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At least 847 records · Page 47

CasDinG is a 5′-3′ dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity

Abstract CRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. Here, we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP-dependent 5′-3′ DNA translocase that unwinds double-stranded (ds)DNA and RNA/DNA hybrids. The crystal structure of CasDinG reveals a superfamily 2 helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these domains, we identified the preferred PAM sequence for the type IV-A system (5′-GNAWN-3′ on the 5′-side of the target) with a plasmid library and performed plasmid clearance assays with domain deletion mutants. Plasmid clearance assays demonstrated that all three domains are essential for type IV-A immunity. Protein expression and biochemical assays suggested the vFeS domain is needed for protein stability and the arch for helicase activity. However, deletion of the N-terminal domain did not impair ATPase, ssDNA binding, or helicase activities, indicating a role distinct from canonical helicase activities that structure prediction tools suggest involves interaction with dsDNA. This work demonstrates CasDinG helicase activity is essential for type IV-A CRISPR immunity as well as the yet undetermined activity of the CasDinG N-terminal domain.

59 BASIC BIOLOGICAL SCIENCES↗

Magnetostriction and damping of forced vibrations in Fe-Mo single and polycrystal alloys

Magnetostriction and damping of forced vibrations in Fe-Mo single and polycrystal alloys is studied and analyzed with respect to existing approaches and experimental data. In this work, our data suggest that a more complex dependence (compared with linear dependence predicted by Smith and Birchak) between damping capacity and magnetostriction takes place for this and possibly other Fe-based ferromagnetic alloys. We believe that more factors related to the structural changes, brought about by the additions (elements added to Fe), which can affect phase stability as well as magnetic and electric contributions influencing property response, should be considered to provide a better correlation between the magnetic and magnetomechanical characteristics of this alloy.

36 MATERIALS SCIENCE↗

Scale-invariant machine-learning model accelerates the discovery of quaternary chalcogenides with ultralow lattice thermal conductivity

We design an advanced machine-learning (ML) model based on crystal graph convolutional neural network that is insensitive to volumes (i.e., scale) of the input crystal structures to discover novel quaternary chalcogenides, AMM'Q 3 (A/M/M' = alkali, alkaline earth, post-transition metals, lanthanides, and Q = chalcogens). These compounds are shown to possess ultralow lattice thermal conductivity (κ l ), a desired requirement for thermal-barrier coatings and thermoelectrics. Upon screening the thermodynamic stability of ~1 million compounds using the ML model iteratively and performing density-functional theory (DFT) calculations for a small fraction of compounds, we discover 99 compounds that are validated to be stable in DFT. Taking several DFT-stable compounds, we calculate their κ l using Peierls–Boltzmann transport equation, which reveals ultralow κ l (<2 Wm -1 K -1 at room temperature) due to their soft elasticity and strong phonon anharmonicity. Our work demonstrates the high efficiency of scale-invariant ML model in predicting novel compounds and presents experimental-research opportunities with these new compounds.

36 MATERIALS SCIENCE↗

Optical pulse-induced ultrafast antiferrodistortive transition in SrTiO 3

The ultrafast dynamics of the antiferrodistortive phase transition in perovskite SrTiO 3 is monitored via time-domain Brillouin scattering. Using femtosecond optical pulses, we initiate a thermally driven tetragonal-to-cubic structural transformation and detect the crystal phase through changes in the frequency of Brillouin oscillations (BO) induced by propagating acoustic phonons. Coupling the measured BO frequency with a spatiotemporal heat diffusion model, we demonstrate that, for a sample kept in the tetragonal phase, deposition of sufficient thermal energy induces a rapid transformation of the heat-affected region to the cubic phase. The initial phase change is followed by a slower reverse cubic-to-tetragonal phase transformation occurring on a timescale of hundreds of picoseconds. Here, we attribute this ultrafast phase transformation in the perovskite to a structural resemblance between atomic displacements of the R-point soft optic mode of the cubic phase and the tetragonal phase, both characterized by anti-phase rotation of oxygen octahedra. The structural relaxation time exhibits a strong temperature dependence consistent with the prediction of the equation of motion describing collective oxygen octahedra rotation based on the energy landscape of the phenomenological Landau theory of phase transitions. Evidence of such a fast structural transition in perovskites can open up new avenues in information processing and energy storage sectors.

