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At least 37 records · Page 2

Mixed-Domain Charge Transport in S-Se Alloys as a Li-S Battery Cathode Material

Lithium-sulfur batteries are emerging candidate systems for the next-generation long-range electric aircraft application owing to their potential to deliver high energy density per weight. Their cathodes are to be made primarily with sulfur, but sulfur by itself has much too low electron conductivity to serve as a useful cathode. An idea that has been suggested to overcome this bottleneck is to alloy sulfur with selenium in the hope that electron mobility, which is thought to improve charge transport at some expense of increased weight and reduced energy density. However, understanding of these alloy structures and their transport mechanism is insufficient, and electron mobility at varying degrees of selenium content is not well charted, which are critical for determining the optimum selenium content and testing whether this strategy is generally feasible. The difficulty of computationally characterizing these alloy systems is rooted in the structure. The structures of both sulfur and selenium exhibit eight-atom rings that pack together in various orientations to form their respective crystals. For one, because these crystals (and presumably their alloys as well) feature multiple polymorphs such that their structural coherence is rather unclear. Secondly, these are also relatively large systems (32 atoms per cell) with low-symmetry, which complicate computation both in terms of accuracy and efficiency. Thirdly, such semi-molecular, semi-crystalline structures lead to a combination of band-transport characteristics and hopping-transport characteristics, each of which is a domain with its own physics and set of computational, theoretical challenges. In addition, there is a general dearth of experimental transport data for sulfur-selenium alloys. In this study, we make a comprehensive attempt to tackle this problem using a wide array of first-principles methods. We generate special quasirandom structures to simulate alloy structures, and compute their first-principles Raman spectra for comparison with experimental data to ensure their structural soundness. We then proceed to use recently developed, state-of-the-art tool (AMSET) in order to efficiently compute electronic mobilities under band transport of pure sulfur, pure selenium, as well as their alloys of various compositions at a reasonable accuracy. We then sample numerous dimer configurations of nearest-neighbor eight-atom-ring-pairs and compute electronic hopping rates between them, which yields hopping mobility. A combination of these efforts lead to a general mapping of electron transport behaviors throughout the alloy range. Preliminary results show that introduction of selenium into sulfur initially damages electron mobility due to disorder but eventually improves it beyond that of pure sulfur with additional selenium content, ultimately peaking at the pure-selenium limit. Band transport dominates for holes in sulfur and electrons in selenium, but in all other cases, hopping transport is dominant. Ongoing efforts include determination of charge concentration and conductivity, as well as performing multiphysics modeling to determine the optimum selenium content for best tradeoff between conductivity and energy density for aircraft range.

Junsoo Park↗

The nature of asteroidal differentiation processes - Implications for primordial heat sources

A review of the geochemical data on basaltic achondrite group meteorites, here defined as diogenites, eucrites, howardites, mesosiderites, main-group pallasites and IIIAB irons, suggests that the following processes and properties were important in determining the compositions of igneous materials on asteroidal sized bodies: (1) inhomogeneities in source rock compositions, (2) variable degrees of partial melting from 5-100%, (3) multiple melt genesis from a single source region, (4) fractional crystallization, and (5) remelting of earlier formed igneous rocks. All of this activity started during or shortly after the major asteroidal accretion phase as suggested by the numerous 4.6 Gyr ages for eucrites and may have lasted for at least 200 m.y. The above properties imply an early, intense heat source that was both spatially and temporally variable. A review of asteroid thermal modeling for various heat sources shows that heating by short-lived Al-26 alone appears to be incapable of supplying the observed geochemical variations.

Mittlefehldt, D. W.↗

Timescale of Petrogenetic Processes Recorded in the Mount Perkins Magma System, Northern Colorado River Extension Corridor, Arizona

