SEARCH · Search NASA

Results for “multiple crystals”

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.

SourceResearch connectionFrom yearThrough year

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

At least 361 records · Page 20

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19

The SARS-CoV-2 3CL protease is a critical drug target for small molecule COVID-19 therapy, given its likely druggability and essentiality in the viral maturation and replication cycle. Based on the conservation of 3CL protease substrate binding pockets across coronaviruses and using screening, we identified four structurally distinct lead compounds that inhibit SARS-CoV-2 3CL protease. After evaluation of their binding specificity, cellular antiviral potency, metabolic stability, and water solubility, we prioritized the GC376 scaffold as being optimal for optimization. We identified multiple drug-like compounds with <10nM potency for inhibiting SARS-CoV-2 3CL and the ability to block SARS-CoV-2 replication in human cells, obtained co-crystal structures of the 3CL protease in complex with these compounds, and determined that they have pan-coronavirus activity. We selected one compound, termed coronastat, as an optimized lead and characterized it in pharmacokinetic and safety studies in vivo. Coronastat represents a new candidate for a small molecule protease inhibitor for the treatment of SARS-CoV-2 infection for eliminating pandemics involving coronaviruses.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Structural basis for varying drug resistance of SARS-CoV-2 M pro E166 variants

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M pro ) has an essential role in the virus lifecycle and, accordingly, it is a target for antiviral drugs. Multiple studies have identified an M pro mutation (E166V) that confers strong resistance to clinically relevant inhibitors, including nirmatrelvir, but the underlying mechanism is not fully understood. Here, we report on crystal structures of SARS-CoV-2 M pro E166V in complex with nirmatrelvir, ensitrelvir, and bofutrelvir. The structures suggest that resistance is caused in part by the loss of a direct hydrogen bond and also, especially for nirmatrelvir, by a steric clash with the substituted valine residue. In comparison, the binding of bofutrelvir shows greater flexibility, which may help alleviate this steric effect and allow bofutrelvir to fit the mutant active site despite the loss of a direct polar contact. Thermal stability analyses also corroborate E166V most severely affecting the binding of nirmatrelvir and, to lesser and different extents, ensitrelvir and bofutrelvir. We further show that E166I causes even more severe nirmatrelvir resistance, whereas E166A and E166L have much milder effects. These studies shed light on the molecular mechanisms of a key M pro drug resistance mutation and may help inform the design of next-generation inhibitors. IMPORTANCE Using a combination of high-resolution X-ray crystallographic and biochemical analyses, we reveal the molecular mechanisms by which a mutation in the severe acute respiratory syndrome coronavirus 2 main protease (M pro ) confers strong resistance against clinically relevant antiviral drugs that inhibit M pro activity. The results presented here may help inform the design of next-generation inhibitors to combat the problem of therapy resistance.

Microbiology↗

DOE OSTI2021

Ice Multiplication by Fragmentation during Quasi-Spherical Freezing of Raindrops: A Theoretical Investigation

Ice multiplication by fragmentation during collision–freezing of supercooled rain or drizzle is investigated. A zero-dimensional dynamical system describes the time evolution of number densities of supercooled drops and ice crystals in a mixed-phase cloud. The characteristic time scale for this collision–freezing ice fragmentation is controlled by the collision efficiency, the number of ice fragments per freezing event, and the available number concentration of supercooled drops. The rate of the process is proportional to the number of supercooled drops available. Thus, ice may multiply extensively, even when the fragmentation number per freezing event is relatively small. The ratio of total numbers of ice particles to those from the first ice, namely, the “ice-enhancement factor,” is controlled both by the number of fragments per freezing event and by the available number concentration of supercooled drops in a similar manner. Especially, when ice fragmentation by freezing of supercooled drops is considered in isolation, the number of originally existing supercooled drops multiplied by the fragmentation number per freezing event yields the eventual number of ice crystals. When supercooled drops are continuously generated by coalescence, ice crystals from freezing fragmentation also continuously increase asymptotically at a rate equal to the generation rate of supercooled drops multiplied by the fragmentation number per freezing event. All these results are expressed by simple analytical forms, thanks to the simplicity of the theoretical model. These parameters can practically be used as a means for characterizing observed mixed-phase clouds.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Complex Adsorption Behavior of Neodymium and Ytterbium on Structurally-Distinct Alumina Surfaces