36 MATERIALS SCIENCE↗

IRMA

IRMA (In)elastic Representation of Materials As S(α,β) evaluations IRMA turns one phonon model into three outputs that usually require three separate tool chains: an evaluated nuclear-data file, predicted neutron-scattering spectra, and scattering kernels for Monte Carlo transport. The three outputs draw on a single, consistent description of the material, so the evaluation, the spectroscopy that can validate it, and the transport that uses it always agree about the physics. Nuclear data. IRMA writes ENDF-6 File 7 thermal scattering evaluations on automatically constructed (α, β) grids. This part reimplements and generalizes NJOY's LEAPR: the classic kernels reproduce freshly generated NJOY2016 tapes digit for digit and published reference tapes to about 1e-4, and the generalized paths add the exact coherent one-phonon term, anisotropic Debye-Waller tensors, coherent elastic for arbitrary crystals, and a per-species partition for polyatomic materials. The tapes feed NJOY, AMPX, FUDGE, and every transport code downstream of them. Neutron spectroscopy. The irma.spectra forward model projects the same physics onto an instrument's kinematics and resolution: INS spectra for VISION and generic indirect geometries, and 2-D S(Q,E) powder maps for direct-geometry spectrometers, from a phonopy model or straight from a phonon DOS. It can be used to predict a proposed measurement before beam time; in analysis, it supplies the calculated single-scattering counterpart of a measured spectrum, from the same material description the evaluation was built from. Monte Carlo transport. The irma.ncrystal exporter writes per-temperature scattering kernels for the companion NCrystal plugin, so McStas, OpenMC, and other NCrystal-aware codes sample the same physics. The exported kernels carry the per-site anisotropic Debye-Waller tensors, keeping directional coherent-elastic physics that NCrystal's standard scalar treatment does not represent. With the same physics inside a transport code, an entire beamline becomes a virtual experiment: IRMA's end-to-end validation ran a custom McStas implementation of the ARCS spectrometer, assembled from the existing McVine and McStas models, against measured data. From a bare crystal structure. The irma mlip front end builds the phonon model itself: a structure file and a choice of potential are enough. Nine pretrained machine-learned interatomic potentials are supported, on a laptop CPU, with no first-principles calculation; an approximate phonon model for a new material costs minutes, not a DFT campaign, and the build emits prefilled inputs for all three outputs. The result is a good starting point rather than a finished evaluation: survey-quality physics with every parameter exposed for review. A converged atomistic calculation enters the same way, as a phonopy model, when higher fidelity is needed.

Ramic, Kemal [Oak Ridge National Laboratory (ORNL)↗

Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces

Understanding the adsorption of isolated metal cations from water on to mineral surfaces is critical for toxic waste retention and cleanup in the environment. Heterogeneous nucleation of metal oxyhydroxides and other minerals on material surfaces is key to crystal growth and dissolution. The link connecting these two areas, namely cation dimerization and polymerization, is far less understood. In this work we apply ab initio molecular dynamics calculations to examine the coordination structure of hydroxide-bridged Cu(II) dimers, and the free energy changes associated with Cu(II) dimerization on silica surfaces. The dimer dissociation pathway involves sequential breaking of two Cu 2+ -OH – bonds, yielding three local minima in the free energy profiles associated with 0-2 OH – bridges between the metal cations, and requires the design of a (to our knowledge) novel reaction coordinate for the simulations. Cu(II) adsorbed on silica surfaces are found to exhibit stronger tendency towards dimerization than when residing in water. Cluster-plus-implicit-solvent methods yield incorrect trends if OH – hydration is not correctly depicted. The predicted free energy landscapes are consistent with fast equilibrium times (seconds) among adsorbed structures, and favor Cu 2+ dimer formation on silica surfaces over monomer adsorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Orbital-spin locking and its optical signatures in altermagnets