The Miocene Mt. Perkins Pluton is a small composite intrusive body emplaced in the shallow crust as four separate phases during the earliest stages of crustal extension. Phase 1 (oldest) consists of isotropic hornblende gabbro and a layered cumulate sequence. Phase 2 consists of quartz monzonite to quartz monzodiorite hosting mafic microgranitoid enclaves. Phase 3 is composed of quartz monzonite and is subdivided into mafic enclave-rich zones and enclave-free zones. Phase 4 consists of aphanitic dikes of mafic, intermediate and felsic compositions hosting mafic enclaves. Phases 2-4 enclaves record significant isotopic disequilibrium with surrounding granitoid host rocks, but collectively enclaves and host rocks form a cogenetic suite exhibiting systematic variations in Nd-Sr-Pb isotopes that correlate with major and trace elements. Phases 2-4 record multiple episodes of magma mingling among cogenetic hybrid magmas that formed via magma mixing and fractional crystallization at a deeper crustal. The mafic end-member was alkali basalt similar to nearby 6-4 Ma basalt with enriched OIB-like trace elements and Nd-Sr-Pb isotopes. The felsic end-member was a subalkaline crustal-derived magma. Phase 1 isotropic gabbro exhibits elemental and isotopic compositional variations at relatively constant SiO2, suggesting generation of isotropic gabbro by an open-system process involving two mafic end-members. One end-member is similar in composition to the OIB-like mafic end-member for phases 2-4; the second is similar to nearby 11-8 Ma tholeiite basalt exhibiting low epsilon (sub Nd), and depleted incompatible trace elements. Phase 1 cumulates record in situ fractional crystallization of an OIB-like mafic magma with isotopic evidence of crustal contamination by partial melts generated in adjacent Proterozoic gneiss. The Mt Perkins pluton records a complex history in a lithospheric scale magma system involving two distinct mantle-derived mafic magmas and felsic magma sourced in the crust. Mixing and fractional crystallization of these magmas at various levels in the crust generated a suite of intermediate composition magmas. U-Pb zircon SHRIMP ages of phase 1 (15.7 +/- 0.2 Ma), phase 3 (15.8 +/- 0.2 Ma) and phase 4 (15.4 +/- 0.3 Ma) document a 100-300k year timescale for petrogenetic processes recorded in the Mt Perkins magma system.

Danielson, Lisa R.↗

The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes

Abstract G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3′-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5′-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗

Cross-Linking Studies of Lysozyme Nucleation

Tetragonal chicken egg white crystals consist of 4(sub 3) helices running in alternating directions, the helix rows having a two fold symmetry with each other. The unit cell consists of one complete tetrameric turn from each of two adjacent helices (an octamer). PBC analysis indicates that the helix intermolecular bonds are the strongest in the crystal, therefore likely formed first. AFM analysis of the (110) surface shows only complete helices, no half steps or bisected helices being found, while AFM line scans to measure the growth step increments show that they are multiples of the 4(sub 3) helix tetramer dimensions. This supports our thesis that the growth units are in fact multiples of the four molecule 4(sub 3) helix unit, the "average" growth unit size for the (110) face being an octamer (two turns about the helix) and the (101) growth unit averaging about the size of a hexamer. In an effort to better understand the species involved in the crystal nucleation and growth process, we have initiated an experimental program to study the species formed in solution compared to what is found in the crystal through covalent cross-linking studies. These experiments use the heterobifunctional cross-linking agent aminoethyl-4-azidonitroanaline (AEANA). An aliphatic amine at one end is covalently attached to the protein by a carbodiimide-mediated reaction, and a photo reactive group at the other can be used to initiate crosslinking. Modifications to the parent structure can be used to alter the distance between the two reactive groups and thus the cross-linking agents "reach". In practice, the cross-linking agent is first coupled to the asp101 side chain through the amine group. Asp101 lies within the active site cleft, and previous work with fluorescent probes had shown that derivatives at this site still crystallize in the tetragonal space group. This was also found to be the case with the AEANA derivative, which gave red tetragonal crystals. The protein now has a reactive group that can be photoactivated at a specific point in the nucleation or crystal growth process to "capture" protein molecules bound within reach of the crosslinking agent. If those bound protein molecules have a defined geometric relationship with the capturing molecule, such as would be found in a crystal, then the photoreacted cross-linking site should be consistent. Random protein interactions, typical of an amorphous precipitate or interaction, would show a random cross-linking reaction. The results of these and other experiments will be presented.