New sources of rare earth elements (REEs) are needed to support a green energy transition. REEs adsorbed to aluminum-rich clays in weathering deposits represent important resources but the mechanisms responsible for their retention and ease of extraction are unresolved. Disordered coordination and co-occurrence of multiple species pose challenges to investigating REE adsorption processes via established spectroscopic methods. In this study, we applied element-specific surface crystallography methods to obtain a new perspective on the complexity of REE adsorption mechanisms and affinities. Alumina (001) and (012) crystal surfaces were utilized to evaluate surface-specific controls on Nd(III) and Yb(III) adsorption behavior. The REEs displayed similar total adsorption to alumina (001) as a mixture of inner- and outer-sphere complexes, but Nd displayed a greater proportion of inner-sphere binding. Adsorption of ordered inner- and outer-sphere REE species was substantially lower on alumina (012). These distinct behaviors reflect differences in the surface functional group charging and topography of the two surfaces. However, alumina (012) also hosted a substantial population of disordered adsorbed species, especially for Nd, potentially associated with Al vacancy surface defects. Here, the accumulation of light versus heavy REEs via adsorption in weathering deposits likely results from multiple, competing reactions affected by clay particle morphology. Leaching procedures for resource recovery should account for differential rates of desorption by coexisting inner- and outer-sphere REE surface complexes.

58 GEOSCIENCES↗

DOE OSTI2021

An investigation of high entropy alloy conductivity using first-principles calculations

The Kubo–Greenwood equation, in combination with the first-principles Korringa–Kohn–Rostoker coherent potential approximation (KKR-CPA) can be used to calculate the DC residual resistivity of random alloys at T = 0 K. We implemented this method in a multiple scattering theory based ab initio package, MuST, and applied it to the ab initio study of the residual resistivity of the high entropy alloy Al x CoCrFeNi as a function of x. The calculated resistivities are compared with experimental data. We also predict the residual resistivity of refractory high entropy alloy MoNbTaV x W. Furthermore, the calculated resistivity trends are also explained using theoretical arguments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Curvilinear Magnonic Crystal Based on 3D Hierarchical Nanotemplates

Curvilinear magnetic nanostructures enable control of magnetization dynamics through geometry-induced anisotropy and chiral interactions, as well as magnetic field modulation. In this work, we report a curvilinear magnonic crystal based on large-area square arrays of truncated nanospikes fabricated by conformal coating of 3D hierarchical templates with permalloy thin films. Brillouin light scattering spectroscopy reveals an anisotropic band structure with multiple dispersive and folded Bloch-type dispersive spin-wave modes as well as nondispersive modes exhibiting direction-dependent frequency shifts and intensity asymmetries along lattice principal axes. Finite element micromagnetic simulations indicate that curvature-induced variations of the demagnetizing field govern the magnonic response, enabling the identification of modes propagating in nanochannels and others localized on nanospike apexes or along the ridges connecting adjacent nanospikes. The combination of geometric curvature and optical probing asymmetry produces directional dependence of magnonic bands, establishing 3D hierarchical templates as a versatile platform for curvature-engineered magnonics.

