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At least 793 records · Page 44

Design principles for site-selective hydroxylation by a Rieske oxygenase

Rieske oxygenases exploit the reactivity of iron to perform chemically challenging C–H bond functionalization reactions. Thus far, only a handful of Rieske oxygenases have been structurally characterized and remarkably little information exists regarding how these enzymes use a common architecture and set of metallocenters to facilitate a diverse range of reactions. Herein, we detail how two Rieske oxygenases SxtT and GxtA use different protein regions to influence the site-selectivity of their catalyzed monohydroxylation reactions. We present high resolution crystal structures of SxtT and GxtA with the native β-saxitoxinol and saxitoxin substrates bound in addition to a Xenon-pressurized structure of GxtA that reveals the location of a substrate access tunnel to the active site. Ultimately, this structural information allowed for the identification of six residues distributed between three regions of SxtT that together control the selectivity of the C–H hydroxylation event. Substitution of these residues produces a SxtT variant that is fully adapted to exhibit the non-native site-selectivity and substrate scope of GxtA. Importantly, we also found that these selectivity regions are conserved in other structurally characterized Rieske oxygenases, providing a framework for predictively repurposing and manipulating Rieske oxygenases as biocatalysts.

59 BASIC BIOLOGICAL SCIENCES↗

Electronic structures, charge transfer, and charge order in twisted transition metal dichalcogenide bilayers

Moiré superlattices of transition metal dichalcogenide (TMD) bilayers have been shown to host correlated electronic states, which arise from the interplay of long wavelength moiré potential and long-range Coulomb interaction. Here, we theoretically investigate structural relaxation and single-particle electronic structure of twisted TMD homobilayer. From the large-scale density functional theory calculation and continuum model with layer degrees of freedom, we find that the out-of-plane gating field creates a tunable charge transfer gap at the Dirac point between the first and second moiré valence bands. We further study the charge orders at the fractional band fillings. In the flat band limit, we find from Monte Carlo simulations a series of charge-ordered insulating states at various fillings $n = \frac{1}{4}, \frac{1}{3}, \frac{1}{2}, \frac{2}{3}, 1$. Further, we predict that gating field induces a phase transition between different electron crystals at fixed filling $n = \frac{1}{2}$ or $\frac{2}{3}$. At half-filling $\textit{n} = 1$, the ground state is a Mott insulator with electronically driven ferroelectricity. This work demonstrates that TMD homobilayer provides a powerful platform for the investigation of tunable charge transfer insulator and charge orders.

36 MATERIALS SCIENCE↗

Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids

The small GTPases H, K, and NRAS are molecular switches indispensable for proper regulation of cellular proliferation and growth. Several mutations in the genes encoding members of this protein family are associated with cancer and result in aberrant activation of signaling processes caused by a deregulated recruitment of downstream effector proteins. In this study, we engineered variants of the Ras-binding domain (RBD) of the C-Raf proto-oncogene, Ser/Thr kinase (CRAF). These variants bound with high affinity with the effector-binding site of Ras in an active conformation. Structural characterization disclosed how the newly identified RBD mutations cooperate and thereby enhance affinity with the effector-binding site in Ras compared with WT RBD. The engineered RBD variants closely mimicked the interaction mode of naturally occurring Ras effectors and acted as dominant-negative affinity reagents that block Ras signal transduction. We report experiments with cancer cells showed that expression of these RBD variants inhibits Ras signaling, reducing cell growth and inducing apoptosis. Using these optimized RBD variants, we stratified patient-derived colorectal cancer organoids with known Ras mutational status according to their response to Ras inhibition. These results revealed that the presence of Ras mutations was insufficient to predict sensitivity to Ras inhibition, suggesting that not all of these tumors required Ras signaling for proliferation. In summary, by engineering the Ras/Raf interface of the CRAF-RBD, we identified potent and selective inhibitors of Ras in its active conformation that outcompete binding of Ras-signaling effectors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Clean 2D superconductivity in a bulk van der Waals superlattice

Alternative route to a 2D superconductor Single layers of transition metal dichalcogenides exhibit exotic properties, including superconductivity. The usual route to obtaining such samples is to exfoliate a three-dimensional (3D) crystal. Devarakonda et al. instead grew a superlattice comprising alternating layers of the transition metal dichalcogenide hexagonal NbS 2 and the material Ba 3 NbS 5 (see the Perspective by Schoop). The inert Ba 3 NbS 5 layers serve to dissociate the superconducting NbS 2 layers from one another, resulting in 2D superconductivity with high carrier mobility. The combination of high mobility and reduced dimensionality may give rise to exotic quantum phases. Science , this issue p. 231 see also p. 170

