Diversity in Atomic Structures of Zeolite-Templated Carbons and the Consequences for Macroscopic Properties

Zeolite-templated carbons (ZTCs) are a family of ordered microporous carbons with extralarge surface areas and micropore volumes, which are synthesized by carbon deposition within the confined spaces of zeolite micropores. There has been great controversy regarding the atomic structures of ZTCs, which encompass two extremes: (1) three-dimensionally connected curved open-blade-type carbon moieties and (2) ideal tubular structures (commonly referred to as "Schwarzites"). In this study, through a combination of experimental analyses and theoretical calculations, we demonstrate that the atomic structure of ZTCs is difficult to define as a single entity, and it widely varies depending on their synthesis conditions. Carbon deposition using a large organic precursor and low-temperature framework densification generates ZTCs predominantly composed of open-blade-type moieties, characterized by low surface curvature and abundant H-terminated edge sites. Meanwhile, synthesis using a small precursor with high-temperature densification produces ZTCs with an increased portion of closed-strut carbon moieties (or closed-fullerene-like nodes), exhibiting large surface curvature and diminished edge sites. The variations in the atomic structure of ZTCs result in significant differences in their macroscopic properties, such as N2/CO2 adsorption, oxidative stability, work function, and electrocatalytic properties, despite the presence of comparable pore structures. Therefore, ZTCs demonstrate the potential to synthesize ordered nanoporous carbons with tunable physicochemical properties.

A Complicated Route from Disorder to Order in Antimony-Tellurium Binary Phase Change Materials

The disorder-to-order (crystallization) process in phase-change materials determines the speed and storage polymorphism of phase-change memory devices. Only by clarifying the fine-structure variation can the devices be insightfully designed, and encode and store information. As essential phase-change parent materials, the crystallized Sb-Te binary system is generally considered to have the cationic/anionic site occupied by Sb/Te atoms. Here, direct atomic identification and simulation demonstrate that the ultrafast crystallization speed of Sb-Te materials is due to the random nature of lattice site occupation by different classes of atoms with the resulting octahedral motifs having high similarity to the amorphous state. It is further proved that after atomic ordering with disordered chemical occupation, chemical ordering takes place, which results in different storage states with different resistance values. These new insights into the complicated route from disorder to order will play an essential role in designing neuromorphic devices with varying polymorphisms.

Resolving Multielement Semiconductor Nanocrystals at the Atomic Level: Complete Deciphering of Domains and Order in Complex CuαZnβSnγSeδ (CZTSe) Tetrapods

Semiconductor nanocrystals (NCs) with high elemental and structural complexity can be engineered to tailor for electronic, photovoltaic, thermoelectric, and battery applications etc. However, this greater complexity causes ambiguity in the atomic structure understanding. This in turn hinders the mechanistic studies of nucleation and growth, the theoretical calculations of functional properties, and the capability to extend functional design across complementary semiconductor nanocrystals. Herein, we successfully deciphered the atomic arrangements of 4 different nanocrystal domains in CuαZnβSnγSeδ (CZTSe) nanocrystals using crucial zone axis analysis on multiple crystals in different orientations. The results show that the essence of crystallographic progression from binary to multielemental semiconductors is actually the change of theoretical periodicity. This transition is caused by decreased symmetry in the crystal instead of previously assumed crystal deformation. We further reveal that these highly complex crystalline entities have highly ordered element arrangements as opposed to the previous understanding that their elemental orderings are random.

Nanocomposites Based on Polyethylene and Nickel Ferrite: Preparation, Characterization, and Properties

Composite materials based on NiFe2O4 nanoparticles and polyethylene matrix have been synthesized by thermal decomposition to expand the application area of high-pressure polyethylene by filling it with nanoscale particles. The synthesized compositions were obtained in the form of a dark gray powder and compressed for further study According to TEM, the average particle size in composites was 2, 3, and 4 nm in samples with a filling of 10%, 20% and 30%. The concentration dependences of the specific electrical resistivity ρV, dielectric permittivity ε, saturation magnetization MS and the parameters of reflection and attenuation of microwave power of the obtained composites were investigated. The threshold for percolation in such materials is found to be within a concentration range of 20…30%. The electronic and atomic structure of composites was studied by methods of Mössbauer spectroscopy, X-ray diffraction and X-ray absorption spectroscopy. The closest atomic environment of nickel and iron in nanoparticles is close to that of crystalline NiFe2O4. The dependence of the nanoparticles size as well as the dependence of the number of tetrahedral or octahedral iron positions in nickel ferrite nanoparticles to their content in polyethylene matrix is established. It is shown that composite materials based on NiFe2O4 nanoparticles and polyethylene matrix can be used as components of electromagnetic compatibility systems.

