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At least 523 records · Page 29

Physical properties and electronic structure of single-crystal KCo 2 As 2

We present a method for producing high quality KCo 2 As 2 crystals, stable in air and suitable for a variety of measurements. X-ray diffraction, magnetic susceptibility, electrical transport and heat capacity measurements confirm the high quality and an absence of long range magnetic order down to at least 2 K. Residual resistivity values approaching 0.25 µΩ cm are representative of the high quality and low impurity scattering, and a Sommerfeld coefficient γ = 7.3 mJ/mol K 2 signifies weaker correlations than the Fe-based counterparts. Together with Hall effect measurements, angle-resolved photoemission experiments reveal a Fermi surface consisting of electron pockets at the center and corner of the Brillouin zone, in line with theoretical predictions and in contrast to the mixed carrier types of other pnictides with the ThCr 2 Si 2 structure. A large, linear magnetoresistance of 200% at 14 T, together with an observed linear and hyperbolic, rather than parabolic, band dispersions are unusual characteristics of this compound.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Abstract Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine hydrolase mechanism mediated by a serine-histidine-aspartate catalytic triad. To elucidate the multi-step PETase catalytic mechanism, we use transition path sampling and likelihood maximization to identify optimal reaction coordinates for the PETase enzyme. We predict that deacylation is likely rate-limiting, and the reaction coordinates for both steps include elements describing nucleophilic attack, ester bond cleavage, and the “moving-histidine” mechanism. We find that the flexibility of Trp185 promotes the reaction, providing an explanation for decreased activity observed in mutations that restrict Trp185 motion. Overall, this study uses unbiased computational approaches to reveal the detailed reaction mechanism necessary for further engineering of an important class of enzymes for plastics bioconversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Real-time correlation of crystallization and segmental order in conjugated polymers

Modulating the segmental order in the morphology of conjugated polymers is widely recognized as a crucial factor for achieving optimal electronic properties and mechanical deformability. However, it is worth noting that the segmental order is typically associated with the crystallization process, which can result in rigid and brittle long-range ordered crystalline domains. To precisely control the morphology, a comprehensive understanding of how highly anisotropic conjugated polymers form segmentally ordered structures with ongoing crystallization is essential, yet currently elusive. To fill this knowledge gap, we developed a novel approach with a combination of stage-type fast scanning calorimetry and micro-Raman spectroscopy to capture the series of specimens with a continuum in the polymer percent crystallinity and detect the segmental order in real-time. Through the investigation of conjugated polymers with different backbones and side-chain structures, we observed a generally existing phenomenon that the degree of segmental order saturates before the maximum crystallinity is achieved. This disparity allows the conjugated polymers to achieve good charge carrier mobility while retaining good segmental dynamic mobility through the tailored treatment. Moreover, the crystallization temperature to obtain optimal segmental order can be predicted based on T g and T m of conjugated polymers. In conclusion, this in-depth characterization study provides fundamental insights into the evolution of segmental order during crystallization, which can aid in designing and controlling the optoelectronic and mechanical properties of conjugated polymers.

36 MATERIALS SCIENCE↗

Origin of metal-insulator transitions in the parent compounds of ruthenium-pnictide superconductors

Here we study the interplay of the structural phase transition, flat electronic band dispersion, and metal-to-insulator transition (MIT) in the parent compounds of the Ru-pnictide superconductors by using first-principles calculations. Our electron and phonon calculations reveal that Ru(P,As) undergo MIT accompanied by orthorhombic to monoclinic distortion at low temperature, but RuSb stays orthorhombic and metallic in agreement with the experimental findings. It is demonstrated that electronic correlation, as treated in DFT + U, DFT + Gutzwiller, and dynamical mean-field theory (DMFT), cannot induce MIT in the undistorted crystal structure. We find that, although small monoclinic distortion can remove the van Hove singularity at the Fermi level, it does not immediately gap out the Fermi surface and a large value of monoclinic distortion is necessary for a clear MIT, suggesting the possibility of an intermediate pseudogapped monoclinic metallic phase. Furthermore, we predict a light-induced two-step insulator-to-metal and structural transitions in the monoclinic phases of RuP and RuAs, which can be tested in future ultrafast pump-probe experiments as an alternative ideal playground to VO 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantitative Analysis of Defects in Silicon

The evaluation and prediction of the conversion efficiency for a variety of silicon samples with differences in structural defects, such as grain boundaries, twin boundaries, precipitate particles, dislocations, etc. are discussed. Quantitative characterization of these structural defects, which were revealed by etching the surface of silicon samples, is performed by using an image analyzer. Due to different crystal growth and fabrication techniques the various types of silicon contain a variety of trace impurity elements and structural defects. The two most important criteria in evaluating the various silicon types for solar cell applications are cost and conversion efficiency.

