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At least 1,171 records · Page 65

Micrometre-scale single-crystalline borophene on a square-lattice Cu(100) surface

Borophene, a crystalline monolayer boron sheet, is a new two-dimensional (2D) quantum material, predicted to feature tunable structure, intriguing physics and to find applications in flexible electronics, energy storage and catalysis. Nanoscale borophene flakes have been synthesized on noble-metal surfaces, but for device fabrication, one needs large single-crystal domains. In this work, we report the synthesis of borophene on a square lattice Cu(100) surface and show that incommensurate coordinations could reduce the borophene-substrate interactions and alter the borophene structures in interesting ways. Micrometer-scale single-crystal domains can form as isolated faceted islands or merge together to achieve full monolayer coverage. We have discovered a new crystal structure of borophene, with ten boron atoms and two hexagonal vacancies in the unit cell. First-principle calculations indicate that charge transfer rather than covalent bonding binds 2D boron to the copper surface, and confirm its integrity and uniformity The electronic band structure features multiple anisotropic tilted Dirac cones, heralding emergent quantum fermions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Characterization of two distinct neutrophil serine protease–binding modes within a Staphylococcus aureus innate immune evasion protein family

Extracellular adherence protein domain (EAPs) proteins are a class of innate immune evasion proteins secreted by the human pathogen Staphylococcus aureus. EAPs are potent and selective inhibitors of cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant neutrophil serine proteases (NSPs). Previous work from our group has shown that the prototypical EAP, EapH1, relies on plasticity within a single inhibitory site to block the activities of CG and NE. However, whether other EAPs follow similar structure–function relationships is unclear. To address this question, we studied the inhibitory properties of the first (Eap1) and second (Eap2) domains of the modular extracellular adherence protein of S. aureus and determined their structures when bound to CG and NE, respectively. We observed that both Eap1 and Eap2 displayed time-dependent inhibition of CG (on the order of 10 -9 M) and of NE (on the order of 10 -10 M). We also found that whereas the structures of Eap1 and Eap2 bound to CG showed an overall inhibitory mode like that seen previously for EapH1, the structures of Eap1 and Eap2 bound to NE revealed a new inhibitory mode involving a distal region of the EAP domain. Using site-directed mutagenesis of Eap1 and Eap2, along with enzyme assays, we confirmed the roles of interfacial residues in NSP inhibition. Taken together, our work demonstrates that EAPs can form structurally divergent complexes with two closely related serine proteases and further suggests that certain EAPs may be capable of inhibiting two NSPs simultaneously.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis

We report multicopper oxidases (MCOs) represent a diverse family of enzymes that catalyze the oxidation of either an organic or a metal substrate with concomitant reduction of dioxygen to water. These enzymes contain variable numbers of cupredoxin domains, two, three or six per subunit, and rely on four copper ions, a single type I copper and three additional copper ions organized in a trinuclear cluster (TNC), with one type II and two type III copper ions, to catalyze the reaction. Here, two crystal structures and the enzymatic characterization of Marinithermus hydrothermalis MCO, a two-domain enzyme, are reported. This enzyme decolorizes Congo Red dye at 70°C in the presence of high halide concentrations and may therefore be useful in the detoxification of industrial waste that contains dyes. In two distinct crystal structures, MhMCO forms the trimers seen in other two-domain MCOs, but differs from these enzymes in that four trimers interact to create a dodecamer. This dodecamer of MhMCO forms a closed ball-like structure and has implications for the sequestration of bound divalent metal ions as well as substrate accessibility. In each subunit of the dodecameric structures, a Trp residue, Trp351, located between the type I and TNC sites exists in two distinct conformations, consistent with a potential role in facilitating electron transfer in the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Imaging the magnetic nanowire cross section and magnetic ordering within a suspended 3D artificial spin-ice