Altermagnets, magnetic materials with zero magnetization and spin-split band structure, have gained tremendous attention recently for their rich physics and potential applications. Here, we report on a microscopic tight-binding model that unveils a unique coupling between orbitals and spins in d-wave altermagnets, which gives rise to momentum-dependent and spin-selective optical absorption. This coupling promotes the controlled optical excitation of up or down spins depending on the polarization direction of linearly polarized light. Such an effect originates from the coupling of orbitals to the sublattice degree of freedom through the crystal field, which is then coupled to spins through the antiferromagnetic interaction. Our crystal field analysis, which is general to any type of altermagnet, helps understand the onset of altermagnetism from a microscopic point of view, and we use our results to propose clear magneto-optical signatures of our predictions. Our findings shine light on the interplay between orbitals and spins in altermagnets, thus paving the way towards novel orbitronic and optospintronic devices.

Vila, Marc↗

Materials Science Experiments on the International Space Station

The Performance Goal for NASA's Microgravity Materials Science Program reads "Use microgravity to establish and improve quantitative and predictive relationships between the structure, processing and properties of materials." The advent of the International Space Station will open up a new era in Materials Science Research including the ability to perform long term and frequent experiments in microgravity. As indicated the objective is to gain a greater understanding of issues of materials science in an environment in which the force of gravity can be effectively switched off. Thus gravity related issues of convection, buoyancy and hydrostatic forces can be reduced and the science behind the structure/processing/properties relationship can more easily be understood. The specific areas of research covered within the program are (1) the study of Nucleation and Metastable States, (2) Prediction and Control of Microstructure (including pattern formation and morphological stability), (3) Phase Separation and Interfacial Stability, (4) Transport Phenomena (including process modeling and thermophysical properties measurement), and (5) Crystal Growth, and Defect Generation and Control. All classes of materials, including metals and alloys, glasses and ceramics, polymers, electronic materials (including organic and inorganic single crystals), aerogels and nanostructures, are included in these areas. The principal experimental equipment available to the materials scientist on the International Space Station (ISS) will be the Materials Science Research Facility (MSRF). Each of these systems will be accommodated in a single ISS rack, which can operate autonomously, will accommodate telescience operations, and will provide real time data to the ground. Eventual plans call for three MSRF racks, the first of which will be shared with the European Space Agency (ESA). Under international agreements, ESA and other partners will provide some of the equipment, while NASA covers launch and integration costs. The MSRF facilities will include modular components, which can be exchanged to provide inserts specifically matched to the engineering requirements of the particular Principal Investigator. To defray costs and avoid duplication of engineering effort NASA is also pursuing the possibility of using facilities provided by international partners. By this means it is anticipated that all of the types of research outlined in the previous paragraph can be done on the ISS.

Gillies, Donald C.↗

Simulation of MEMS for the Next Generation Space Telescope

The NASA Goddard Space Flight Center (GSFC) is developing optical micro-electromechanical system (MEMS) components for potential application in Next Generation Space Telescope (NGST) science instruments. In this work, we present an overview of the electro-mechanical simulation of three MEMS components for NGST, which include a reflective micro-mirror array and transmissive microshutter array for aperture control for a near infrared (NIR) multi-object spectrometer and a large aperture MEMS Fabry-Perot tunable filter for a NIR wide field camera. In all cases the device must operate at cryogenic temperatures with low power consumption and low, complementary metal oxide semiconductor (CMOS) compatible, voltages. The goal of our simulation efforts is to adequately predict both the performance and the reliability of the devices during ground handling, launch, and operation to prevent failures late in the development process and during flight. This goal requires detailed modeling and validation of complex electro-thermal-mechanical interactions and very large non-linear deformations, often involving surface contact. Various parameters such as spatial dimensions and device response are often difficult to measure reliably at these small scales. In addition, these devices are fabricated from a wide variety of materials including surface micro-machined aluminum, reactive ion etched (RIE) silicon nitride, and deep reactive ion etched (DRIE) bulk single crystal silicon. The above broad set of conditions combine to be a formidable challenge for space flight qualification analysis. These simulations represent NASA/GSFC's first attempts at implementing a comprehensive strategy to address complex MEMS structures.

