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At least 721 records · Page 40

Evolution of the SARS-CoV -2 proteome in three dimensions (3D) during the first 6 months of the COVID -19 pandemic

Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein–protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Here detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein–protein and protein–nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.

59 BASIC BIOLOGICAL SCIENCES↗

Widespread opportunities for materials engineering of nanocrystals: Synthetically tailorable effects and methodologies

Since their initial development, semiconductor nanocrystals (NCs) and metal nanoparticles (NPs) have become widely utilized in a variety of applications, including solar energy harvesting, lighting, catalysis, biomedical imaging, and targeted cancer treatments. Because of their reduced dimensionality, NCs and NPs have vastly different optical and electronic properties than their bulk counterparts, and the properties often depend heavily on the NC or NP surface. Surface defects and ligands alter the optoelectronic properties of NCs and NPs and affect their interaction with the environment, allowing tailoring of their properties without changing the overall chemical composition. In this review, we discuss research progress focusing on optoelectronic properties of NPs and NCs and their respective applications. We highlight how different surface treatments and ligand functionalization of nanomaterials can influence these applications.

36 MATERIALS SCIENCE↗

Theoretical underpinnings of CP-violation at the high-energy frontier

We present a general analysis for the discovery potential of CP-violation (CPV) searches in scattering processes at TeV-scale colliders in an effective field theory framework, using the SMEFT basis for higher dimensional operators. In particular, we systematically examine the CP-violating sector of the SMEFT framework in some well motivated limiting cases, based on flavour symmetries of the underlying heavy theory. We show that, under naturality arguments of the underlying new physics (NP) and in the absence of (or suppressed) flavour-changing interactions, there is only a single operator, Q tΦ = Φ † Φ($\overline{q}$ 3 t) $\tilde{\phi}$ which alters the top-Yukawa coupling, that can generate a non-vanishing CP-violating effect from tree-level SM×NP interference terms. We find, however, that CPV from Q tΦ = Φ † Φ($\overline{q}$ 3 t) $\tilde{\phi}$ is expected to be at best of Ο (1%) and, therefore, very challenging if at all measurable at the LHC or other future high-energy colliders. We then conclude that a potentially measurable CP-violating effect of Ο (10%) can arise in high-energy scattering processes only if flavour-changing interactions are present in the underlying NP; in this case a sizable CPV can be generated at the tree-level by pure NP×NP effects and not from SM×NP interference. We provide several examples of CPV at the LHC and at a future e + s - collider to support these statements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Chemical Signatures of Seasonally Unique Anthropogenic Influences on Organic Aerosol Composition in the Central Amazon

Urbanization and fires perturb the quantities and composition of fine organic aerosol in the central Amazon, with ramifications for radiative forcing and public health. These disturbances include not only direct emissions of particulates and secondary organic aerosol (SOA) precursors, but also changes in the pathways through which biogenic precursors form SOA. The composition of ambient organic aerosol is complex and incompletely characterized, encompassing millions of potential structures relatively few of which have been synthesized and characterized. Through analysis of submicron aerosol samples from the Green Ocean Amazon (GoAmazon2014/5) field campaign by two-dimensional gas chromatography coupled with machine learning, ~1300 unique compounds were traced and characterized over two seasons. Fires and urban emissions produced chemically and interseasonally distinct impacts on product signatures, with only ~50% of compounds observed in both seasons. Seasonally unique populations point to the importance of aqueous processing in Amazonian aerosol ageing, but further mechanistic insights are impeded by limited product identity knowledge. Further, less than 10% of compounds were identifiable at an isomer-specific level. Overall, the findings (i) provide compositional characterization of anthropogenic influence on submicron organic aerosol in the Amazon, (ii) identify key season-to-season differences in chemical signatures, and (iii) highlight high-priority knowledge gaps in current speciated knowledge.

54 ENVIRONMENTAL SCIENCES↗

Interlayer separation in hydrogen titanates enables electrochemical proton intercalation