Rectangular-Phase Tellurene on Ni(111) from Monolayer Films to Periodic Striped Patterns

As an emerging member of monoelemental two-dimensional (2D) materials, 2D tellurium (tellurene) has recently attracted intensive attention due to its polymorphism arising from the multivalent nature and fascinating properties such as wide-range band gaps, high carrier mobilities, etc. Herein, we predict the formation of a rectangular-phase tellurene on Ni(111) by first-principles density functional theory (DFT) calculations and realize its direct syntheses and characterizations by molecular beam epitaxy (MBE) and scanning tunneling microscopy (STM). We reveal that the monolayer rectangular tellurene and underlying Ni(111) substrate are strongly coupled, along with good lattice registry along two mutually perpendicular directions, which serves as the key driving force for the tellurene formation. We also uncover the unique morphological transitions of Te/Ni(111) from rectangular tellurene monolayer, to uniform periodic striped patterns at the second layer, and then to thick striped patterns. This work should offer valuable insights for the substrate-mediated syntheses of monoelemental 2D materials, thus propelling their phase engineering and intriguing property explorations.

Influence of the Hydrogen Doping Method on the Atomic Structure, Mechanical Properties and Relaxation Behaviors of Metallic Glasses

The interaction of metallic glasses (MGs) with hydrogen can trigger many interesting physical, chemical and mechanical phenomena. However, atomic-scale understanding is still lacking. In this work, molecular dynamics (MD) simulations are employed to study the atomic structure, mechanical properties and relaxation behaviors of H-doped Ni50Al50 MGs doped by two methods. The properties of H-doped MGs are determined not only by the hydrogen content but also by the doping method. When H atoms are doped into the molten state of samples, H atoms can fully diffuse and interact with metallic atoms, resulting in loose local atomic structures, homogeneous deformation and enhanced β relaxation. In contrast, when H atoms are doped into as-cast MGs, the H content is crucial in affecting the atomic structure and mechanical properties. A small number of H atoms has little influence on the elastic matrix, while the percolation of shear transformation zones (STZs) is hindered by H atoms, resulting in the delay of shear band (SB) formation and an insignificant change in the strength. However, a large number of H atoms can make the elastic matrix loose, leading to the decrease in strength and the transition of the deformation mode from SB to homogeneous deformation. The H effects on the elastic matrix and flow units are also applied to the dynamic relaxation. The deformability of H-doped Ni50Al50 MGs is enhanced by both H-doping methods; however, our results reveal that the mechanisms are different.

Atomic structure of intermetallic compound Nb5Si3by new cluster transformation analysis method

The structure of Nb₅Si₃at the atomic level is fundamental for identifying its complicated structure in atomic simulations and for further understanding the phase selection behaviors during the solidification of Nb-Si alloys. In this study, the structure of Nb₅Si₃was investigated using deep-learning molecular dynamic simulations. The idealβNb₅Si₃is characterized by Nb-centered Voronoi polyhedrons (VPs) <0,0,12,3>, <0,0,12,2>, and Si-centered VPs <0,2,8,2>, <0,2,8,0>. Most initial VPs are distorted at high temperatures due to intense thermal perturbation. A new cluster transformation analysis (CTA) method was proposed to evaluate the stability of ideal VPs against perturbation and predict the possible transformations of the initial VPs in atomic simulations. Most transformations of the initial VPs inβNb₅Si₃originate from distortions at the edges of the Nb-centered VPs and the faces/vertices of the Si-centered VPs. The distorted VPs inβNb₅Si₃at high temperatures are dominated by <0,1,10,4>, <0,1,10,5>, <0,2,8,1> and <1,2,5,3> VPs, which are predicted as the primary transformations by the CTA.

Intermetallic Nanocrystal Discovery through Modulation of Atom Stacking Hierarchy

A library of compositionally and structurally well-defined Au-Cu alloy nanocrystals has been prepared via scanning probe block copolymer lithography. These libraries not only allow one to map compositional and structure space but also the conditions (e.g., cooling rate) required to access specific structures. This approach enabled the realization of a previously unobserved architecture, an intermetallic nanoprism, that is a consequence of hierarchical atom stacking. These structures exhibit distinctive diffraction patterns characterized by non-integer-index, forbidden spots, which serve as a diagnostic indicator of such structures. Inspection of the library's pseudospherical particles reveals a high-strain cubic-tetragonal interfacial configuration in the outer regions of the intermetallic nanocrystals. Since it is costly and time-consuming to explore the nanomaterials phase space via conventional wet-chemistry, this parallel kinetic-control approach, which relies on substrate- and positionally isolated particles, may lead to the rapid discovery of complex nanocrystals that may prove useful in applications spanning catalysis and plasmonic sensing.

Recent Developments of Microscopic Study for Lanthanide and Manganese Doped Luminescent Materials

Luminescent materials are indispensable for applications in lighting, displays and photovoltaics, which can transfer, absorb, store and utilize light energy. Their performance is closely related with their size and morphologies, exact atomic arrangement, and local configuration about photofunctional centers. Advanced electron microscopy-based techniques have enabled the possibility to study nanostructures with atomic resolution. Especially, with the advanced micro-electro-mechanical systems, it is able to characterize the luminescent materials at the atomic scale under various environments, providing a deep understanding of the luminescent mechanism. Accordingly, this review summarizes the recent achievements of microscopic study to directly image the microstructure and local environment of activators in lanthanide and manganese (Ln/Mn²⁺ )-doped luminescent materials, including: 1) bulk materials, the typical systems are nitride/oxynitride phosphors; and 2) nanomaterials, such as nanocrystals (hexagonal-phase NaLnF₄ and perovskite) and 2D nanosheets (Ca₂ Ta₃ O₁₀ and MoS₂ ). Finally, the challenges and limitations are highlighted, and some possible solutions to facilitate the developments of advanced luminescent materials are provided.