Forsythe, Elizabeth↗

Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site

As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the activesite FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer–Tropsch-type chemistry). The CC bond forming capabilities of nitrogenase suggest that multiple CO or COderived ligands bind to the active site. Herein, we report a crystal structure with two CO ligands coordinated to the FeMo-cofactor of the molybdenum nitrogenase at 1.33 resolution. In addition to the previously observed bridging CO ligand between Fe2 and Fe6 of the FeMo-cofactor, a new ligand binding mode is revealed through a second CO ligand coordinated terminally to Fe6. While the relevance of this state to nitrogenase-catalyzed reactions remains to be established, it highlights the privileged roles for Fe2 and Fe6 in ligand binding, with multiple coordination modes available depending on the ligand and reaction conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the optoelectronic properties of doped 2D organic-inorganic halide perovskite quantum wells: towards efficient quantum well IR photodetectors

Metal halide perovskite (MHP) multiple quantum wells which consist of multilayers of alternate organic and inorganic layers exhibit large exciton binding energies due to the dielectric confinement between the inorganic and organic layers. These naturally formed multiple quantum wells have strong spin-orbit coupling (SOC) due to the presence of heavy elements in their crystal structures. Although the fundamental properties of 2D MHPs are far from being entirely understood, it is widely accepted that their band edge absorption coefficient results from strong exciton interactions. However, studies demonstrating how different exciton interactions and doping effects influence electronic traps and disorder on the band edge absorption coefficient of 2D MHPs have not been demonstrated. Understanding these interactions in MHPs will allow us to access low energy optical transitions for the fabrication of solution processable short-to-mid-wavelength IR photodetectors (1 – 8 μm). Moreover, upon doping, it is possible to move the Fermi energy into the conduction band (CB) to favorably promote the transport of charges in a working device. Herein, we study the development of 2D MHPs having strong SOC, high carrier mobility, and tunable quantum well structures. Our studies shed light on the design and modulation of fundamental physical phenomena by carefully elucidating the role of dopants (n-type and p-type), exciton heterogeneity, orientation, structure, and bias stress effects on the performance of MHPs as potential IR photodetectors.

36 MATERIALS SCIENCE↗

Characteristics of a dynamic holographic sensor for shape control of a large reflector

Design of a distributed holographic interferometric sensor for measuring the surface displacement of a large segmented reflector is proposed. The reflector's surface is illuminated by laser light of two wavelengths and volume holographic gratings are formed in photorefractive crystals of the wavefront returned from the surface. The sensor is based on holographic contouring with a multiple frequency source. It is shown that the most stringent requirement of temporal stability affects both the temporal resolution and the dynamic range. Principal factor which limit the sensor performance include the response time of photorefractive crystal, laser power required to write a hologram, and the size of photorefractive crystal.

Welch, Sharon S.↗

Peak effect and dynamics of stripe- and pattern-forming systems on a periodic one-dimensional substrate

Here we examine the ordering, pinning, and dynamics of two-dimensional pattern-forming systems interacting with a periodic one-dimensional substrate. In the absence of the substrate, particles with competing long-range repulsion and short-range attraction form anisotropic crystal, stripe, and bubble states. When the system is tuned across the stripe transition in the presence of a substrate, we find that there is a peak effect in the critical depinning force when the stripes align and become commensurate with the substrate. Under an applied drive, the anisotropic crystal and stripe states can exhibit soliton depinning and plastic flow. When the stripes depin plastically, they dynamically reorder into a moving stripe state that is perpendicular to the substrate trough direction. We also find that when the substrate spacing is smaller than the widths of the bubbles or stripes, the system forms pinned stripe states that are perpendicular to the substrate trough direction. The system exhibits multiple reentrant pinning effects as a function of increasing attraction, with the anisotropic crystal and large bubble states experiencing weak pinning but the stripe and smaller bubble states showing stronger pinning. We map out the different dynamic phases as a function of filling, the strength of the attractive interaction term, the substrate strength, and the drive, and demonstrate that the different phases produce identifiable features in the transport curves and particle orderings.