Science & Technology - Other Topics↗

Strain‐Driven Stabilization of a Room‐Temperature Chiral Multiferroic with Coupled Ferroaxial and Ferroelectric Order

Noncollinear ferroic materials are sought after as testbeds to explore the intimate connections between topology and symmetry, which result in electronic, optical, and magnetic functionalities not observed in collinear ferroic materials. For example, ferroaxial materials have rotational structural distortions that break mirror symmetry and induce chirality. When ferroaxial order is coupled with ferroelectricity arising from a broken inversion symmetry, it offers the prospect of electric-field-control of the ferroaxial distortions and opens up new tunable functionalities. However, chiral multiferroics, especially ones stable at room temperature, are rare. A strain-stabilized, room-temperature chiral multiferroic phase in single crystals of BaTiS 3 is reported here. Using first-principles calculations, the stabilization of this multiferroic phase having P6 3 space group for biaxial tensile strains exceeding 1.5% applied on the basal ab-plane of the room temperature P6 3 cm phase of BaTiS 3 is predicted. The chiral multiferroic phase is characterized by rotational distortions of TiS 6 octahedra around the long c-axis and polar displacement of Ti atoms along the c-axis. Furthermore, the ferroaxial and ferroelectric distortions and their domains in P6 3 -BaTiS 3 are directly resolved using atomic resolution scanning transmission electron microscopy. Landau-based phenomenological modeling predicts a strong coupling between the ferroelectric and the ferroaxial order making P6 3 -BaTiS 3 an attractive test bed for achieving electric-field-control of chirality.

Chalcogenide↗

Virtual texture analysis to investigate the deformation mechanisms in metal microstructures at the atomic scale

Understanding the deformation behavior of metallic materials at high strain rates requires the characterization of plasticity contributors such as twins, phase transformed regions, and dislocations. However, predicting the contributions from phase transformation and twinning relies on a complete understanding of the selection of variants for various loading orientations and the evolution of their volume fractions. This manuscript presents a new virtual texture (VirTex) analysis approach to characterize phase transformation and twinning variants in deformed microstructures generated using molecular dynamics (MD) simulations. Furthermore, the VirTex method involves the construction of a rotation matrix to calculate the angle/axis pairs and misorientation angles for each atom in the microstructure. Any changes in the orientation angle from angle/axis pairs and/or structure types are analyzed to determine the nucleation and evolution of variants in the microstructure. The study uses shock deformed single-crystal Fe, Ta, and Cu to analyze the variant selections for phase transformation or twinning or both in BCC and FCC systems. In addition, the VirTex analysis is able to characterize the phase transformation and twinning variants in nanocrystalline Fe and Ta microstructures. Besides characterizing variants, orientation mapping also provides an accelerated and on-the-fly approach for quantifying twin fractions in MD microstructures.

36 MATERIALS SCIENCE↗

The effects of Venus' thermal structure on buoyant magma ascent

The recent Magellan images have revealed a broad spatial distribution of surface volcanism on Venus. Previous work in modeling the ascent of magma on both Venus and Earth has indicated that the planetary thermal structure significantly influences the magmatic cooling rates and thus the amount of magma that can be transported to the surface before solidification. In order to understand which aspects of the thermal structure have the greatest influence on the cooling of ascending magma, we have constructed magma cooling curves for both plutonic and crack buoyant ascent mechanisms, and evaluated the curves for variations in the planetary mantle temperature, thermal gradient curvature with depth, surface temperature gradient, and surface temperature. The planetary thermal structure is modeled as T/T(sub 0) = 1-tau(1-Z/Z(sub 0)(exp n), where T is the temperature, T(sub 0) is the source depth temperature, tau = 1-(T(sub s)/T(sub 0)) where T(sub s) is the planetary surface temperature, Z is the depth, Z(sub 0) is the source depth, and n is a constant that controls thermal gradient curvature with depth. The equation is used both for mathematical convenience and flexibility, as well as its fit to the thermal gradients predicted by the cooling half-space models. We assume a constant velocity buoyant ascent, body-averaged magma temperatures and properties, an initially crystal-free magma, and the same liquidus and solidus for both Venus and Earth.

