cavities (FPCs), are particularly attractive for a microreactor environment because of their high temperature stability, and FPCs also enable higher frequency interrogation with a lower sensitivity to radiation-induced drift. This report describes multiple interrogation systems, but the best interrogation system for a given situation will depend on the specific microreactor application, including the desired acoustic vibrational amplitudes, modes, and resonant frequencies. Initial experiments included fabricating three FPCs, tack-welding these FPCs to stainless-steel pipes or rods and performing room-temperature acoustic sensing tests to capture the vibrational frequency content. Peaks were identified in the measured frequency spectra and compared with the theoretical fundamental frequencies obtained from Euler-Bernoulli beam theory. Two of the three FPCs measured vibrational frequencies that generally matched those obtained from theory. Future work will include similar testing on pipes or other microreactor components with intentional flaws to evaluate the ability to determine changes in resonant frequencies. Finally, these tests will be repeated at high temperatures, potentially with an applied thermomechanical stress, to include environmental conditions similar to those for a microreactor application.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