97 MATHEMATICS AND COMPUTING↗

Optical second harmonic generation in anisotropic multilayers with complete multireflection of linear and nonlinear waves using ♯SHAARP.ml package

Abstract Optical second harmonic generation (SHG) is a nonlinear optical effect widely used for nonlinear optical microscopy and laser frequency conversion. Closed-form analytical solution of the nonlinear optical responses is essential for evaluating materials whose optical properties are unknown a priori. A recent open-source code, ♯SHAARP. si , can provide such closed form solutions for crystals with arbitrary symmetries, orientations, and anisotropic properties at a single interface. However, optical components are often in the form of slabs, thin films on substrates, and multilayer heterostructures with multiple reflections of both the fundamental and up to ten different SHG waves at each interface, adding significant complexity. Many approximations have therefore been employed in the existing analytical approaches, such as slowly varying approximation, weak reflection of the nonlinear polarization, transparent medium, high crystallographic symmetry, Kleinman symmetry, easy crystal orientation along a high-symmetry direction, phase matching conditions and negligible interference among nonlinear waves, which may lead to large errors in the reported material properties. To avoid these approximations, we have developed an open-source package named Second Harmonic Analysis of Anisotropic Rotational Polarimetry in Multilayers (♯SHAARP. ml ). The reliability and accuracy are established by experimentally benchmarking with both the SHG polarimetry and Maker fringes using standard and commonly used nonlinear optical materials as well as twisted 2-dimensional heterostructures.

36 MATERIALS SCIENCE↗

Molecular dynamics simulations of radiation cascade evolution near cellular dislocation structures in additively manufactured stainless steels

The dislocation dense cellular structures observed in additively manufactured (AM) stainless steels can allow these materials to have enhanced strength and ductility compared to conventionally manufactured materials. Effective design of radiation resistant materials often necessitates creating microstructures containing of a high density of dislocations that act as sinks for radiation induced defects. This work uses molecular dynamics simulations to study the impact of pre-existing defects on radiation damage in stainless steel 316L fabricated by the laser powder bed fusion process. The evolution of synthetically generated dislocations in a crystal system in response to multiple radiation collision cascades suggest that dislocation dense regions reduce the probability of surviving point defects forming clusters. This finding seems to result from the dislocation cores’ ability to absorb point defects, thereby limiting the formation of clusters during the recombination phase. However, after successive cascades, the ability of the dislocation entanglement to prevent defect formation is diminished and defect cluster formation trends to an equilibrium. Accordingly, it is hypothesized that in an experimental setting the dislocation cells will initially act as neutral sinks for point defects, potentially delaying the onset of radiation damage effects; but, these structures will be degraded due to radiation-enhanced diffusion and lose their effectiveness at doses above 1.5–2 displacements per atom. Nevertheless, the ability to produce complex and feature-specific microstructures suggests promise for the design of radiation tolerant materials using AM methods.

36 MATERIALS SCIENCE↗

Crystalline Peptoid Nanofibers with a Single-Unit Cell Cross Section

Ultranarrow crystalline one-dimensional nanostructures formed from soft materials facilitate precise structural control in nanomaterial design, which is essential for biomedicine and nanotechnology applications. Systematic control of their hierarchical structure is challenging due to the complexities of simultaneously manipulating multiple noncovalent interactions at such small scales. We employed a polypeptoid crystal motif as a supramolecular synthon to engineer ultranarrow crystalline nanofibers constrained to a single lattice axis by incorporating a single ionizable side chain into the hydrophobic core of a nanosheet-forming peptoid. Cryogenic transmission electron microscopy of the nanofibers revealed detailed molecular arrangements of a unit-cell cross-section and the presence of distinct pH-dependent lattice isoforms that resulted in morphological transformations. Molecular dynamics simulations demonstrated that the ionizable side chain plays a critical role in changing the local conformation of the unit cell, which further impacts the dimensionality of hierarchical structures. Moreover, these fibers were readily functionalized with biological ligands to afford one-dimensional (1D) protein arrays. This approach for the high-precision bottom-up assembly of ultranarrow 1D nanostructures offers significant potential for developing novel biomimetic nanostructures.