Density Functional Studies on the Atomistic Structure and Properties of Iron Oxides: A Parametric Study

With the aim to find the best simulation routine to accurately predict the ground-state structures and properties of iron oxides (hematite, magnetite, and wustite) using density functional theory (DFT) with Hubbard-U correction, a significant amount of DFT calculations were conducted to investigate the influence of various simulation parameters (energy cutoff, K-point, U value, magnetization setting, smearing value, etc.) and pseudopotentials on the structures and properties of iron oxides. With optimized simulation parameters, the obtained equation of state, lattice constant, bulk moduli, and band gap is much closer to the experimental values compared with previous studies. Due to the strong coupling between the 2p orbital of O and the 3d orbital of Fe, it was found that Hubbard-U correction obviously improved the results for all three kinds of iron oxides including magnetite which has not yet been tested with U correction before, but the U value should be different for different oxides (3 ev, 4 ev, 4 ev for hematite, magnetite, and wustite, respectively). Two kinds of spin magnetism settings for FeO are considered, which should be chosen according to different calculation purposes. The detailed relationship between the parameter settings and the atomic structures and properties were analyzed, and the general principles for future DFT calculation of iron oxides were provided.

Investigation on Atomic Bonding Structure of Solution-Processed Indium-Zinc-Oxide Semiconductors According to Doped Indium Content and Its Effects on the Transistor Performance

The atomic composition ratio of solution-processed oxide semiconductors is crucial in controlling the electrical performance of thin-film transistors (TFTs) because the crystallinity and defects of the random network structure of oxide semiconductors change critically with respect to the atomic composition ratio. Herein, the relationship between the film properties of nitrate precursor-based indium-zinc-oxide (IZO) semiconductors and electrical performance of solution-processed IZO TFTs with respect to the In molar ratio was investigated. The thickness, morphological characteristics, crystallinity, and depth profile of the IZO semiconductor film were measured to analyze the correlation between the structural properties of IZO film and electrical performances of the IZO TFT. In addition, the stoichiometric and electrical properties of the IZO semiconductor films were analyzed using film density, atomic composition profile, and Hall effect measurements. Based on the structural and stoichiometric results for the IZO semiconductor, the doping effect of the IZO film with respect to the In molar ratio was theoretically explained. The atomic bonding structure by the In doping in solution-processed IZO semiconductor and resulting increase in free carriers are discussed through a simple bonding model and band gap formation energy.

Theory-Guided Modulation of Optimal Silver Nanoclusters toward Efficient CO2 Electroreduction

Electrochemical CO₂ reduction reaction (CO₂RR), when powered with intermittent but renewable energies, holds an attractive potential to close the anthropogenic carbon cycle through efficiently converting the exorbitantly discharged CO₂ to value-added fuels and/or chemicals and consequently reduce the greenhouse gas emission. Through systematically integrating the density functional theory calculations, the modeling statistics of various proportions of CO₂RR-preferred electroactive sites, and the theoretical work function results, it is found that the crystallographically unambiguous Ag nanoclusters (NCs) hold a high possibility to enable an outstanding CO₂RR performance, particularly at an optimal size of around 2 nm. Motivated by this, homogeneously well-distributed ultrasmall Ag NCs with an average size of ∼2 nm (2 nm Ag NCs) were thus synthesized to electrochemically promote CO₂RR, and the results demonstrate that the 2 nm Ag NCs are able to achieve a significantly larger CO partial current density [j_(CO)], an impressively higher CO Faraday efficiency of over 93.8%, and a lower onset overpotential (η) of 146 mV as well as a remarkably higher energy efficiency of 62.8% and a superior stability of 45 h as compared to Ag nanoparticles (Ag NPs) and bulk Ag. Both theoretical computations and experimental results clearly and persuasively demonstrate an impressive promotion effect of the crystallographically explicit atomic structure for electrochemically reducing CO₂ to CO, which exemplifies a novel design approach to more benchmark metal-based platforms for advancing the practically large-scale CO₂RR application.

Atomic-Scale Insights into the Lateral and Vertical Epitaxial Growth in Two-Dimensional Pd2Se3-MoS2 Heterostructures

Two-dimensional (2D) materials form heterostructures in both the lateral and vertical directions when two different materials are interfaced, but with totally different bonding mechanisms of covalent in-plane to van der Waal's layered interactions. Understanding how the competition between lateral and vertical forces influences the epitaxial growth is important for future materials development of complex mixed layered heterostructures. Here, we use atomic-resolution annular dark-field scanning transmission electron microscopy to study the detailed atomic arrangements at mixed 2D heterostructure interfaces composed of two semiconductors with distinctly different crystal symmetry and elemental composition, Pd₂Se₃:MoS₂, in order to understand the role of different chemical bonds on the resultant epitaxy. Pd₂Se₃ is grown off the step edge in bilayer MoS₂, and the vertical and lateral epitaxial relationships of the Pd₂Se₃-MoS₂ heterostructures are investigated. We find that the similarity of geometry at the interface with one metal (Pd or Mo) atoms bonded with two chalcogens (S or Se) are the crucial factors to make the atomically stitched lateral junction of 2D heterostructures. In addition, the vertical van der Waal interactions that are normally dominant in layered materials can be overcome by in-plane forces if the interfacial atomic stitching is high in quality and low in defect density. This knowledge should help guide the approaches for improving the epitaxy in mixed 2D heterostructures and seamless stitching of in-plane 2D heterostructures with various complex monolayer structures.