Sakimoto, S. E. H.↗

Nepheline Crystallization Studies and the Structural Integrity of the Residual (SIR) - FY 2022 Study Glasses

In FY22 a set of 367 HLW glasses with compositions representative of the Waste Treatment and Immobilization Plant (WTP) processing region were aggregated and analyzed with the Structural Integrity of the Residual (SIR) model developed by the Savannah River National Laboratory (SRNL). An additional 12 glasses targeting 27 – 37 wt % alumina (in glass) and at waste loadings up to ~70 wt % were fabricated and added to the database. Collectively, this data set was analyzed with regression statistics and partitioning functions to reveal correlations between boron release and the chemical composition. FY22 results indicate that the SIR theoretical alkali-silicate precipitation term, Al 2 O 3 and B 2 O 3 concentration, and SIR computed non-bridging oxygen are significant predictors of chemical durability. A statistical model using the SIR parameters was shown to have greater overall accuracy than the nepheline discriminator model while maintaining false predictions of pour durability below 1%. In FY23, we will continue this work to focus on refining the SIR with glass compositions that challenge the SIR correlation terms, namely the theoretical crystalline precipitation and non-bridging oxygen terms.

36 MATERIALS SCIENCE↗

From Design to Device: Challenges and Opportunities in Computational Discovery of p -Type Transparent Conductors

A high-performance p -type transparent conductor (TC) does not yet exist but could lead to advances in a wide range of optoelectronic applications and enable new architectures for, e.g., next-generation photovoltaic (PV) devices. High-throughput computational material screenings have been a promising approach to filter databases and identify new p -type TC candidates and some of these predictions have been experimentally validated. However, most of these predicted candidates do not have experimentally achieved properties on par with n -type TCs used in solar cells and therefore have not yet been used in commercial devices. Thus, there is still a significant divide between transforming predictions into results that are actually achievable in the laboratory and an even greater lag in scaling predicted materials into functional devices. In this perspective, we outline some of the major disconnects in this materials discovery process—from scaling computational predictions into synthesizable crystals and thin films in the laboratory to scaling laboratory-grown films into real-world solar devices—and share insights to inform future strategies for TC discovery and design. Published by the American Physical Society 2024

14 SOLAR ENERGY↗

Structure-Function and Nearest Neighbor Interactions of the Cytochrome b 6 f Complex

Test prediction from our (i) high resolution (2.5 Å) structure of cyanobacterial cytochrome b 6 f complex (Structure, 22, 1008-1015, 2014), and (ii) analysis of quinone/quinol traffic within the b 6 f complex (Biophys. J., 107, 1620-1628, 2014) concerning the rate-limiting step in the linear (non-cyclic) electron transport chain. It was concluded that it arises from access of plastoquinol, the electron/proton donor, to the high potential electron carriers, i. e., the Fe 2 S 2 and cytochrome f proteins. The directed motion of the quinol proceeds via a narrow channel on the lumen or electrochemically positive, p- (lumen) side of the b 6 f complex which was defined by crystal structures of the b 6 f complex with quinol analogue inhibitors (J. Mol. Biol., 370, 39-52, 2007).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational Design of Interlayers for Thermally Stable Compositionally Graded Coatings on Nickel Alloys

To extend the service life of Ni-based superalloys, refractory metal coatings are often used. However, direct bonding between metals with dissimilar crystal structure promotes brittle intermetallic phase formation. This work presents a computational thermodynamic framework for high throughput design of functionally graded interlayers to suppress deleterious phases that may form at the interlayer. The Thermo-Calc software package was used to screen candidate metallic interlayer elements based on stability of solid-solution phases. Vanadium was identified as a promising interlayer due to its consistent suppression of intermetallic phases. Temperature-dependent phase diagram mapping between 600 and 1000 °C guided selection of a compositional pathway that significantly reduced intermetallic formation compared to directly joining the Ni-based and Nb refractory alloys. Time–temperature–transformation analysis was performed to assess whether equilibrium-predicted phases are kinetically accessible along regions of the graded path where non-solid-solution phases are not fully suppressed. The methodology was further applied to additional Ni-based alloy and coating systems, illustrating its transferability as an approach for rapid computational design of graded interlayers in dissimilar high-temperature materials.