Artificial spin-ice systems are patterned arrays of magnetic nanoislands arranged into frustrated geometries and provide insight into the physics of ordering and emergence. The majority of these systems have been realized in two-dimensions, mainly due to the ease of fabrication, but with recent developments in advanced nanolithography, three-dimensional artificial spin ice (ASI) structures have become possible, providing a new paradigm in their study. Such artificially engineered 3D systems provide new opportunities in realizing tunable ground states, new domain wall topologies, monopole propagation, and advanced device concepts, such as magnetic racetrack memory. Direct imaging of 3DASI structures with magnetic force microscopy has thus far been key to probing the physics of these systems but is limited in both the depth of measurement and resolution, ultimately restricting measurement to the uppermost layers of the system. In this work, a method is developed to fabricate 3DASI lattices over an aperture using two-photon lithography, thermal evaporation, and oxygen plasma exposure, allowing the probe of element-specific structural and magnetic information using soft x-ray microscopy with x-ray magnetic circular dichroism (XMCD) as magnetic contrast. The suspended polymer–permalloy lattices are found to be stable under repeated soft x-ray exposure. Analysis of the x-ray absorption signal allows the complex cross section of the magnetic nanowires to be reconstructed and demonstrates a crescent-shaped geometry. Measurement of the XMCD images after the application of an in-plane field suggests a decrease in magnetic moment on the lattice surface due to oxidation, while a measurable signal is retained on sub-lattices below the surface.

36 MATERIALS SCIENCE↗

Photonic ring resonator notch filters for astronomical OH line suppression

Photonic ring resonator arrays used as notch filters are a promising novel solution to improve the signal-to-noise ratio of ground-based astronomical observations by suppressing OH emission lines in the near-infrared (NIR) wavelength range (0.9-2.5 μm). We aim to fabricate a series of ring resonators connected by a waveguide, each with its resonance wavelength and full-width-half-maximum (FWHM) matched with one of the OH emission lines. The fundamental structure of ring resonator-based notch filters is a ring resonator evanescently coupled to a waveguide. Due to the optical loss of the ring resonator, the transmission of light through the waveguide will be suppressed at the resonance wavelength of the ring resonator. The degree of suppression can be controlled by varying the coupling strength between the waveguide and the ring resonator, while the resonance wavelength can be controlled by the geometry and size of the ring. However, since a single ring resonator has multiple modes each with a different wavelength separated by its free spectral range (FSR), the additional suppression at other wavelengths may undermine the signal. Therefore, the ideal FSR off the ring resonators needs to be larger than the measurement window. For this application, we aim the FSR to be 1 larger than 30 nm . Our initial measurement results revealed two major challenges for this application. First, the FSR of the ring resonators is limited by the bending loss of ring resonators. In a standard 220 nm silicon-on-insulator material platform, the FSR of ring resonators cannot exceed 30 nm; Second, due to the wafer thickness variation and fabrication inaccuracy, the achievable accuracy in the resonance wavelength of a fabricated single ring resonator is only ~1.5 nm. In this work, we report our novel solutions to the above two challenges. For the first one, we have developed a novel structure based on the Vernier effect to greatly raise the FSR of ring resonators. Serially coupled Vernier ring structures is a typical approach to increase the FSR without encountering bending loss, but it requires restrictive matching of the coupling and optical loss of the rings and any imperfect matching can result in even noisier signals. On the contrary, our structure, as shown in shown in Fig. 1, does not require the restrictive matching. The signals of two output ports in our structure marked in Fig. 1 will be added together to form the final output signal, and Fig. 2 shows the finite-difference time-domain (FDTD) simulation results of the final output signal. As can be seen, the FSR of the entire structure is well-beyond 60 nm with little noise at other wavelengths. For the second one, we have developed an easy-to-implement method to permanently tune the resonance wavelengths of ring resonators within 0.1 nm accuracy. The tuning mechanism is based on the property of hydrogen silsesquioxane (HSQ) resist. As a negative tone electron beam resist, HSQ upon exposure will cross-link and eventually form SiO2. The refractive 2 index of HSQ resist and formed SiO2 are slightly different , enabling the tuning. By having a thin layer of HSQ resist on top of ring resonator structures followed by SiO2 cladding, the resonance wavelengths of ring resonators can be post-tuned Advances in Optical Astronomical Instrumentation 2019, edited by Simon Ellis, Céline d'Orgeville, Downloaded From: https://www.spiedigitallibrary.org/conference-proceedings-of-spie on 23 Sep 2020 Terms of Use: https://www.spiedigitallibrary.org/terms-of-use through electron beam exposure. We have found that, within 5 nm tuning range, the resonance wavelength shift and dosage applied obeys a linear relationship. So a simple calibration beforehand can result in resonance wavelength tuning within 0.1 nm accuracy. The transmission spectra of a 3-ring device before and after tuning is shown in Fig. 3.