Atomistic origin of nano-silver paracrystalline structure: molecular dynamics and x-ray diffraction studies

Classical molecular dynamics (MD) and x-ray diffraction (XRD) have been used to establish the origin of the paracrystalline structure of silver nanoparticles at the atomic scale. Models based on the face-centred cubic structure have been computer generated and their atomic arrangements have been optimized by the MD with the embedded-atom model (EAM) potential and its modified version (MEAM). The simulation results are compared with the experimental XRD data in reciprocal and real spaces, i.e. the structure factor and the pair distribution function. The applied approach returns the structural models, defined by the Cartesian coordinates of the constituent atoms. It has been found that most of the structural features of Ag nanoparticles are better reproduced by the MEAM. The presence of vacancy defects in the structure of the Ag nanoparticles has been considered and the average concentration of vacancies is estimated to be 3 at.%. The average nearest-neighbour Ag-Ag distances and the coordination numbers are determined and compared with the values predicted for the bulk Ag, demonstrating a different degree of structural disorder on the surface and in the core, compared to the bulk crystalline counterpart. It has been shown that the paracrystalline structure of the Ag nanoparticles has origin in the surface disorder and the disorder generated by the presence of the vacancy defects. Both sources lead to network distortion that propagates proportionally to the square root of the interatomic distances.

Atomic structure and Mott nature of the insulating charge density wave phase of 1T-TaS2

Using x-ray pair distribution function (PDF) analysis and computer modeling, we explore structure models for the complex charge density wave (CDW) phases of layered 1T-TaS₂that both well capture their atomic-level features and are amenable to electronic structure calculations. The models give the most probable position of constituent atoms in terms of 3D repetitive unit cells comprising a minimum number of Ta-S layers. Structure modeling results confirm the emergence of star-of-David (SD) like clusters of Ta atoms in the high-temperature incommensurate (IC) CDW phase and show that, contrary to the suggestions of recent studies, the low-temperature commensurate (C) CDW phase expands upon cooling thus reducing lattice strain. The C-CDW phase is also found to preserve the stacking sequence of Ta-S layers found in the room temperature, nearly commensurate (NC) CDW phase to a large extent. DFT based on the PDF refined model shows that bulk C-CDW 1T-TaS₂also preserves the insulating state of individual layers of SD clusters, favoring the Mott physics description of the metal-to-insulator (NC-CDW to C-CDW) phase transition in 1T-TaS₂. Our work highlights the importance of using precise crystal structure models in determining the nature of electronic phases in complex materials.

Unraveling the Complexity of Nano-Dispersoids in the Oxide Dispersion Strengthened Alloy 617

Nanocrystalline oxides are mainly responsible for Ni-base oxide dispersion strengthened (ODS) superalloys excellent thermo-mechanical properties. To establish the microstructural correlations between the metallic matrix and various oxide dispersoids, we report here the atomic-scale structure and chemistry of the complex nano-oxide dispersoids. Ultrahigh-resolution Cs-aberration-corrected scanning transmission electron microscopy (STEM) based techniques have been used to resolve nano-dispersoids in the Alloy 617 ODS. These nano-oxides, interestingly, possess a variety of high-angle annular dark-field (HAADF) contrasts, that is, bright, dark, and bi-phases. Both the light and heavy atoms have been found to be present in Y–Al–O complex-oxide nanostructures in varying quantities and forming a characteristic interface with the metallic matrix. In overcoming the limitation of conventional STEM-HAADF imaging, the integrated differential phase-contrast imaging technique was employed to investigate the oxygen atoms along with other elements in the dispersoids and its interface with the matrix. The most intriguing aspect of the study is the discovery of a few atoms thick Al2O3 interlayer (shell) around a monoclinic Y–Al–O core in the Ni-matrix. On the other hand, when the dispersoid is a hexagonal type Y–Al–O complex, the interface energy is already low, maintaining a semi-coherent interface and it was devoid of a shell.

The Cation Distributions of Zn-doped Normal Spinel MgFe2O4 Ferrite and Its Magnetic Properties

Determining the exact occupation sites of the doping ions in spinel ferrites is vital for tailoring and improving their magnetic properties. In this study, the distribution and occupation sites of cations in MgFe₂O₄ and Zn-doped MgFe₂O₄ ferrite are imaged by Cs-STEM. The experimental STEM images along [001], [011] and [111] orientations suggest that the divalent Mg²⁺ cations occupy all A sites, and the trivalent Fe³⁺ cations occupy all B sites in MgFe₂O₄ ferrite prepared by electrospinning, which is consistent with the normal spinel structure. We further clarify that the preferred sites of dopant Zn²⁺ ions are Fe³⁺ crystallographic sites in the Zn-doped MgFe₂O₄ ferrite nanofibers. Magnetic measurements show that Zn doping affects the spin states of the Fe³⁺, and the Fe³⁺-O²⁻-Fe³⁺ super-exchange interaction leads to enhancements in the magnetization and reduction in the Curie temperature. Our work should contribute a significant step toward eventually realizing the practical application of doped spinel ferrites.