36 MATERIALS SCIENCE↗

Magnetic structure and spin dynamics of the quasi-two-dimensional antiferromagnet Zn-doped copper pyrovanadate

We report magnetic properties of the antiferromagnet Zn x Cu 2-x V 2 O 7 (ZnCVO) with x ≈ 0.06 have been thoroughly investigated on powder and single-crystal samples. The crystal structure determination using powder x-ray and neutron diffraction confirms that our ZnCVO samples are isostructural with β-Cu 2 V 2 O 7 (β-CVO) with a small deviation in the lattice parameters. Macroscopic magnetic property measurements also confirm the similarity between the two compounds. The Cu 2+ spins were found to align along the crystallographic c axis, antiparallel to their nearest neighbors connected by the leading exchange interaction J 1 . Spin dynamics reveals a typical symmetric spin-wave dispersion with strong interactions in the bc plane and weak interplane coupling. The exchange interaction analysis indicates that the spin network of ZnCVO is topologically consistent with the previous DFT prediction but the values of leading exchange interactions are contradictory. Furthermore, rather than the predicted 2D honeycomb structure, the spin network in ZnCVO could be better described by the anisotropic 2D spin network composed of J 1 , J 5 , and J 6 interactions, four bonds per one spin site, coupled by weak interplane interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Micro-spectroscopic and freezing characterization of ice-nucleating particles collected in the marine boundary layer in the eastern North Atlantic

Abstract. Formation of atmospheric ice plays a crucial role in the microphysical evolution of mixed-phase and cirrus clouds and thus climate. How aerosol particles impact ice crystal formation by acting as ice-nucleating particles (INPs) is a subject of intense research activities. To improve understanding of atmospheric INPs, we examined daytime and nighttime particles collected during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) field campaign conducted in summer 2017. Collected particles, representative of a remote marine environment, were investigated for their propensity to serve as INPs in the immersion freezing (IMF) and deposition ice nucleation (DIN) modes. The particle population was characterized by chemical imaging techniques such as computer-controlled scanning electron microscopy with energy-dispersive X-ray analysis (CCSEM/EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine-structure spectroscopy (STXM/NEXAFS). Four major particle-type classes were identified where internally mixed inorganic–organic particles make up the majority of the analyzed particles. Following ice nucleation experiments, individual INPs were identified and characterized by SEM/EDX. The identified INP types belong to the major particle-type classes consisting of fresh sea salt with organics or processed sea salt containing dust and sulfur with organics. Ice nucleation experiments show IMF events at temperatures as low as 231 K, including the subsaturated regime. DIN events were observed at lower temperatures of 210 to 231 K. IMF and DIN observations were analyzed with regard to activated INP fraction, ice-nucleation active site (INAS) densities, and a water activity-based immersion freezing model (ABIFM) yielding heterogeneous ice nucleation rate coefficients. Observed IMF and DIN events of ice formation and corresponding derived freezing rates demonstrate that the marine boundary layer aerosol particles can serve as INPs under typical mixed-phase and cirrus cloud conditions. The derived IMF and DIN parameterizations allow for implementation in cloud and climate models to evaluate predictive effects of atmospheric ice crystal formation.

54 ENVIRONMENTAL SCIENCES↗

Importance of bulk excitations and coherent electron-photon-phonon scattering in photoemission from PbTe(111): Ab initio theory with experimental comparisons

This paper presents a fully ab initio many-body photoemission framework that includes coherent three-body electron-photon-phonon scattering to predict the transverse momentum distributions and the mean transverse energies (MTEs) of bulk photoelectrons from single-crystal photocathodes. The need to develop such a theory stems from the lack of studies that provide complete understanding of the underlying fundamental processes governing the transverse momentum distribution of photoelectrons emitted from single crystals. For example, initial predictions based on density-functional theory calculations of effective electron masses suggested that the (111) surface of PbTe would produce very small MTEs (≤ 15 meV), whereas our experiments yielded MTEs ten to twenty times larger than these predictions and also exhibited a lower photoemission threshold than predicted. The ab initio framework presented in this paper correctly reproduces both the magnitude of the MTEs from our measurements in PbTe(111) and the observed photoemission below the predicted threshold. Our results show that both photoexcitations into states that propagate in the bulk of the material and coherent many-body electron-photon-phonon scattering processes, which initial predictions ignored, play surprisingly important roles in photoemission from PbTe(111). Lastly, from the lessons learned, we recommend a procedure for rapid computational screening of potential single-crystal photocathodes for applications in next-generation ultrafast electron diffraction and X-ray free-electron lasers, which will enable significant advances in condensed matter research.