Astronomical optics↗

A Frequency Domain Methodology for Quantitative Evaluation of Diffuse Wavefield With Applications to Seismic Imaging

Abstract Ambient Noise Imaging (ANI) of subsurface structures relies on seismic interferometry of diffuse seismic wavefields. However, the lack of effective methods to quantify and identify highly diffuse waves hampers applications of ANI, particularly in evaluating seismic attenuation and monitoring structural changes with high temporal resolution. Conventional ANI approaches require data normalization, which effectively suppresses the non‐diffuse component with large amplitude but also results in significant loss of amplitude and phase information in the continuous seismic records. In this study, we propose a frequency domain method to quantitatively evaluate the degree of diffuseness of seismic wavefields by analyzing their statistical characteristics of modal amplitudes for stationarity and randomness. Tests on synthetic waveform and field nodal records show that the proposed method can effectively distinguish between diffuse and non‐diffuse waveforms for either single‐ or three‐component data. As an application, we identify a 60‐s‐long diffuse coda of a local M 2.2 earthquake recorded by a dense nodal array on the San Jacinto Fault Zone, and successfully extract high‐quality dispersion curve andQ‐value without performing data normalization. These results are consistent with those obtained by conventional methods that assess the correlation between coherency and the Green's function, and by modeling ballistic waves generated by road traffic. Our proposed method can advance the imaging of subsurface velocity and attenuation structures as well as monitoring temporal changes for scientific studies and engineering applications.

Geochemistry & Geophysics↗

Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair

G-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. The G-protein, MMAA, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B 12 -dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the complex assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nano-assembly, which reveals a dramatic 180° rotation of the B 12 domain, exposing it to solvent. The complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the MMAA-MMUT interfaces we identify here.

59 BASIC BIOLOGICAL SCIENCES↗

3D imaging of magnetic domains in Nd 2 Fe 14 B using scanning hard X-ray nanotomography

Nanoscale structural and electronic heterogeneities are prevalent in condensed matter physics. Investigating these heterogeneities in 3D has become an important task for understanding material properties. To provide a tool to unravel the connection between nanoscale heterogeneity and macroscopic emergent properties in magnetic materials, scanning transmission X-ray microscopy (STXM) is combined with X-ray magnetic circular dichroism. A vector tomography algorithm has been developed to reconstruct the full 3D magnetic vector field without any prior noise assumptions or knowledge about the sample. Two tomographic scans around the vertical axis are acquired on single-crystalline Nd 2 Fe 14 B pillars tilted at two different angles, with 2D STXM projections recorded using a focused 120 nm X-ray beam with left and right circular polarization. Image alignment and iterative registration have been implemented based on the 2D STXM projections for the two tilts. Dichroic projections obtained from difference images are used for the tomographic reconstruction to obtain the 3D magnetization distribution at the nanoscale.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting

Abstract The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.

Jaiswal, Rahul↗

Revealing Mesoscale Ionomer Membrane Structure by Tender Resonant X-ray Scattering

Nafion, a perfluorosulfonic acid ionomer, has been well-studied for decades due to its key role as an ion-conductive membrane in electrochemical energy conversion and storage applications. When hydrated, this membrane phase separates into a complex hierarchical nanostructure with hydrophilic domains that facilitate ion transport. Hard X-ray scattering has been a powerful technique in understanding Nafion due to its capabilities in capturing the ionomer’s nanophase separated structure, which gives rise to contrast between polymer and water domains. More recently, resonant X-ray scattering, which tunes to elemental absorption edges to provide specificity on constituent elements, has been explored to highlight key interactions related to the sulfonic acid groups within its structure. Here, in this work, we study the Nafion nanostructure by combining hard X-ray scattering and tender resonant X-ray scattering (TReXS) at the sulfur K-edge to reveal a mesoscopic feature corresponding to a correlation length of approximately 40 nm that has been challenging to resolve with hard X-ray studies. Additionally, we study the effect of the dispersion solvent composition that plays a key role in the formation of this mesoscale feature. Notably, TReXS can attain high contrast to decipher this mesoscale morphology even for dry polymer membranes under a vacuum, which typically have reduced contrast for hard X-rays. We find that the correlation length of this mesoscale feature decreases with increasing water fraction in the dispersion, which is the opposite trend exhibited by the smaller intercrystalline feature in the same membranes. This study showcases the utility of TReXS to uncover multiscale morphological details in functional polymers that are not always revealed by other methods like hard X-ray scattering. We illustrate this with Nafion, which is a relevant ion-conducting polymer for electrochemical technologies.