Electrochemical proton intercalation into titanium oxides is typically limited to the near-surface region, necessitating the use of nanostructured high surface area materials to obtain high capacities. Here, we investigate the role of materials structure to extend intercalation beyond the near-surface region. Employing a series of hydrogen titanates (HTOs), we find that electrochemical protonation capacity significantly increases with interlayer structural protonation. The maximum capacity of ~80 mA h g -1 is achieved with H 2 Ti 3 O 7 , which also undergoes reversible structural and optical changes during the de/intercalation process. Using quasi-elastic neutron scattering, we show that structural protons are highly confined in the HTO interlayer with only localized, but not translational, dynamics. Electrochemical protonation leads to a contraction of theH 2 Ti 3 O 7 interlayer without causing significant strain in the two-dimensional titanate layers. Density functional theory calculations indicate more favorable adsorption energy for intercalated protons in H 2 Ti 3 O 7 as compared to HTOs with fewer structural protons. Here, we hypothesize that interlayer structural protons are the structural feature responsible for the high electrochemical protonation capacity in H 2 Ti 3 O 7 because they effectively decrease the interconnections between the titanate layers. This enables facile compensation of the electrochemically introduced strain via one-dimensional interlayer contraction. These results demonstrate the special structural requirements for bulk proton intercalation in titanium oxides, and offer a new materials design strategy for high energy density aqueous energy storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Superior metal storage behavior of Zn-containing porous carbon nanostructures for Na and Li metal batteries

Na and Li metals are ideal anodes for high-energy rechargeable batteries. However, their poor coulombic efficiency and the associated safety issues due to dendritic metal deposition and large volume changes during metallic plating/stripping are the major causes that persistently hinder their practical energy-storage applications. Herein, Zn-containing carbon nanostructures derived from typical zeolitic imidazolate framework-8 (ZIF-8) are proposed as advanced metal anode materials for both Na and Li metal batteries. In this study; the three-dimensional interconnected porous surfaces confine metallic Na and Li within the nanostructures, filling the carbon scaffold, and covering the electrode surface to form stable solid electrolyte interphases. Based on the metal nucleation and growth results obtained through various electrochemical tests, Zn incorporation and pore morphology have been revealed to be the key factors that regulate the metal nucleation and metallic plating/stripping during cycling. Thus, the incorporation of Zn in the closed pores of a carbon nanostructure improves the cycle performance, even in carbonate electrolytes, and produces stable Na and Li metallic anodes for next-generation rechargeable batteries.

25 ENERGY STORAGE↗

Plasma gradient effect on direct laser acceleration

The transfer of a high-intensity laser pulse energy to a high-energy electron beam via the direct laser acceleration mechanism is shown to be significantly enhanced through control of the plasma density gradient. Experiments performed using the OMEGA EP facility's high-intensity beams altered the plasma density and gradients by changing the Mach number and the angle of the gas-jet nozzle to the laser axis. When a long density gradient at the rear of the target is used, the total high-energy electron number measured was enhanced by 4.5 times compared to a shorter rear gradient. Complementary two-dimensional simulations, which follow the laser field evolution and the corresponding electron dynamics, strongly support the key trends observed in the experiment. The effect is twofold, the long density gradient provides the longest acceleration distance while it minimizes the formation of the sheath field as the electron beam exits into the vacuum. This study shows the importance of tailoring the plasma density.

Laser plasma interactions↗

Toroidal modeling of plasma flow damping and density pump-out by RMP during ELM mitigation in HL-2A

Reduction of both the plasma density and toroidal flow speed, due to application of the predominantly n = 1 (n is the toroidal mode number) resonant magnetic perturbation (RMP) for controlling the edge localized mode in the HL-2A tokamak, is numerically investigated utilizing the quasi-linear initial-value code MARS-Q (Liu et al 2013 Phys. Plasmas 20 042503). Simulation results reveal that the neoclassical toroidal viscosity (NTV) due to three dimensional fields plays the key role in modifying the plasma momentum and particle transport in the HL-2A discharge. By comparing the modeling results with the measured density pump-out in the experiment, the electron NTV particle flux model, in combination with the free-boundary condition for the axisymmetric change of the density at the plasma edge, is found to yield the best agreement in terms of both the pump-out level and the overall time scale. Further sensitivity studies show that the simulated density pump-out level is reasonably robust against variations in the model assumptions, including the particle diffusion model and the non-ambipolar versus ambipolar NTV particle flux. The latter however affects the time scale for reaching the steady state solution. Finally, it is found that the plasma edge-peeling response, the NTV torque, as well as the plasma momentum and particle transport, all are sensitive to the toroidal phase difference between the upper and lower rows of the RMP coil currents in HL-2A, with the 30 ∘ coil phasing producing the minimal side effects on the plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Seeing through nuclear fuel: Three-dimensional, nondestructive X-ray microscopy and volumetric analyses of neutron-irradiated TRISO-coated fuel kernels