Mott, Brent↗

Improving Data and Prediction Quality of High-Throughput Perovskite Synthesis with Model Fusion

Combinatorial fusion analysis (CFA) is an approach for combining multiple scoring systems using the rank-score characteristic function and cognitive diversity measure. One example is to combine diverse machine learning models to achieve better prediction quality. In this work, we apply CFA to the synthesis of metal halide perovskites containing organic ammonium cations via inverse temperature crystallization. Using a data set generated by high-throughput experimentation, four individual models (support vector machines, random forests, weighted logistic classifier, and gradient boosted trees) were developed. We characterize each of these scoring systems and explore 66 possible combinations of the models. When measured by the precision on predicting crystal formation, the majority of the combination models improves the individual model results. The best combination models outperform the best individual models by 3.9 percentage points in precision. In addition to improving prediction quality, we demonstrate how the fusion models can be used to identify mislabeled input data and address issues of data quality. In particular, we identify example cases where all single models and all fusion models do not give the correct prediction. Experimental replication of these syntheses reveals that these compositions are sensitive to modest temperature variations across the different locations of the heating element that can hinder or enhance the crystallization process. In summary, we demonstrate that model fusion using CFA can not only identify a previously unconsidered influence on reaction outcome but also be used as a form of quality control for high-throughput experimentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Affinity of Nicotinoids to a Model Nicotinic Acetylcholine Receptor (nAChR) Binding Pocket in the Human Brain

The binding affinity of nicotinoids to the binding residues of the a4ß2 variant of the nicotinic acetylcholine receptor (nAChR) was identified as a strong predictor of the nicotinoid’s addictive character. Using ab-iniito calculations for model binding pockets of increasing size comprising of 3, 6, and 14 amino acids (3AA, 6AA, and 14AA) that are derived from the crystal structure, the differences in binding affinity of 6 nicotinoids, namely nicotine (NIC), nornicotine (NOR), anabasine (ANB), anatabine (ANT), myosmine (MYO), and cotinine (COT) were correlated to their previously reported doses required for increases in intracranial self-stimulation (ICSS) thresholds, a metric for their addictive function. By employing the many body decomposition, the differences in the binding affinities of the various nicotinoids could be attributed mainly to the proton exchange energy between the Pyridine and non-Pyridine rings of the nicotinoids and the interactions between them and a handful of proximal amino acids, namely Trp156, Trpß57, Tyr100, and Tyr204. Interactions between the guest nicotinoid and the amino acids of the binding pocket were found to be mainly classical in nature, except for those between the nicotinoid and Trp156. The larger pockets were found to model binding structures more accurately and predicted the addictive character of all nicotinoids while smaller models, which are more computationally feasible, would only predict the addictive character of nicotinoids that are similar to nicotine. Here, the present study identifies the binding affinity of the guest nicotinoid to the host binding pocket as a strong descriptor of the nicotinoid’s addiction potential and as such it can be employed as a fast screening technique for the potential addiction of nicotine analogs.