36 MATERIALS SCIENCE↗

Structure and Antigenicity of the Porcine Astrovirus 4 Capsid Spike

Porcine astrovirus 4 (PoAstV4) has been recently associated with respiratory disease in pigs. In order to understand the scope of PoAstV4 infections and to support the development of a vaccine to combat PoAstV4 disease in pigs, we designed and produced a recombinant PoAstV4 capsid spike protein for use as an antigen in serological assays and for potential future use as a vaccine antigen. Structural prediction of the full-length PoAstV4 capsid protein guided the design of the recombinant PoAstV4 capsid spike domain expression plasmid. The recombinant PoAstV4 capsid spike was expressed in Escherichia coli, purified by affinity and size-exclusion chromatography, and its crystal structure was determined at 1.85 Å resolution, enabling structural comparisons to other animal and human astrovirus capsid spike structures. The recombinant PoAstV4 capsid spike protein was also used as an antigen for the successful development of a serological assay to detect PoAstV4 antibodies, demonstrating that the recombinant PoAstV4 capsid spike retains antigenic epitopes found on the native PoAstV4 capsid. These studies lay a foundation for seroprevalence studies and the development of a PoAstV4 vaccine for swine.

Virology↗

Precise Modulation of CO 2 Sorption in Ti 8 Ce 2 –Oxo Clusters: Elucidating Lewis Acidity of the Ce Metal Sites and Structural Flexibility

Investigating the structure-property correlation in porous materials is a fundamental and consistent focus in various scientific domains, especially within sorption research. Metal oxide clusters with capping ligands, characterized by intrinsic cavities formed through specific solid-state packing, demonstrate significant potential as versatile platforms for sorption investigations due to their precisely tunable atomic structures and inherent long-range order. This study presents a series of Ti 8 Ce 2 -oxo clusters with subtle variations in coordinated linkers and explores their sorption behavior. Notably, Ti 8 Ce 2 -BA (BA denotes benzoic acid) manifests a distinctive two-step profile during CO 2 adsorption, accompanied by a hysteresis loop. This observation marks a new instance within the metal oxide cluster field. Of intrigue, the presence of unsaturated Ce(IV) sites was found to be correlated with the stepped sorption property. Moreover, the introduction of an electrophilic fluorine atom, positioned ortho or para to the benzoic acid, facilitated precise control over gate pressure and stepped sorption quantities. Advanced in-situ techniques systematically unraveled the underlying mechanism behind this unique sorption behavior. The findings elucidate that robust Lewis base-acid interactions are established between CO 2 molecules and Ce ions, consequently altering the conformation of coordinated linkers. Conversely, the F atoms primarily contribute to gate pressure variation by influencing the Lewis acidity of the Ce sites. This research advances the understanding in fabricating metal-oxo clusters with structural flexibility and provides profound insights into their host-guest interaction motifs. Furthermore, these insights hold substantial promise across diverse fields and offer valuable guidance for future adsorbent designs grounded in fundamental theories of structure-property relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Primordial black hole dark matter: A quantitative parameter sensitivity comparison across formation mechanisms and particle candidates