Natesh, R.↗

Ginzburg-Landau theory for the solid-liquid interface of bcc elements

Consideration is given to a simple order-parameter theory for the interfacial tension of body-centered-cubic solids in which the principal order parameter is the amplitude of the density wave at the smallest nonzero reciprocal-lattice vector of the solid. The parameters included in the theory are fitted to the measured heat of fusion, melting temperature, and solid-liquid density difference, and to the liquid structure factor and its temperature derivative at freezing. Good agreement is found with experiment for Na and Fe and the calculated anisotropy of the surface tension among different crystal faces is of the order of 2 percent. On the basis of various assumptions about the universal behavior of bcc crystals at melting, the formalism predicts that the surface tension is proportional to the heat of fusion per surface atom.

Shih, W. H.↗

Reduction of Defects in Germanium-Silicon

Crystals grown without being in contact with a container have superior quality to otherwise similar crystals grown in direct contact with a container, especially with respect to impurity incorporation, formation of dislocations, and residual stress in crystals. "Detached" or "dewetted" Bridgman growth is similar to regular Bridgman growth in that most of the melt is in contact with the crucible wall, but the crystal is separated from the wall by a small gap, typically of the order of 10-100 microns. Ge1-xSix crystals have been repeatedly grown detached in pBN crucibles. Detached-grown crystals exhibited superior structural quality as evidenced by measurements of etch pit density, synchrotron white beam X-ray topography and double axis X-ray diffraction. Experiments have also been conducted to assess the effect of pressure differential across the meniscus in sealed crucibles. The experiments were in agreement with calculations which predicted that stable detachment will only occur in crucibles with a high wetting angle and over a relatively narrow range of pressure differential. Calculations also indicate that the conditions for stable detached growth are greatly expanded in a microgravity environment.

Volz, M. P.↗

A Case Study of the Glycoside Hydrolase Enzyme Mechanism Using an Automated QM-Cluster Model Building Toolkit

Glycoside hydrolase enzymes are important for hydrolyzing the β-1,4 glycosidic bond in polysaccharides for deconstruction of carbohydrates. The two-step retaining reaction mechanism of Glycoside Hydrolase Family 7 (GH7) was explored with different sized QM-cluster models built by the Residue Interaction Network ResidUe Selector (RINRUS) software using both the wild-type protein and its E217Q mutant. The first step is the glycosylation, in which the acidic residue 217 donates a proton to the glycosidic oxygen leading to bond cleavage. In the subsequent deglycosylation step, one water molecule migrates into the active site and attacks the anomeric carbon. Residue interaction-based QM-cluster models lead to reliable structural and energetic results for proposed glycoside hydrolase mechanisms. The free energies of activation for glycosylation in the largest QM-cluster models were predicted to be 19.5 and 31.4 kcal mol −1 for the wild-type protein and its E217Q mutant, which agree with experimental trends that mutation of the acidic residue Glu217 to Gln will slow down the reaction; and are higher in free energy than the deglycosylation transition states (13.8 and 25.5 kcal mol −1 for the wild-type protein and its mutant, respectively). For the mutated protein, glycosylation led to a low-energy product. This thermodynamic sink may correspond to the intermediate state which was isolated in the X-ray crystal structure. Hence, the glycosylation is validated to be the rate-limiting step in both the wild-type and mutated enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electron-phonon coupling and superconductivity in the doped topological crystalline insulator ( Pb 0.5 Sn 0.5 ) 1 – x In x Te