Construction of Al-Mg-Zn Interatomic Potential and the Prediction of Favored Glass Formation Compositions and Associated Driving Forces

An interatomic potential is constructed for the ternary Al-Mg-Zn system under a proposed modified tight-binding scheme, and it is verified to be realistic. Applying this ternary potential, atomistic simulations predict an intrinsic glass formation region in the composition triangle, within which the glassy alloys are more energetically favored in comparison with their solid solution counterparts. Kinetically, the amorphization driving force of each disordered state is derived to correlate the readiness of its glass-forming ability in practice; thus, an optimal stoichiometry region is pinpointed around Al₃₅Mg₃₅Zn₃₀. Furthermore, by monitoring the structural evolution for various (Al₅₀Mg₅₀)_1−xZn_x (x = 30, 50, and 70 at.%) compositions, the optimized-glass-former Al₃₅Mg₃₅Zn₃₀ is characterized by both the highest degree of icosahedral ordering and the highest phase stability among the investigated compositions. In addition, the icosahedral network in Al₃₅Mg₃₅Zn₃₀ exhibits a much higher cross-linking degree than that in Al₂₅Mg₂₅Zn₅₀. This suggests that there is a certain correlation between the icosahedral ordering and the larger glass-forming ability of Al₃₅Mg₃₅Zn₃₀. Our results have significant implications in clarifying glass formation and hierarchical atomic structures, and in designing new ternary Al-Mg-Zn glassy alloys with high GFA.

Molecular basis of multistep voltage activation in plant two-pore channel 1

Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge-bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca2+ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.

Reconfiguring Organic Color Centers on the sp2 Carbon Lattice of Single-Walled Carbon Nanotubes

Organic color centers (OCCs) are atomic defects that can be synthetically created in single-walled carbon nanotube hosts to enable the emission of shortwave infrared single photons at room temperature. However, all known chemistries developed thus far to generate these quantum defects produce a variety of bonding configurations, posing a formidable challenge to the synthesis of identical, uniformly emitting color centers. Herein, we show that laser irradiation of the nanotube host can locally reconfigure the chemical bonding of aryl OCCs on (6,5) nanotubes to significantly reduce their spectral inhomogeneity. After irradiation the defect emission narrows in distribution by ∼26% to yield a single photoluminescence peak. We use hyperspectral photoluminescence imaging to follow this structural transformation on the single nanotube level. Density functional theory calculations corroborate our experimental observations, suggesting that the OCCs convert from kinetic structures to the more thermodynamically stable configuration. This approach may enable localized tuning and creation of identical OCCs for emerging applications in bioimaging, molecular sensing, and quantum information sciences.

Experimental and Theoretical Study of Possible Collective Electronic States in Exfoliable Re-Doped NbS2

Metallic transition-metal dichalcogenides (TMDs) are rich material systems in which the interplay between strong electron-electron and electron-phonon interactions often results in a variety of collective electronic states, such as charge density waves (CDWs) and superconductivity. While most metallic group V TMDs exhibit coexisting superconducting and CDW phases, 2H-NbS₂ stands out with no charge ordering. Further, due to strong interlayer interaction, the preparation of ultrathin samples of 2H-NbS₂ has been challenging, limiting the exploration of presumably rich quantum phenomena in reduced dimensionality. Here, we demonstrate experimentally and theoretically that light substitutional doping of NbS₂ with heavy atoms is an effective approach to modify both interlayer interaction and collective electronic states in NbS₂. Very low concentrations of Re dopants (<1%) make NbS₂ exfoliable (down to monolayer) while maintaining its 2H crystal structure and superconducting behavior. In addition, first-principles calculations suggest that Re dopants can stabilize some native CDW patterns that are not stable in pristine NbS₂.

Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions

We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions. Present applications include polymer-based nanocomposites with nanofillers in the form of cylinders and spheres of varied concentration and size, extremely confined and maximally packed assemblies in two and three dimensions, and terminally grafted macromolecules. The main simulator is accompanied by a descriptor that identifies the similarity of computer-generated configurations with respect to reference crystals in two or three dimensions. The Simu-D simulator-descriptor can be an especially useful tool in the modeling studies of the entropy- and energy-driven phase transition, adsorption, and self-organization of polymer-based systems under a variety of conditions.

Transition from High-Entropy to Conventional Alloys: Which Are Better?

The study of the transition from high-entropy alloys (HEAs) to conventional alloys (CAs) composed of the same alloying components is apparently important, both for understanding the formation of HEAs and for proper evaluation of their potential with respect to that of the corresponding CAs. However, this transition has thus far been studied in only two types of alloy systems: crystalline alloys of iron group metals (such as the Cantor alloy and its derivatives) and both amorphous (a-) and crystalline alloys, TE-TL, of early (TE = Ti, Zr, Nb, Hf) and late (TL = Co, Ni, Cu) transition metals. Here, we briefly overview the main results for the transition from HEAs to CAs in these alloy systems and then present new results for the electronic structure (ES), studied with photoemission spectroscopy and specific heat, atomic structure, thermal, magnetic and mechanical properties of a-TE-TL and Cantor-type alloys. A change in the properties of the alloys studied on crossing from the HEA to the CA concentration range mirrors that in the ES. The compositions of the alloys having the best properties depend on the alloy system and the property selected. This emphasizes the importance of knowing the ES for the design of new compositional complex alloys with the desired properties.