The three-dimensional (3D) characterization of nuclear fuel with X-ray microscopy has historically proven difficult, due to uranium’s high attenuation of easily accessible X-rays, both in a laboratory setting and at a synchrotron user facility. However, this imaging modality provides nondestructive information that can be used to investigate morphological changes arising from external stimuli (e.g., neutron irradiation, high-temperature testing). Using an appropriate X-ray energy spectrum and an adequate X-ray filter, suitable transmissions through properly sized nuclear fuel specimens can be achieved. Here, in this study, we present the methods and results of using a commercially available, laboratory-based X-ray microscope (XRM) to examine the extent of 3D morphological changes of tristructural isotropic (TRISO)-coated fuel particles, specifically uranium oxide/uranium carbide fuel kernels, after high-temperature neutron irradiation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Low-Cost Preform and Molding Processes

The entry cost for prototyping a composite component for manufacture using automated, high rate processes is prohibitively expensive in many cases, especially for small business, where tooling costs may be several $100k. Discussions with industry also indicate that many small companies, tier 1 and 2 suppliers, have an interest to mold composite parts but do not want to deal with the capital cost, material handling issues, and labor associated with dry fiber preforming operations. While the molders may locate near the end user for logistics reasons, it may be more cost effective for the performer to remain regional and invest in capital equipment to support preform automation, thus keeping costs to a minimum. This project was designed to explore and demonstrate several options to meet these industry needs. Dry fiber preforming approaches were evaluated which allow for low pressure resin infusion, single sided tooling options such a vacuum assisted resin transfer molding (VARTM) or low pressure resin transfer molding (RTM-light). Unlike sheet molding compound, SMC compression molding where typical molding pressures of 1000 psi are required to push material into the desired location; positioning of a dry fiber preform into the desired location on the tool allows for low molding pressures of 10-50 psi. Lower molding pressures allow for use of low cost, additive fabrication of polymeric tooling. Polymeric tooling is suitable for rapid part prototyping and limited production. Dry fiber preforming approaches evaluated included use of commercial chopped strand mat, robotic chopper gun deposition, and continuous fiber preform augmentation using tailored fiber placement (TFP). Use of chopped strand mat does not require a robotic deposition method, however a cutting table is generally required and there is typically 20-30% scrap generation. While various fiber areal weights are available, the preform is not readily optimized for minimal fiber use or weight savings. In contrast, a robotic chopper gun approach allows for localized deposition where fiber is required to meet structural requirements. The robotic method is highly automated and minimizes fiber scrap, however the capital cost of the equipment and engineering labor for programming can result in higher preform cost compared to chopped strand mat in certain cases depending on preform complexity. Dry fiber preforming using the robotic chopper gun method allows for creation of three dimensional forms. This approach may be ideal for molding in-house, or if the preforms stack together densely to allow for efficient shipping. Applications evaluated for this program considered trade-off between fabrication of a fully 3D preform versus production of a flat preform which is designed to readily drape into the final desired shape. Such a preform design greatly simplifies robotic programming and requires no specialized tooling. The flat preforms are easily stacked and shipped to the final molding location. Flat preforms are much easier to augment with TFP continuous fiber to provide local reinforcement. The demonstration and evaluation of these preforming and tooling methods were completed on three component applications. The first application was a battery box cover for an electric vehicle which was highly three dimensional. The second demonstrator article was comprised of complex contours and was used to demonstrate the use of TFP and RTM-light molding process. The third demonstration article was the roof of an operator’s cab for large construction equipment. The roof is relatively flat however it is comprised of complex changes in thickness which clearly demonstrate the advantage of robotic chopper gun approach as compared to using numerous preform layers of chopped strand mat. The cost trades for the various preforming methods are summarized to help guide the reader as to preforming method considerations. Finally, these demonstrations all used glass fiber roving. A fourth, exploratory task was added to evaluate the ability to make preforms using Zoltek’s carbon fiber split tow roving. We were able to adapt the chopper gun to make flat preforms for laminate testing, but further development effort would be required to make suitable preforms.