Here, we present a neutron-scattering study of phonons in single crystals of ( Pb 0.5 Sn 0.5 ) 1 – x In x Te with x = 0 (metallic, but nonsuperconducting) and x = 0.2 (nonmetallic normal state, but superconducting). We map the phonon dispersions (more completely for x = 0 ) and find general consistency with theoretical calculations, except for the transverse and longitudinal optical (LO) modes at the Brillouin-zone center. At low temperature, both modes are strongly damped but sit at a finite energy ( ≈ 4 meV in both samples), shifting to higher energy at room temperature. These modes are soft due to a proximate structural instability driven by the sensitivity of Pb-Te and Sn-Te p -orbital hybridization to off-center displacements of the metal atoms. The impact of the soft optical modes on the low-energy acoustic modes is inferred from the low thermal conductivity, especially at low temperature. Given that the strongest electron-phonon coupling is predicted for the LO mode, which should be similar for both studied compositions, it is intriguing that only the In-doped crystal is superconducting. In addition, we observe elastic diffuse (Huang) scattering that is qualitatively explained by the difference in Pb-Te and Sn-Te bond lengths within the lattice of randomly distributed Pb and Sn sites. We also confirm the presence of anomalous diffuse low-energy atomic vibrations that we speculatively attribute to local fluctuations of individual Pb atoms between off-center sites.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Polaritonic Chern Insulators in Monolayer Semiconductors

Systems with strong light-matter interaction open up new avenues for studying topological phases of matter. Examples include exciton polaritons, mixed light-matter quasiparticles, where the topology of the polaritonic band structure arises from the collective coupling between matter wave and optical fields strongly confined in periodic dielectric structures. Distinct from light-matter interaction in a uniform environment, the spatially varying nature of the optical fields leads to a fundamental modification of the well-known optical selection rules, which were derived under the plane wave approximation. Here, in this study, we identify polaritonic Chern insulators by coupling valley excitons in transition metal dichalcogenides to photonic Bloch modes in a dielectric photonic crystal slab. We show that polaritonic Dirac points, which are markers for topological phase transition points, can be constructed from the collective coupling between valley excitons and photonic Dirac cones in the presence of both time-reversal and inversion symmetries. Lifting exciton valley degeneracy by breaking time-reversal symmetry leads to gapped polaritonic bands with nonzero Chern numbers. Through numerical simulations, we predict polaritonic chiral edge states residing inside the topological gaps. Our Letter paves the way for the further study of strong exciton-photon interaction in nanophotonic structures and for exploring polaritonic topological phases and their practical applications in polaritonic devices.

74 ATOMIC AND MOLECULAR PHYSICS↗

New Theoretical Technique Developed for Predicting the Stability of Alloys

When alloys are being designed for aeronautical and other applications, a substantial experimental effort is necessary to make incremental changes in the desired alloy properties. A scheme to narrow the field to the most promising candidates would substantially reduce the high cost of this experimental screening. Such a method for determining alloy properties, called the BFS (Bozzolo, Ferrante, and Smith) method, has been developed at the NASA Lewis Research Center. This method was used to calculate the thermal stability and mechanical strength of 200 alloys of Ni3Al, with Cu and Au impurities forming ternary and quaternary compounds. With recent advances in the method, almost any metallic impurity and crystal structure can be addressed. In addition, thermal effects can be addressed with Monte Carlo techniques. At present, an experimental program is in progress to verify these results. The method identified a small number of the most promising candidates from the 200 alloys with the largest negative heat of formation and the highest bulk modulus. This calculation required only 5 min of CPU time on a VAX computer. It is clear that semi-empirical methods have achieved the level of development and reliability to warrant examining this new approach to the problem of alloy design. The present work was meant to demonstrate, perhaps in a rather simple way, this power. This type of application of atomistic simulation methods can narrow the gap and improve the feedback between theoretical predictions and laboratory experimentation.