Nitrogen-Containing Gas Sensing Properties of 2-D Ti2N and Its Derivative Nanosheets: Electronic Structures Insight

In this work, the potentials of two-dimensional Ti2N and its derivative nanosheets Ti2NT2(T=O, F, OH) for some harmful nitrogen-containing gas (NCG) adsorption and sensing applications have been unveiled based on the quantum-mechanical Density Functional Theory calculations. It is found that the interactions between pure Ti2N and NCGs (including NO, NO2, and NH3 in this study) are very strong, in which NO and NO2 can even be dissociated, and this would poison the substrate of Ti2N monolayer and affect the stability of the sensing material. For the monolayer of Ti2NT2(T=O, F, OH) that is terminated by functional groups on surface, the adsorption energies of NCGs are greatly reduced, and a large amount of charges are transferred to the functional group, which is beneficial to the reversibility of the sensing material. The significant changes in work function imply the good sensitivity of the above mentioned materials. In addition, the fast response time further consolidates the prospect of two-dimensional Ti2NT2 as efficient NCGs' sensing materials. This theoretical study would supply physical insight into the NCGs' sensing mechanism of Ti2N based nanosheets and help experimentalists to design better 2-D materials for gas adsorption or sensing applications.

Terahertz Wave Absorption Property of all Mixed Organic-Inorganic Hybrid Perovskite Thin Film MA(Sn, Pb)(Br, I)3 Fabricated by Sequential Vacuum Evaporation Method

All mixed hybrid perovskite (MA(Sn, Pb)(Br,I)3) thin film was fabricated by sequential vacuum evaporation method. To optimize the first layer with PbBr2 and SnI2, we performed different annealing treatments. Further, MA(Sn, Pb)(Br, I)3 thin film was synthesized on the optimized first layer by evaporating MAI and post-annealing. The formed hybrid perovskite thin film exhibited absorptions at 1.0 and 1.7 THz with small absorbance (<10%). Moreover, no chemical and structural defect-incorporated absorption was found. In this study, the possibility of changing terahertz absorption frequency through the mixture of metal cations (Sn+ and Pb+) and halogen anions (Br- and I-) was verified.

Effect of Substrate Types on the Structure of Vertical Graphene Prepared by Plasma-Enhanced Chemical Vapor Deposition

Although the structure of vertical graphene (VG) is important for various applications, the growth mechanism of VG is not yet fully clear. Here, the impacts of electrical conductivity of substrate on the morphology and structure of VG prepared by plasma-enhanced chemical vapor deposition are studied by scanning electron microscopy and Raman spectroscopy. The results show that VG with greater thickness can be grown on substrate with better electrical conductivity in the same growth time. Even though longer deposition time leads to more VG, more defects might develop in VG, especially at the position furthest away from the substrates. The change of morphology and structure of VG is closely correlated with strength of electric field near the substrate surface, which offers a new approach for orderly growing of VG. The discoveries not only shed light on the growth mechanism of VG, but also are beneficial for promoting the applications of VG.

Approximate Atomic Green Functions

In atomic and many-particle physics, Green functions often occur as propagators to formally represent the (integration over the) complete spectrum of the underlying Hamiltonian. However, while these functions are very crucial to describing many second- and higher-order perturbation processes, they have hardly been considered and classified for complex atoms. Here, we show how relativistic (many-electron) Green functions can be approximated and systematically improved for few- and many-electron atoms and ions. The representation of these functions is based on classes of virtual excitations, or so-called excitation schemes, with regard to given bound-state reference configurations, and by applying a multi-configuration Dirac-Hartree-Fock expansion of all atomic states involved. A first implementation of these approximate Green functions has been realized in the framework of Jac, the Jena Atomic Calculator, and will facilitate the study of various multi-photon and/or multiple electron (emission) processes.

Extended Hückel Semi-Empirical Approach as an Efficient Method for Structural Defects Analysis in 4H-SiC

This paper presents an efficient method to calculate the influence of structural defects on the energy levels and energy band-gap for the 4H-SiC semiconductor. The semi-empirical extended Hückel method was applied to both ideal 4H-SiC crystal and different structures with defects like vacancies, stacking faults, and threading edge dislocations. The Synopsys QuatumATK package was used to perform the simulations. The results are in good agreement with standard density functional theory (DFT) methods and the computing time is much lower. This means that a structure with ca. 1000 atoms could be easily modeled on typical computing servers within a few hours of computing time, enabling fast and accurate simulation of non-ideal atomic structures.