3D hierarchical templates↗

DOE OSTI2023

In Situ Attenuated Total Reflectance Infrared Spectroelectrochemistry (ATR-IR-SEC) for the Characterization of Molecular Redox Processes on Surface-Proximal Doped Silicon ATR Crystal Working Electrodes

In situ mid-infrared spectroscopy is a powerful technique for understanding the mechanism of CO 2 reduction (CO 2 R) catalysts because it enables the direct detection of catalytic intermediates and products. Moreover, spectroelectrochemistry (SEC), the coupling of spectroscopy with electrochemistry, allows spectroscopic changes to be correlated with applied potentials to reveal potential-dependent intermediates that are often relevant to photoelectrochemical reactions. Hybrid photoelectrodes, comprised of a narrow bandgap semiconductor, like silicon (Si), with a covalently-linked molecular catalyst, are a promising platform for sunlight-driven catalysis, but characterization of the catalytic mechanism(s) is challenging under photoelectrochemical conditions, particularly when the catalyst is present in monolayer or less concentrations. Here, we have developed a new strategy to use multiple-reflection attenuated total reflectance IR spectroscopy (ATR-IR) coupled with electrochemistry to characterize catalysts directly integrated with a semiconductor surface under applied potential. We show that by surface-proximal n-type or p-type doping of the top ~100-200 nm of the crystal surface, Si ATR crystals can be used simultaneously as the internal reflection element and semiconductor working electrode for ATR-IR-SEC measurements. The surface-proximal doping strategy yields a quasi-equipotential surface with excellent infrared transparency that would have been compromised by free carrier absorption if the crystal was uniformly doped. This approach permits the catalytically-active functionalized surface to be directly probed without modification and overcomes signal-to-noise limitations of other strategies that use separately deposited working electrodes on Si ATR crystals. Proof-of-concept ATR-IR-SEC spectra were collected during the reduction and oxidation of monolayers of Re- and Ru-based transition metal carbonyl complexes, respectively, verifying the viability of the technique to probe redox processes associated with CO 2 R catalysts on Si electrode surfaces with high sensitivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Single Crystals of Vanadium Oxides as a Lens for Understanding Structural and Electronic Phase Transformations, Ion Transport, Chemo-Mechanical Coupling, and Electrothermal Neuronal Emulation

Vanadium oxides cystallize in a diverse array of structures and compositions arising from the redox versatility of vanadium, variable covalency of V−O bonds, and myriad coordination geometries. Their open frameworks present abundant interstitial sites that enable insertion of guest-ions. In such compounds, V3d electron and spin localization and disorder couple strongly to structural preferences. The rich structural diversity manifests as a “rugged” free energy landscape with multiple interconvertible polymorphs. Such a landscape sets up structural, electronic, and magnetic transitions that underpin the promise of these materials as ion-insertion battery electrodes; compact primitives for brain-inspired computing, and heterogeneous catalysts. Here, we examine the structural and compositional diversity, electronic instabilities, defect dynamics, structure transformations, mechanical properties, and surface structure of vanadium oxides using single crystals as a distinctive lens. Single crystals enable the measurement of structure−function correlations without the ensemble and orientational averaging inevitable in polycrystalline materials. Their well-defined surfaces further enable examination of facet-dependent reactivity toward molecular adsorbates, ion fluxes, and lattice (mis)matched solids. We provide a comprehensive account of vanadium-oxide single-crystal studies, from delineation of common structural motifs to single-crystal growth techniques, topochemical modification strategies, mechanisms underpinning electronic instabilities, and implementation as electrothermal neurons and battery electrode materials.

Ponis, John [Texas A&M University, College Station↗

DOE OSTI2023

True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications

The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet–triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Evolution of texture and internal stresses within polycrystalline rock salt using in situ 3D synchrotron computed tomography and 3D X-ray diffraction

Over time rock salt caverns have been extensively used as reliable repositories for hazardous waste such as nuclear waste, oil or compressed gases. Undisturbed rock salt deposits in nature are usually impermeable and have very low porosity. However, rock salt formations under excavation stresses can develop crack networks, which increase their porosities; and in the case of a connected crack network within the media, rock salt may become permeable. Although the relationship between the permeability of rock salt and the applied stresses has been reported in the literature, a microscopic study that investigates the properties influencing this relationship, such as the evolution of texture and internal stresses, has yet to be conducted. This study employs in situ 3D synchrotron micro-computed tomography and 3D X-ray diffraction (3DXRD) on two small-scale polycrystalline rock salt specimens to investigate the evolution of the texture and internal stresses within the specimens. The 3DXRD technique measures the 3D crystal structure and lattice strains within rock salt grains. The specimens were prepared under 1D compression conditions and have shown an initial {111} preferred texture, a dominant {110}$\langle1\bar{1}0\rangle$ slip system and no fully connected crack network. The {111} preferred texture under the unconfined compression experiment became stronger, while the {111}$\langle1\bar{1}0\rangle$ slip system became more prominent. The specimens did not have a fully connected crack network until applied axial stresses reached about 30 MPa, at a point where the impermeability of the material becomes compromised due to the development of multiple major cracks.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Computing diffraction patterns of microstructures from phase-field simulations