Source record↗

Electrochemical Oxidation in Garnet-Type Solid Electrolyte by Formation of Point Defects

All-solid-state batteries hold greater promise for improving safety and energy density over conventional battery technology employing organic liquid electrolytes. One of the required features of a Li + conducting solid electrolyte is electrochemical stability, attained thermodynamically or kinetically, within the targeted operating voltage and temperature ranges. Therefore, understanding of the oxidative or reductive degradation mechanism is important to allow the design of stable solid electrolyte materials. This work contributes to building an understanding of the oxidative degradation mechanism in lithium solid electrolytes at cell operating conditions. Here, we have focused on resolving the oxidative decomposition mechanism of Al-doped lithium garnet Li 6.28 Al 0.24 La 3 Zr 2 O 12 (LLZO) as a state-of-the-art inorganic ceramic electrolyte. By combining experimental and computational analyses, we show that oxidation of LLZO occurs by simultaneous loss of oxygen and lithium from the structure, resulting in substoichiometric LLZO, at a moderate temperature (80 °C) and a high electrode potential (4.3 V vs Li/Li + ). Based on X-ray absorption and diffraction analyses, we find that the zirconium coordination shells in LLZO contract while the crystal structure experiences positive chemical strain upon electrochemical oxidation. The results from ex situ structural characterization of both the local structure and crystal symmetry are supported by a substoichiometric LLZO with lithium and oxygen vacancies, modeled by density functional theory (DFT) calculations. These chemical and structural changes in LLZO suppress effective lithium-ion conductivity by an order of magnitude. Formation of lithium and oxygen vacancies in LLZO upon electrochemical oxidation is different from prior thermodynamic predictions of phase decomposition of LLZO. The difference here is that the experiments were conducted at near-room temperature, which can hinder the kinetics of phase separation, and thus, the resultant LLZO solid electrolyte is still single-phase but substoichiometric in Li and O. In conclusion, these findings contribute an important degradation mechanism of the electrolyte, relevant for practical operational conditions of solid-state batteries.

36 MATERIALS SCIENCE↗

Machine learning accelerated prediction of Ce-based ternary compounds involving antagonistic pairs

The discovery of novel quantum materials within ternary phase spaces containing antagonistic pairs such as Fe with Bi, Pb, In, and Ag, presents significant challenges yet holds great potential. In this work, we investigate the stabilization of these immiscible pairs through the integration of Cerium (Ce), an abundant rare-earth and cost-effective element. By employing a machine learning (ML)-guided framework, particularly crystal graph convolutional neural networks (CGCNN), combined with first-principles calculations, we efficiently explore the composition/structure space and predict 9 stable and 37 metastable Ce-Fe-X (X=Bi, Pb, In, and Ag) ternary compounds. Our findings include the identification of multiple new stable and metastable phases, which are evaluated for their structural and energetic properties. These discoveries not only contribute to the advancement of quantum materials but also offer viable alternatives to critical rare earth elements, underscoring the importance of Ce-based intermetallic compounds in technological applications.

36 MATERIALS SCIENCE↗

Bipartite chromatin recognition by Hop1 from two diverged Holozoa

In meiosis, ploidy reduction is driven by a complex series of DNA breakage and recombination events between homologous chromosomes, orchestrated by meiotic HORMA domain proteins (HORMADs). Meiotic HORMADs possess a central chromatin binding region (CBR) whose architecture varies across eukaryotic groups. Here, we determine high-resolution crystal structures of the meiotic HORMAD CBR from two diverged aquatic Holozoa,Schistosoma mansoniandPatiria miniata, which reveal tightly associated plant homeodomain (PHD) and winged helix-turn-helix (wHTH) domains. We show that PHD–wHTH CBRs bind duplex DNA through their wHTH domains, and identify key residues that disrupt this interaction. Combining experimental and predicted structures, we show that the CBRs’ PHDs likely interact with the tail of histone H3, and may discriminate between unmethylated and trimethylated H3 lysine 4. Finally, we show that Holozoa Hop1 CBRs bind nucleosomes in vitro in a bipartite manner involving both the PHD and wHTH domain. Our data reveal how meiotic HORMADs with PHD–wHTH CBRs can bind chromatin and potentially discriminate between chromatin states to drive meiotic recombination to specific chromosomal regions.