Homology modeling and global computational mutagenesis of human myosin VIIa

Usher syndrome type 1B (USH1B) is a genetic disorder caused by mutations in the unconventional Myosin VIIa (MYO7A) protein. USH1B is characterized by hearing loss due to abnormalities in the inner ear and vision loss due to retinitis pigmentosa. Here, we present the model of human MYO7A homodimer, built using homology modeling, and refined using 5 ns molecular dynamics in water. Global computational mutagenesis was applied to evaluate the effect of missense mutations that are critical for maintaining protein structure and stability of MYO7A in inherited eye disease. We found that 43.26% (77 out of 178 in HGMD) and 41.9% (221 out of 528 in ClinVar) of the disease-related missense mutations were associated with higher protein structure destabilizing effects. Overall, most mutations destabilizing the MYO7A protein were found to associate with USH1 and USH1B. Particularly, motor domain and MyTH4 domains were found to be most susceptible to mutations causing the USH1B phenotype. Our work contributes to the understanding of inherited disease from the atomic level of protein structure and analysis of the impact of genetic mutations on protein stability and genotype-to-phenotype relationships in human disease.

Atomic structure, tensile property, and dislocation behavior of Fe-W interfaces from molecular dynamics simulation

Molecular dynamic simulations based on a recently constructed potential reveal that quasi-repeating patterns could appear in both Fe(110)/W(110) and W(110)/Fe(110) interfaces, and that three kinds of atomic displacements of Fe atoms because of the Fe-W interaction intrinsically bring about the interesting quasi-repeating patterns of the Fe-W interfaces. It is also found that the Fe-W interface becomes more brittle with less critical strains under tensile loading than pure Fe or W, which is fundamentally attributed to the movement of the interface dislocations as a result of the lattice mismatch between Fe and W. Interestingly, the dislocation loops could be formed in the Fe-W interface under tensile loading due to the pinning of the100edge dislocations by the edge dislocations of1/2111, whereas no dislocation loop would be generated in pure Fe or W.

Recent Progress in Engineering the Atomic and Electronic Structure of Electrocatalysts via Cation Exchange Reactions

In the past few decades, tremendous advances have been made in electrocatalysis due to the rational design of electrocatalysts at the nanoscale level. Further development requires engineering electrocatalysts at the atomic level, which is a grand challenge. Here, the recent advances in cation exchange strategy, which is a powerful tool for fine-tuning atomic structure of electrocatalysts via surface faceting, heteroatom doping, defects formation, and strain modulation, are the main focus. Proper atomic structure engineering effectively adjusts the electronic structure, and thus enhances the electronic conductivity and facilitates the adsorption/desorption of reaction intermediates. By virtue, the cation exchange strategy greatly boosts the intrinsic and apparent activities of electrocatalysts and shows a great potential toward design of new energy conversion devices, such as water splitting devices and metal-air batteries. It is believed that cation exchange offers new insights and opportunities for the rational design of a new generation of electrocatalysts.

Aquaporin-7: A Dynamic Aquaglyceroporin With Greater Water and Glycerol Permeability Than Its Bacterial Homolog GlpF

Xenopus oocytes expressing human aquaporin-7 (AQP7) exhibit greater osmotic water permeability and 3H-glycerol uptake vs. those expressing the bacterial glycerol facilitator GlpF. AQP7-expressing oocytes exposed to increasing extracellular [glycerol] under isosmolal conditions exhibit increasing swelling rates, whereas GlpF-expressing oocytes do not swell at all. To provide a structural basis for these observed physiological differences, we performed X-ray crystallographic structure determination of AQP7 and molecular-dynamics simulations on AQP7 and GlpF. The structure reveals AQP7 tetramers containing two monomers with 3 glycerols, and two monomers with 2 glycerols in the pore. In contrast to GlpF, no glycerol is bound at the AQP7 selectivity filter (SF), comprising residues F74, G222, Y223, and R229. The AQP7 SF is resolved in its closed state because F74 blocks the passage of small solutes. Molecular dynamics simulations demonstrate that F74 undergoes large and rapid conformational changes, allowing glycerol molecules to permeate without orientational restriction. The more rigid GlpF imposes orientational constraints on glycerol molecules passing through the SF. Moreover, GlpF-W48 (analogous to AQP7-F74) undergoes rare but long-lasting conformational changes that block the pore to H2O and glycerol.

Probing the Atomic-Scale Structure of Amorphous Aluminum Oxide Grown by Atomic Layer Deposition

Atomic layer deposition (ALD) is a well-established technique for depositing nanoscale coatings with pristine control of film thickness and composition. The trimethylaluminum (TMA) and water (H₂O) ALD chemistry is inarguably the most widely used and yet to date, we have little information about the atomic-scale structure of the amorphous aluminum oxide (AlO_x) formed by this chemistry. This lack of understanding hinders our ability to establish process-structure-property relationships and ultimately limits technological advancements employing AlO_x made via ALD. In this work, we employ synchrotron high-energy X-ray diffraction (HE-XRD) coupled with pair distribution function (PDF) analysis to characterize the atomic structure of amorphous AlO_x ALD coatings. We combine ex situ and in operando HE-XRD measurements on ALD AlO_x and fit these experimental data using stochastic structural modeling to reveal variations in the Al-O bond length, Al and O coordination environment, and extent of Al vacancies as a function of growth conditions. In particular, the local atomic structure of ALD AlO_x is found to change with the substrate and number of ALD cycles. The observed trends are consistent with the formation of bulk Al₂O₃ surrounded by an O-rich surface layer. We deconvolute these data to reveal atomic-scale structural information for both the bulk and surface phases. Overall, this work demonstrates the usefulness of HE-XRD and PDF analysis in improving our understanding of the structure of amorphous ALD thin films and provides a pathway to evaluate how process changes impact the structure and properties of ALD films.