36 MATERIALS SCIENCE↗

Using Computer Simulations to Optimize Biofuel Production

The DOE strives to ensure America's security and prosperity by addressing energy challenges. NREL shares this goal and tries to achieve a clean energy world. Fossil fuels are problematic for both organizations. Using them endangers American security. Their supply is finite and burning them causes environmental damage. Biofuels are a good alternative to fossil fuels. They are renewably produced on American soil and can lower greenhouse gas emissions. Also, cars and planes need no costly mechanical adjustments to use biofuels. However, the fuels themselves are expensive. For my SULI project, I reduced the cost of biofuels by optimizing the production process through computer simulations. Existing simulations were accurate but slow. One simulation takes up to eight hours, and researchers must do hundreds. My solution reduces the computing time. I treated the biomass particles in the simulation as one-dimensional. That simplified the simulation equations, making them easier for the computer to solve. Still, biomass particles are three-dimensional. The 1D assumption was wrong and produced inaccurate results. To maintain accuracy while increasing speed, I developed a method to convert 1D simulation results into usable 3D data. I adjusted the 1D simulation until the output matched the 3D results for a specific environment. I found out how much the simulation changed when the environment changed. Machine learning algorithms defined a relationship between 1D and 3D data for all environments. This lets scientists convert fast 1D simulation results into valid 3D data.

1D↗

Revealing the three-dimensional structure of microbunched plasma-wakefield-accelerated electron beams

Abstract Plasma wakefield accelerators use tabletop equipment to produce relativistic femtosecond electron bunches. Optical and X-ray diagnostics have established that their charge concentrates within a micrometre-sized volume, but its sub-micrometre internal distribution, which critically influences gain in free-electron lasers or particle yield in colliders, has proven elusive to characterize. Here, by simultaneously imaging different wavelengths of coherent optical transition radiation that a laser-wakefield-accelerated electron bunch generates when exiting a metal foil, we reveal the structure of the coherently radiating component of bunch charge. The key features of the images are shown to uniquely correlate with how plasma electrons injected into the wake: by a plasma-density discontinuity, by ionizing high- Z gas-target dopants or by uncontrolled laser–plasma dynamics. With additional input from the electron spectra, spatially averaged coherent optical transition radiation spectra and particle-in-cell simulations, we reconstruct coherent three-dimensional charge structures. The results demonstrate an essential metrology for next-generation compact X-ray free-electron lasers driven by plasma-based accelerators.

43 PARTICLE ACCELERATORS↗

Exfoliation of Cu-Containing Poly(triazine imide): From Three-Dimensional to Two-Dimensional Particle Morphology

Controlling the morphological parameters of extended covalent organic frameworks remains challenging and represents an important yet often elusive metric of consideration. Typically, carbon nitride materials possess local ordering but remain largely amorphous in terms of their long-range order and orientation. This study probes the synthesis of a crystalline carbon nitride, poly(triazine imide) lithium bromide which possesses an atomically-precise extended structure, and demonstrates its exfoliation into a two-dimensional hexagonal sheet-like morphology. Furthermore, a previously unreported carbon nitride material, poly(triazine imide) copper bromide, or PTI-CuBr, was developed through an additional flux-assisted cation-exchange process and is shown to retain its internal Cu cations during solvothermal exfoliation. Characterization by dynamic light scattering and high-angle annular dark-field scanning electron microscopy reveals the morphological changes and captures the high aspect ratio of the thin carbon nitride sheets with <10 nm thickness while maintaining hundreds of nm in width. Additional characterization by energy-dispersive spectroscopy and X-ray photoelectron spectroscopy confirms that the Cu:Br:N molar ratio was maintained within the extended layers throughout the exfoliation process. This top-down synthesis approach differs from typical methods that isolate thin sheets for subsequent metal−cation coordination and illustrates the importance of maintaining oxygen-free conditions to minimize copper clustering. Thus, this new approach is demonstrated to provide a consistent and more homogeneous occupancy of the PTI pore spaces throughout the carbon nitride framework.

Exfoliation↗

Controllable topological insulator phases in litharge-phase InBi monolayer

Despite recent advances of layered square-net topological material models that possess ideal semimetallic electronic structures and promising potential in material applications, the identification of experimentally accessible two-dimensional square-net materials with related topological properties has proven challenging. Due to the highly tunable physical and topological properties of III-V semiconductors, we revisit the class of III-V materials and observe that the litharge-phase InBi is a layered square-net material and can be exfoliated into the InBi monolayer. We present a comprehensive first-principles study of the energy landscape of the InBi monolayer. We identify a paraelastic phase and three ferroelastic phases and study their topological properties. Specifically, we show that the paraelastic InBi monolayer is a trivial insulator due to the orbital-ordering-induced band inversion occurring between states with the same parity. Substituting one Bi atom per cell with another V-group element (N, P, As) or applying an electric field that breaks the inversion symmetry and changes the orbital onsite energy, the paraelastic InBi monolayer can be driven into the topological insulator phase. Furthermore, one of the ferroelastic phases of pure InBi, which can be obtained by gently straining the paraelastic phase, also possesses such topological insulating properties. Furthermore, these results provide several experimentally accessible routes to tune the nontrivial topology in the InBi monolayer, including creating heterostructures with piezoelectric or ferroelectric substrates and applying mechanical strain, making the InBi monolayer an ideal platform to study the interplay of reduced dimensionality, square-net chemical bonding networks, and band topology.