Primordial black holes (PBHs) in the asteroid-mass window ( 10 17 – 10 22 g ) can account for all of the dark matter without violating any observational constraint, yet are routinely dismissed as fine-tuned. I put that dismissal to the test by applying three complementary sensitivity measures uniformly across a broad landscape: three noninflationary PBH production mechanisms, six classes of inflationary PBH models, and seven particle dark matter benchmarks, all evaluated against the same observable target. Three distinct naturalness universality classes emerge, determined entirely by the analytic structure of the abundance map rather than by the nature of the dark matter candidate. Biased-domain-wall PBHs, in their least model-dependent (free- V b ) form, have the same low sensitivity, Δ = 4.5 , as off-resonance weakly interacting massive particles and freeze-in particles ( Δ = 2 ), a sensitivity that, because it is constant over the entire parameter space of the construction, also coincides trivially with its own Wilson-normalized average within that parameter space (Section Definition and conventions), an equivalence that concerns only the space over which Δ is computed and is not a naturalness statement about the construction as a whole; a further reduction to Δ = 2 is possible only under the additional, independently motivated but not required, assumption that the domain-wall bias is generated by Planck-suppressed operators; early matter-domination PBHs occupy an intermediate tier alongside coannihilating weakly interacting massive particles (WIMPs), unified by a structural identity in which the sensitivity measure equals the logarithm of the ratio of the formation scale to the matter–radiation equality scale; first-order phase transition PBHs, once the more accurate super-exponential collapse probability is used in place of the single-exponential approximation, instead belong to the same highly sensitive tier as resonant WIMP annihilation and single-field inflationary collapse, for a structurally distinct reason; single-field ultraslow-roll inflationary collapse is severely tuned for a distinct reason: a double exponential in which the power spectrum amplitude is itself exponentially sensitive to the inflaton potential coefficients, on top of the exponential collapse sensitivity of the abundance map. My main conclusion is that the claim that PBH dark matter is generically fine-tuned conflates the worst case with a landscape spanning every naturalness tier. The Barbieri-Giudice sensitivity computed here and the Wilson-normalized measure of Iovino and Riotto answer distinct and mutually consistent questions about the same construction, a distinction I clarify within the two-layer decomposition.

Profumo, Stefano [University of California, Santa ↗

The human coronavirus HCoV-229E S-protein structure and receptor binding

The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S-protein function is maintained is not understood. Reported are the X-ray crystal structures of Class III-V RBDs in complex with human aminopeptidase N (hAPN), as well as the electron cryomicroscopy structure of the 229E S-protein. The structures show that common core interactions define the specificity for hAPN and that the peripheral RBD sequence variation is accommodated by loop plasticity. The results provide insight into immune evasion and the cross-species transmission of 229E and related coronaviruses. We also find that the 229E S-protein can expose a portion of its helical core to solvent. This is undoubtedly facilitated by hydrophilic subunit interfaces that we show are conserved among coronaviruses. These interfaces likely play a role in the S-protein conformational changes associated with membrane fusion.

59 BASIC BIOLOGICAL SCIENCES↗

Competing magnetic and nonmagnetic states in monolayer VSe 2 with charge density wave

The field of two-dimensional ferromagnets has been reinvigorated by the discovery of VSe 2 monolayer grown on van der Waals substrates, which is reported to be ferromagnetic with a Curie point higher than 330 K. However, the ferromagnetic and nonmagnetic states of pristine monolayer VSe 2 are highly debated. Here, employing density functional theory, Wannier function calculations, and the band unfolding method, we explore the electronic structure of monolayer VSe 2 with a $\sqrt{3} × \sqrt{7}$ charge density wave (CDW). Certain qualitative aspects of the calculated unfolded band dispersion and unfolded Fermi surface of monolayer VSe 2 with the $\sqrt{3} × \sqrt{7}$ CDW in the nonmagnetic state agree well with previous angle-resolved photoemission spectroscopy results, albeit with uncertainty about whether these experiments probed single or multiple domains. Specifically, we find that an isolated CDW domain naturally induces a strong breaking of the threefold symmetry of the electronic structure. In addition we find that, relative to the undistorted structure, the CDW structure shows a strong competition between nonmagnetic and various magnetic states, with an energy difference less than 5 meV/f.u. For the CDW structure in the antiferromagnetic state, the band dispersions and Fermi surface are similar to those in the nonmagnetic state, while the unfolded bands of the ferromagnetic CDW state display a sizable exchange splitting. These results indicate the possibility of various antiferromagnetic fluctuations in VSe 2 to coexist and compete with ferromagnetic order and the experimentally reported CDW order. In this work, our calculations build insights for exploring the interplay between magnetism and CDW behaviors more generally in transition metal dichalcogenides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