The diffraction pattern of a material contains information not only on the crystal structures of its constituting phases, but also on its mesoscale spatial distributions of phases, grains, and ferroelastic, ferroelectric, and ferromagnetic domains. While diffraction patterns from experiments such as X-ray diffraction are presented in the reciprocal or Fourier space, mesoscale microstructure models such as the phase-field method naturally produce real-space images of spatial distribution of chemical composition, structural, and ferroic domains. Although one could rather readily compute the Fourier amplitudes of chemical and structural domain distributions generated by mesoscale simulations, they only contain information about the length scale and alignment of the real-space chemical and structure domains. Therefore, a direct comparison between diffraction experiments and mesoscale microstructure simulations is not possible. Here, we develop a theoretical approach to directly compute the crystal diffraction patterns of microstructures predicted by phase-field simulations. In particular, we consider five representative examples of microstructure patterns involving purely compositional domains, a single pair of tetragonal twin structures, multiple twin variants in a hexagonal system, ferroelectric polar vortices, and polycrystalline grains. The results are compared with previous experimental observations as well as X-ray diffraction experiments performed in the present study. Furthermore, the theoretical framework allows one to directly connect material microstructures and diffraction patterns predicted from phase-field simulations and the corresponding diffraction patterns from experiments, and thus providing guidance to experimental diffraction characterization and interpretation of microstructures.

36 MATERIALS SCIENCE↗

DOE OSTI2026

ALS mutations disrupt self-association between the ubiquilin STI1 hydrophobic groove and internal placeholder sequences

Ubiquilins are molecular chaperones that play multifaceted roles in proteostasis, with point mutations in UBQLN2 leading to altered phase-separation properties and amyotrophic lateral sclerosis (ALS). Our mechanistic understanding of this essential process has been hindered by a lack of structural information on the STI1 domain, which is essential for ubiquilin chaperone activity and phase separation. Here, we present the first crystal structure of a ubiquilin-family STI1 domain bound to a transmembrane domain (TMD), and show that ALS mutations disrupt the STI1-TMD interaction. We further demonstrate that ubiquilins contain multiple conserved internal sequences that bind to the STI1 domain, including the PXX-repeat region that is a hotspot for ALS mutations. We propose that these placeholder sequences prevent solvent exposure of the STI1 hydrophobic groove and contribute to the multivalency that drives ubiquilin phase-separation. Together, this work provides a new paradigm for understanding how STI1 domains modulate ubiquilin chaperone activity and phase separation, and offers insights into the molecular basis of ALS pathogenesis.

Onwunma, Joan [Univ. of Toledo, OH (United States)↗

DOE OSTI2025

Thermodynamically leveraged solventless aerobic deconstruction of polyethylene-terephthalate plastics over a single-site molybdenum-dioxo catalyst