60 APPLIED LIFE SCIENCES↗

Vacancy-Mediated Increases in Brine–Salt Surface Energies

Salt formations have been explored for the permanent isolation of spent nuclear fuel based on their high thermal conductivity, self-healing nature, and low hydraulic permeability to brine flow. Vacancy defect concentrations in salt complicate fracture mechanics not driven by dislocation dynamics and can influence the resulting surface structure. Classical molecular dynamic simulations were used to simulate tensile testing of salt crystals (halite) with vacancy defect concentrations of up to 0.5 defects/nm 3 . Increasing defect concentrations resulted in a decrease in ultimate tensile strength and fracture surface energies, driven by increased surface roughness rather than changes in the amount of surface area. Brine–salt surface energies of the fractured surfaces were 0.22 to 0.26 J/m 2 , significantly higher than values reported for atomically flat (100) surfaces at the same brine composition. This change in surface energy increased the brine–salt dihedral angle by ~27°. The dihedral angle threshold for percolation in salt is 60°, and a 27° increase due to rough fracture surfaces identifies a reduction in porosity percolation and a decrease in salt permeability. Therefore, bedded salt and salt domes may be even more stable than those previously predicted from dihedral angle calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electronic and magnetic properties of the topological semimetal SmMg 2 Bi 2

Dirac semimetals show nontrivial physical properties and can host exotic quantum states like Weyl semimetals and topological insulators under suitable external conditions. Here, by combining angle-resolved photoemission spectroscopy measurements (ARPES) and first-principle calculations, we demonstrate that the Zintl-phase compound SmMg 2 Bi 2 is in close proximity to a topological Dirac semimetallic state. ARPES results show a Dirac-like band crossing at the zone center near the Fermi level (E F ), which is further confirmed by first-principle calculations. Theoretical studies also reveal that SmMg 2 Bi 2 belongs to a Z 2 topological class and hosts spin-polarized states around the E F . Zintl's theory predicts that the valence state of Sm in this material should be Sm 2+ , however, we detect many Sm-4f multiplet states (flat-bands) whose energy positions and relative intensities suggest the presence of both dominant Sm 2+ and minor Sm 3+ . The small concentration (2.5%) of Sm 3+ in the bulk of a crystal is inferred to arise from Sm vacancies in the crystal. It is also evident that these flat bands and other dispersive states are strongly hybridized when they cross each other. Due to the presence of Sm 3+ ions, the temperature dependence of the magnetic susceptibility χ (T) shows a Curie-Weiss-like contribution in the low-temperature region, in addition to the Van Vleck-like behavior expected for the Sm 2+ ions. The present study will help to better understand the electronic structure, magnetism, and transport properties of related materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Martensitic Transformation in Fe x Mn 80-x Co 10 Cr 10 High-Entropy Alloy

High-entropy alloys and even medium-entropy alloys are an intriguing class of materials in that structure and property relations can be controlled via alloying and chemical disorder over wide ranges in the composition space. Employing density-functional theory combined with the coherent-potential approximation to average over all chemical configurations, we tune free energies between face-centered-cubic and hexagonal-close-packed phases in Fe x Mn 80 - x Co 10 Cr 10 systems. Within Fe-Mn-based alloys, we show that the martensitic transformation and chemical short-range order directly correlate with the face-centered-cubic and hexagonal-close-packed energy difference and stacking-fault energies, which are in quantitative agreement with recent observation of two phase region (face-centered cubic and hexagonal closed pack) in a polycrystalline high-entropy alloy sample at x = 40 at.%. Our predictions are further confirmed by single-crystal measurements on a x = 40 at.% using transmission-electron microscopy, selective-area diffraction, and electron-backscattered-diffraction mapping. The results herein offer an understanding of transformation-induced or twinning-induced plasticity in this class of high-entropy alloys and a design guide for controlling the physics at the electronic level.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Lines of Bound States in the Continuum in Monodisperse Microsphere Structures