36 MATERIALS SCIENCE↗

Factors Affecting the Plasticity of Sodium Chloride, Lithium Fluoride, and Magnesium Oxide Single Crystals

A study was made of the relative magnitude of the effects of various factors on the ductility of single crystals of sodium chloride (NaCl), lithium fluoride (LiF), and magnesium oxide (MgO). Specimen treatments included water-polishing, varying cleavage rate, annealing, quenching, X-irradiation, surface coating, aging, and combinations of some of these treatments. The mechanical behavior of the crystals was studied in flexure and in compression, the latter study being performed at both constant strain rate and constant load. Etch-pit studies were carried out to provide some pertinent information on the results of pretreatment on the dislocation concentration and distribution in the vicinity of the surface. The load deformation curves for these ionic single crystals show an initial region of very low slope which proved to be due to anelastic deformation. The extent of initial anelastic deformation is modified by specimen pretreatment in a way that suggests that this deformation is the result of expansion of cleaved-in dislocation loops, which can contract on the removal of the stress. The effects of the various pretreatments on the load and deflection at fracture are in accord with the prediction one might make with regard to their effect on the nucleation of fatal surface cracks. For NaCl, increases in ductility are always accompanied by increases in strength. The creep constants for NaCl are a function of treatments which affect the bulk structure but are not a function of treatments which only affect the surface.

Stearns, Carl A.↗

First-principles study of an S = 1 quasi one-dimensional quantum molecular magnetic material

We use density functional theory to study the structural, magnetic, and electronic structures of the organometallic quantum magnet NiCl 2-4 SC (NH 2 ) 2 (DTN). Recent work has demonstrated the quasi one-dimensional nature of the molecular crystal and studied its quantum phase transitions at low temperatures. The system includes a magnetoelectric (ME) coupling and, when doped with Br, the presence of an exotic Bose-glass state. Using the generalized gradient approximation with inclusion of a van der Waals term to account for weak intermolecular forces and by introducing a Hubbard U term to the total energy, we systematically show that our calculations reproduce the magnetic anisotropy, the intermolecular exchange coupling strength, and the magnetoelectric effect in DTN, which have been observed in previous experiments. Further analysis of the electronic structure gives insight into the underlying magnetic interactions, including what mechanisms may be causing the ME effect. Using this computationally efficient model, we predict what effect applying an electric field might have on the magnetic properties of this quantum magnet.

1-dimensional spin chains↗

Data Science Enabled Enabled Discovery of Superconductors (Final Progress Report)

This Final Technical Report describes efforts by 4 PIs at the University of Florida (Peter Hirschfeld, Richard Hennig, Greg Stewart and James Hamlin), over the period September 2019-August 2023, to use data science and machine learning techniques to discover new conventional superconductors. The PIs constructed a discovery loop with two theorists and two experimentalists to: develop algorithms to machine learn descriptors correlating strongly with the critical temperature Tc (PI's Peter Hirschfeld, UF Physics and Richard Hennig, UF Materials Science and En), synthesize and measure properties of promising materials, and feed back the knowledge gained into the prediction algorithm. This work was motivated by the theoretical prediction and experimental discovery of high-pressure, high-pressure hydride superconductors, and to find ways to recreate the high critical temperatures in these systems at ambient pressure. Highlights from the grant include: 1) a new equation for Tc in terms of moments of the electron-phonon spectral function, improving on the so-called Allen-Dynes equation (1975); 2) study of the metastable A15 superconductor Nb3Si, formed under explosive compression at ~1000GPa to determine the kinetic barrier to the ground state structure; 3) the development of ultra-fast machine-learned atomic potentials for molecular dynamics, and 4) the discovery of superconductivity at 19K in WB2 arising from metastable defect structures in the crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High electron mobility of Al x Ga1− x N evaluated by unfolding the DFT band structure

We calculate the alloy-disorder-limited electron mobility of AlxGa1−xN from first principles. AlxGa1−xN is a technologically important ultra-wide-bandgap alloy with promise in light emitting diodes and high-power transistors. Alloying introduces statistical disorder, which causes electrons to scatter between different crystal-momentum states, leading to a reduction in mobility for intermediate alloy compositions. The corresponding lifetime, which appears as an energy broadening in the band structure, can be evaluated by unfolding the band structure from the supercell basis to the primitive-cell basis. We fit the first-principles band broadening with a model scattering potential and evaluate the low-field electron mobility using the semiclassical Boltzmann transport equation in the relaxation-time approximation. Our calculated mobility is in agreement with experimental values. We also find the lowest alloy-scattering electron mobility (total electron mobility) across the entire composition range to be 186 cm2/V s (136 cm2/V s), which is comparable to the highest electron mobility predicted in the competitor system, β-(AlxGa1−x)2O3. Our results elucidate the intrinsic limits imposed by alloy disorder on electron transport in AlxGa1−xN.

Pant, Nick (ORCID:0000000254506045)↗