2-dimensional systems↗

Dimensional Control of Octahedral Tilt in SrRuO 3 via Infinite-Layered Oxides

Manipulation of octahedral distortion at atomic scale is an effective means to tune the ground states of functional oxides. Previous work demonstrates that strain and film thickness are variable parameters to modify the octahedral parameters. However, selective control of bonding geometry by structural propagation from adjacent layers is rarely studied. Here we propose a new route to tune the ferromagnetism in SrRuO 3 (SRO) ultrathin layers by oxygen coordination of adjacent SrCuO 2 (SCO) layers. The infinite-layered CuO 2 exhibits a structural transformation from “planar-type” to “chain-type” with reduced film thickness. Two orientations dramatically modify the polyhedral connectivity at the interface, thus altering the octahedral distortion of SRO. The local structural variation changes the spin state of Ru and orbital hybridization strength, leading to a significant change in the magnetoresistance and anomalous Hall resistivity. Furthermore, these findings could launch investigations into adaptive control of functionalities in quantum oxide heterostructures using oxygen coordination.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Self‐consistent transport simulation of boron dust particle injection in the peripheral plasma in Large Helical Device

Abstract The trajectories and the ablation positions of boron dust particles dropped from an impurity powder dropper in the peripheral plasma in the Large Helical Device (LHD) were calculated using a three‐dimensional edge plasma simulation code (EMC3‐EIRENE) and a dust transport simulation code (DUSTT). The simulation shows that the trajectory of the boron dust particles is deflected at the upper divertor leg due to the effect of the hydrogen plasma flow, and the ablation positions of the dust particles in an ergodic layer change toward the outboard side of the torus for higher plasma densities. The effect of the boron ion flow in the divertor leg on the deflection is investigated by coupling the two codes self‐consistently. The simulation predicts that the boron ions in the divertor leg, which are produced by sputtering on the divertor plates, which do not affect the change in the ablation positions. It also shows that the ablation positions move toward the inboard side and approach the Last Closed Flux Surface (LCFS) in case of increased boron dust drop rates, which is caused by the lowered plasma flow in the upper divertor leg due to the lowered electron temperature by radiation cooling by the dropped dust particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Hysteresis curves reveal the microscopic origin of cooperative CO 2 adsorption in diamine-appended metal–organic frameworks

Diamine-appended metal-organic frameworks (MOFs) of the form Mg 2 (dobpdc)(diamine) 2 adsorb CO 2 in a cooperative fashion, exhibiting an abrupt change in CO 2 occupancy with pressure or temperature. This change is accompanied by hysteresis. While hysteresis is suggestive of a first-order phase transition, we show that hysteretic temperature-occupancy curves associated with this material are qualitatively unlike the curves seen in the presence of a phase transition; they are instead consistent with CO 2 chain polymerization, within one-dimensional channels in the MOF, in the absence of a phase transition. Here, our simulations of a microscopic model reproduce this dynamics, providing a physical understanding of cooperative adsorption in this industrially important class of materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Extrinsic n-type doping of Cd 3 As 2 thin films

Cd 3 As 2 provides an excellent platform for studying the physics of three-dimensional Dirac semimetals due to its stability as well as its compatibility with thin film growth. Crystals made using both bulk and thin film synthesis are unintentionally doped n-type, and other than introducing Zn to reduce the carrier concentration, no efforts have been reported to alter this intrinsic doping without major changes to the band structure. Here, group VI elements Te and Se are introduced during epitaxy to increase the electron concentration of the films. Starting from an unintentionally doped electron concentration of 1–2 × 10 17 cm -3 , concentrations of up to 3 × 10 18 cm -3 are achieved. Analysis of Shubnikov–de Haas oscillations reveals good agreement in calculated effective mass and Fermi velocity of highly doped films with unintentionally doped single crystals with similar electron concentrations. The density functional theory is also performed to study the effects of group VI substitutions and confirms no strong perturbations in the electronic structure. This work ultimately demonstrates tunability in the carrier concentration using extrinsic dopants without substantial changes in the band structure, allowing for intentional design of Fermi-level position for device applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