Incorporating epitaxially grown active semiconductor media into self-assembled microsphere crystals has remained a major challenge as the curved geometry of the spheres is incompatible with conventional planar growth and patterning techniques. As a result, active photonic devices based on such self-assembled structures, which have other desirable properties such as enabling the rapid assembly of large area systems, have been elusive. Here, we numerically demonstrate an alternative route to creating high-Q resonances in microsphere-based nanophotonic assemblies compatible with standard optical gain materials. We show that close-packed layers of monodisperse microspheres can exhibit symmetry bandgaps, regardless of their layer stacking order. Thus, this microsphere environment can be used to create lines of bound states in the continuum (BICs) of an embedded slab made of active material. Using a realistic ZnS@SiO 2 (core-shell) architecture and sphere diameters compatible with scalable colloidal assembly, we predict sharp spectral features in angle-resolved transmission that trace these lines of BICs and persist in the presence of some fabrication disorder. Altogether, in enabling the integration of unpatterned epitaxial gain slabs with large-area colloidal microsphere assemblies, this approach opens a practical path toward active, dynamically reconfigurable photonic devices that leverage BIC physics for narrow-linewidth lasing and enhanced light–matter interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles

The successful self-assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally-designed, nanoscale components. This 3D DNA tile owes its “tensegrity” nature to its three rotationally-stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter-junction regions, corresponding to two thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed [Z + 2/3] turn inter-junction segments, yielding right-handed, antiparallel, “J1” junctions. Here, we report here a minimal DNA triangle motif consisting of 3-bp inter-junction segments, or one third of a helical turn. Here, we find that the minimal motif exhibits a reversed morphology with a left-handed tertiary structure mediated by a locally-parallel Holliday junction—the L1 junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. We identify a Rule of Thirds by which supramolecular chirality can be programmed through inter-junction DNA segment length. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under-explored class of self-assembling, chiral nanomaterials for topological processes in biological systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Observation of topological Dirac fermions and surface states in superconducting BaSn3

The interplay between topological electronic structure and superconductivity has attracted tremendous research interests recently as they could induce topological superconductivity (TSCs) which may be used to realize topological qubits for quantum computation. Among various TSC candidates, superconducting BaSn 3 (T c ~ 4.4K) has been predicted to be a topological Dirac semimetal (TDS) hosting two pairs of Dirac points along the Γ-A direction. Here, by combining the use of angle-resolved photoemission spectroscopy and ab initio calculations, we identified the predicted topological Dirac fermions and confirmed the TDS nature of the compound. In addition, we observed surface states connecting the Dirac points. Our observations demonstrate BaSn 3 as a superconductor with nontrivial topological electronic structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Interstitial Nature of Mn 2+ Doping in 2D Perovskites

Halide perovskites doped with magnetic impurities (such as the transition metals Mn 2+ , Co 2+ , Ni 2+ ) are being explored for a wide range of applications beyond photovoltaics, such as spintronic devices, stable light-emitting diodes, single-photon emitters, and magneto-optical devices. However, despite several recent studies, there is no consensus on whether the doped magnetic ions will predominantly replace the octahedral B-site metal via substitution or reside at interstitial defect sites. Here, by performing correlated nanoscale X-ray microscopy, spatially and temporally resolved photoluminescence measurements, and magnetic force microscopy on the inorganic 2D perovskite Cs 2 PbI 2 Cl 2 , we show that doping Mn 2+ into the structure results in a lattice expansion. The observed lattice expansion contrasts with the predicted contraction expected to arise from the B-site metal substitution, thus implying that Mn 2+ does not replace the Pb 2+ sites. Photoluminescence and electron paramagnetic resonance measurements confirm the presence of Mn 2+ in the lattice, while correlated nano-XRD and X-ray fluorescence track the local strain and chemical composition. Density functional theory calculations predict that Mn 2+ atoms reside at the interstitial sites between two octahedra in the triangle formed by one Cl – and two I – atoms, which results in a locally expanded structure. These measurements show the fate of the transition metal dopants, the local structure, and optical emission when they are doped at dilute concentrations into a wide band gap semiconductor.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