Life Sciences & Biomedicine - Other Topics↗

KCo 2 As 2 : A new portal for the physics of high-purity metals

High-quality single crystals of KCo 2 As 2 with the body-centered tetragonal ThCr 2 Si 2 structure were grown using KAs self flux. Structural, magnetic, thermal, and electrical transport properties were investigated. No clear evidence for any phase transitions was found in the temperature range 2–300 K. The in-plane electrical resistivity ρ versus temperature T is highly unusual, showing a T 4 behavior below 30 K and an anomalous positive curvature up to 300 K, which is different from the linear behavior expected from the Bloch-Grüneisen theory for electron scattering by acoustic phonons. This positive curvature has been previously observed in the in-plane resistivity of high-conductivity layered delafossites such as PdCoO 2 and PtCoO 2 . The in-plane ρ(T → 0) = 0.36μΩ cm of KCo 2 As 2 is exceptionally small for this class of compounds. The material also exhibits a magnetoresistance at low T which attains a value of about 40% at T = 2 K and magnetic field H = 80 kOe. The magnetic susceptibility χ of KCo 2 As 2 is isotropic and about an order of magnitude smaller than the values for the related compounds SrCo 2 As 2 and BaCo 2 As 2 . The χ increases above 100 K, which is found from our first-principles calculations to arise from a sharp peak in the electronic density of states just above the Fermi energy E F . Heat capacity C p (T) data at low T yield an electronic density of states N(E F ) that is about 36% larger than predicted by the first-principles theory. The C p (T) data near room temperature suggest the presence of excited optic vibration modes, which may also be the source of the positive curvature in ρ(T). Angle-resolved photoemission spectroscopy measurements are compared with the theoretical predictions of the band structure and Fermi surfaces. In conclusion, our results show that KCo 2 As 2 provides a new avenue for investigating the physics of high-purity metals.

36 MATERIALS SCIENCE↗

Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain

Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.

59 BASIC BIOLOGICAL SCIENCES↗

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

59 BASIC BIOLOGICAL SCIENCES↗

Application of Dislocation Theory to Minimize Defects in Artificial Solids Built with Nanocrystal Building Blocks

Conspectus. Oriented atomic attachment of colloidal inorganic nanocrystals represents a powerful synthetic method for preparing complex inorganic superstructures. Examples include fusion of nanocrystals into dimer and superlattice structures. If the attachment were perfect throughout, then the resulting materials would have single crystal-like alignment of the individual nanocrystals' atomic lattices. While individual colloidal nanocrystals typically are free of many defects, there are a multitude of pathways that can generate defects upon nanocrystal attachment. These attachment generated defects are typically undesirable, and thus developing strategies to favor defect-free attachment or heal defective interfaces are essential. There may also be some cases where attachment-derived defects are desirable. In this Account, we summarize our current understanding of how these defects arise, in order to offer guidance to those who are designing nanocrystal derived solids. The small size of inorganic nanocrystals means short diffusion lengths to the surface, which favor the formation of nanocrystal building blocks with pristine atomic structures. Upon attachment, however, there are numerous pathways that can lead to atomic scale defects, and bulk crystal dislocation theory provides an invaluable guide to understanding these phenomena. As an example, an atomic step edge can be incorporated into the interface leading to an extra half-plane of atoms, known as an edge dislocation. These dislocations can be well described by the Burgers vector description of dislocations, which geometrically identifies planes in which a dislocation can move. Our in situ measurements have verified that bulk dislocation theory predictions for 1D defects hold true at few-nanometer length scales in PbTe and CdSe nanocrystal interfaces. Ultimately, the applicability of dislocation theory to nanocrystal attachment enables the predictive design of attachment to prevent or facilitate healing of defects upon nanocrystal attachment. We applied similar logic to understand formation of planar (2D) defects such as stacking faults upon nanocrystal attachment. Again concepts from bulk crystal defect crystallography can identify attachment pathways that can prevent or deterministically form planar defects upon nanocrystal attachment. The concepts we discuss work well for identifying favorable attachment geometries for nanocrystal pairs ; however it is currently unclear how to translate these ideas to near-simultaneous multiparticle attachment. Geometric frustration, which prevents nanocrystal rotation, and yet-to-be considered defect generation pathways unique to multiparticle attachment complicate defect-free superlattice attachment. New imaging methods now allow for the direct observation of local attachment trajectories and may enable improved understanding of such multiparticle phenomena. With further refinement, a unified framework for understanding and ultimately eliminating structural defects in fused nanocrystal superstructures may well be achievable in coming years.

77 NANOSCIENCE AND NANOTECHNOLOGY↗