Here, we describe the solventless catalytic deconstruction of polyethylene-terephthalate (PET) under an aerobic atmosphere, mediated by an earth-abundant, low-cost activated carbon (AC)-supported single-site molybdenum-dioxo catalyst (AC/MoO 2 ). Catalytic amounts of AC/MoO 2 selectively convert waste PET into its monomer, terephthalic acid (TPA), within 4 h at 265 °C with yields as high as 94% under 1 atm air. Pure crystalline TPA product sublimes from the reaction hot zone, crystallizing on the reactor cold zone, thus avoiding the need for separation and purification steps. This process does not employ any hazardous/toxic reducing agents or solvents, and the catalyst can be recycled multiple times without loss of activity, rendering this process highly atom-efficient. According to computational and experimental mechanistic studies, the AC/MoO 2 catalyst mediates a thermoneutral metal-catalyzed β-scission step, followed by an exothermic step that converts the vinyl benzoate intermediate to TPA and acetaldehyde using trace amounts of moisture in the air. The formation of gaseous acetaldehyde makes the isolation of TPA from the reaction mixture facile and industrially favorable, especially since solvents are unnecessary. The present methodology is also extended to the deconstruction of other frequently used polyester plastics, polybutylene terephthalate (PBT), polyethylene naphthalate (PEN), and polyethylene furanoate (PEF), and operates equally well with post-consumer waste products. Notably, this process is also compatible with plastic mixtures of polyesters with polyolefins, polyamides, and polycarbonates, leading to the selective conversion of each polyester to the corresponding monomer, leaving the residual polymer unchanged and polyester-free.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

FRAM Isotopic Analysis of High-Resolution CZT Data

H3D Inc. has introduced a new type of CZT detectors that has resolution several times better than that of a typical, single crystal CZT detector. The better resolution has made it easier for software codes to analyze its spectra for isotopic composition of nuclear materials. The Fixed-energy Response-function Analysis with multiple efficiency (FRAM) is one of such software codes. The good peak resolution of the H3D CZT detectors allows the current FRAM v.6.1 and earlier to successfully analyze uranium spectra with minimal modification of the parameter sets and get reasonable results. (A parameter set governs how an analysis is performed.) The exceptionally large high-energy tail of the peaks makes it difficult to achieve good uranium results and impossible to successfully analyze plutonium spectra. The FRAM code needed to be modified to better fit the high-energy tail of the peaks in order to analyze plutonium data and to get better uranium analysis results. Results of this modification, encoded in beta version FRAM v.7.0i, are reported herein.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Mechanical Actuation via Homeomorphic Transformations of Topological Solitons within Polymer Coatings

Abstract Topological solitons are currently under investigation for their exotic properties, especially in nonlinear physics, optics, and material sciences. However, challenges of robust generation and limited stability over time have hindered their practical uses. To address this issue, an approach is developed to form structured arrays of solitons in films of polymerizable liquid crystals. Their complex molecular architecture is preserved by in situ photopolymerization forming a stable liquid crystal network. Most excitingly, their properties are advanced to include responsiveness functions. When thermally actuated, these topological solitons mediate the reconfiguration of surface topographies. Complex shape changes occur depending on the intrinsic complex spatial distribution of the director, which may even lead to full shape inversion and topographical changes as high as ≈40% of the initial thickness. Conversely, the shape changes provide information on the initial director profile, which is consistent with the mathematical model. The soliton‐containing polymer coatings are applicable in multiple domains, ranging from tunable optics to haptics, and from shape‐coupled sensing systems to temperature‐coupled heat management.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021)

We discuss a method for recovering complex structure factors from many simultaneously excited Bragg beam intensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unitary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

High Supersaturation in the Wake of Falling Hydrometeors: Implications for Cloud Invigoration and Ice Nucleation

Aerosol particles, cloud droplets, and ice crystals, coupled through the supersaturation field, play an important role in the buoyancy and life cycle of convective clouds. This letter reports laboratory observations of copious cloud droplets and ice crystals formed in the wake of a warm, falling water drop, which is a laboratory surrogate for a relatively warm hydrometeor in atmospheric clouds, such as a graupel particle in the wet growth regime. Aerosols were activated in the regions of very high supersaturation due to mixing in the wake. A mechanism is explored for attaining very high supersaturations capable of activating significant fractions of the interstitial aerosols within the lifetime of a convective cloud. The latent heat released from the activation of interstitial aerosols and subsequent growth may provide an additional source of buoyancy for cloud invigoration and may lead to larger concentrations of ice crystals.

54 ENVIRONMENTAL SCIENCES↗