Lee, Yen Jea↗

Broadly cross-reactive human antibodies that inhibit genogroup I and II noroviruses

The rational development of norovirus vaccine candidates requires a deep understanding of the antigenic diversity and mechanisms of neutralization of the virus. Here, we isolate and characterize a panel of broadly cross-reactive naturally occurring human monoclonal IgMs, IgAs and IgGs reactive with human norovirus (HuNoV) genogroup I or II (GI or GII). We note three binding patterns and identify monoclonal antibodies (mAbs) that neutralize at least one GI or GII HuNoV strain when using a histo-blood group antigen (HBGA) blocking assay. The HBGA blocking assay and a virus neutralization assay using human intestinal enteroids reveal that the GII-specific mAb NORO-320, mediates HBGA blocking and neutralization of multiple GII genotypes. The Fab form of NORO-320 neutralizes GII.4 infection more potently than the mAb, however, does not block HBGA binding. The crystal structure of NORO-320 Fab in complex with GII.4 P-domain shows that the antibody recognizes a highly conserved region in the P-domain distant from the HBGA binding site. Dynamic light scattering analysis of GII.4 virus-like particles with mAb NORO-320 shows severe aggregation, suggesting neutralization is by steric hindrance caused by multivalent cross-linking. Aggregation was not observed with the Fab form of NORO-320, suggesting that this clone also has additional inhibitory features.

59 BASIC BIOLOGICAL SCIENCES↗

Torsional force microscopy of van der Waals moirés and atomic lattices

In a stack of atomically thin van der Waals layers, introducing interlayer twist creates a moiré superlattice whose period is a function of twist angle. Changes in that twist angle of even hundredths of a degree can dramatically transform the system’s electronic properties. Setting a precise and uniform twist angle for a stack remains difficult; hence, determining that twist angle and mapping its spatial variation is very important. Techniques have emerged to do this by imaging the moiré, but most of these require sophisticated infrastructure, time-consuming sample preparation beyond stack synthesis, or both. In this work, we show that torsional force microscopy (TFM), a scanning probe technique sensitive to dynamic friction, can reveal surface and shallow subsurface structure of van der Waals stacks on multiple length scales: the moirés formed between bi-layers of graphene and between graphene and hexagonal boron nitride (hBN) and also the atomic crystal lattices of graphene and hBN. In TFM, torsional motion of an Atomic Force Microscope (AFM) cantilever is monitored as it is actively driven at a torsional resonance while a feedback loop maintains contact at a set force with the sample surface. TFM works at room temperature in air, with no need for an electrical bias between the tip and the sample, making it applicable to a wide array of samples. It should enable determination of precise structural information including twist angles and strain in moiré superlattices and crystallographic orientation of van der Waals flakes to support predictable moiré heterostructure fabrication.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Ladderlike Switched-Path Optical Delay Lines

Switched-path adjustable optical delay lines with ladderlike configurations proposed for use in photonically controlling phases of radio signals in radiating elements of phased-array antennas and in adaptive filtering of signals. Lines relatively simple, compact, easy to fabricate, and inexpensive. Switchable delay blocks stacked like building blocks to form incrementally adjustable delay lines. Delay lines also stacked to form high-density multiple-channel delay systems. To reduce number of blocks, heights of blocks increased successively by factor of 2, similar to crystal arrangement described in article "Switched-Polarization Birefringent Optical Delay Lines" (NPO-19412).

Yao, Xiaotian Steve↗

Silicon Membrane Mirrors with Electrostatic Shape Actuators

Efforts are under way to develop deformable mirrors equipped with microscopic electrostatic actuators that would be used to maintain their reflective surfaces in precise shapes required for their intended applications. Unlike actuators that depend on properties of materials (e.g., piezoelectric and electrostrictive actuators), electrostatic actuators are effective over a wide temperature range. A mirror of the present type would be denoted a MEMSDM (for microelectromechanical system deformable mirror). The reflective surface of such a mirror would be formed on a single-crystal silicon membrane that would be attached by posts to a silicon actuator membrane that would, in turn, be attached by posts to a rigid silicon base (see figure). The actuator membrane would serve as the upper electrode of a capacitor. Multiple lower electrodes, each occupying a conveniently small fraction of the total area, would be formed on an electrically insulating oxide layer on the base, thereby defining a multiplicity of actuator pixels. The actuator membrane would be corrugated in a pattern that would impart mechanical compliance needed for relaxation of operational and fabrication-induced stresses and to minimize the degree of nonlinearity of deformations. The compliance afforded by the corrugations would also help to minimize the undesired coupling of deformations between adjacent pixels (a practical goal being to keep the influence coefficient between adjacent pixels below 10 percent).

Yang, Eui-Hyeok↗