Giant Thickness-Tunable Bandgap and Robust Air Stability of 2D Palladium Diselenide

Uncovering the thickness-dependent electronic property and environmental stability for 2D materials are crucial issues for promoting their applications in high-performance electronic and optoelectronic devices. Herein, the extrahigh air stability and giant tunable electronic bandgap of chemical vapor deposition (CVD)-derived few-layer PdSe₂ on Au foils, by using scanning tunneling microscope/spectroscopy (STM/STS), are reported. The robust stability of 2D PdSe₂ is uncovered by the observation of nearly defect/adsorption-free atomic lattices on long-time air-exposed samples. A one-to-one correspondence between the electronic bandgap (from ≈1.15 to ≈0 eV) and thickness of PdSe₂ /Au (from bilayer to bulk) is established. It is also revealed that few-layer semiconducting PdSe₂ flakes present zero-gap edges, induced by hybridization of Pd 4d and Se 4p orbitals. This work hereby provides straightforward evidence for the thickness-tunable electronic property and air stability of 2D semiconductors, thus shedding light on their applications in next-generation electronic devices.

Structure-mining: screening structure models by automated fitting to the atomic pair distribution function over large numbers of models

A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search criteria and performs structure refinements on them without human intervention. It supports both X-ray and neutron PDFs. Tests on various material systems show the effectiveness and robustness of the algorithm in finding the correct atomic crystal structure. It works on crystalline and nanocrystalline materials including complex oxide nanoparticles and nanowires, low-symmetry and locally distorted structures, and complicated doped and magnetic materials. This approach could greatly reduce the traditional structure searching work and enable the possibility of high-throughput real-time auto-analysis PDF experiments in the future.

The atomic structure of the Bergman-type icosahedral quasicrystal based on the Ammann-Kramer-Neri tiling

In this study, the atomic structure of the ternary icosahedral ZnMgTm quasicrystal (QC) is investigated by means of single-crystal X-ray diffraction. The structure is found to be a member of the Bergman QC family, frequently found in Zn-Mg-rare-earth systems. The ab initio structure solution was obtained by the use of the Superflip software. The infinite structure model was founded on the atomic decoration of two golden rhombohedra, with an edge length of 21.7 Å, constituting the Ammann-Kramer-Neri tiling. The refined structure converged well with the experimental diffraction diagram, with the crystallographic R factor equal to 9.8%. The Bergman clusters were found to be bonded by four possible linkages. Only two linkages, b and c, are detected in approximant crystals and are employed to model the icosahedral QCs in the cluster approach known for the CdYb Tsai-type QC. Additional short b and a linkages are found in this study. Short interatomic distances are not generated by those linkages due to the systematic absence of atoms and the formation of split atomic positions. The presence of four linkages allows the structure to be pictured as a complete covering by rhombic triacontahedral clusters and consequently there is no need to define the interstitial part of the structure (i.e. that outside the cluster). The 6D embedding of the solved structure is discussed for the final verification of the model.

Local- and Intermediate-Range Structures on Ordinary and Exotic Phase-Change Materials by Anomalous X-ray Scattering

Local- and intermediate-range atomic structures were investigated on amorphous phases of an ordinary phase-change material, Ge₂Sb₂Te₅ (GST), and an exotic one, Cu₂GeTe₃ (CGT), by using anomalous X-ray scattering close to K absorption edges of each element to find a fast amorphous-crystalline phase-change mechanism. The obtained data were analyzed by using reverse Monte Carlo modeling to obtain partial structure factors, partial pair distribution functions, and three-dimensional atomic configurations. Ring statistics were carefully examined to clarify the similarity and difference compared with the corresponding crystal structures, and it was found that amorphous GST has a number of four-membered rings indicating fragments of crystal structure, and amorphous CGT has a remarkable number of three-membered rings showing a collapse of crystal structures composed of purely six-membered rings. A persistent homology analysis was carried out and long-range ring structures of the constituent elements were observed in the amorphous phase, which may originate from fragments of crystal structures with a long-range periodicity.

3D Structure and Function of Glycosyltransferases Involved in N-glycan Maturation

Glycosylation is the most ubiquitous post-translational modification in eukaryotes. N-glycan is attached to nascent glycoproteins and is processed and matured by various glycosidases and glycosyltransferases during protein transport. Genetic and biochemical studies have demonstrated that alternations of the N-glycan structure play crucial roles in various physiological and pathological events including progression of cancer, diabetes, and Alzheimer’s disease. In particular, the formation of N-glycan branches regulates the functions of target glycoprotein, which are catalyzed by specific N-acetylglucosaminyltransferases (GnTs) such as GnT-III, GnT-IVs, GnT-V, and GnT-IX, and a fucosyltransferase, FUT8s. Although the 3D structures of all enzymes have not been solved to date, recent progress in structural analysis of these glycosyltransferases has provided insights into substrate recognition and catalytic reaction mechanisms. In this review, we discuss the biological significance and structure-function relationships of these enzymes.

Anisotropic Growth and Scanning Tunneling Microscopy Identification of Ultrathin Even-Layered PdSe2 Ribbons

Palladium diselenide (PdSe₂ ) is an emerging 2D layered material with anisotropic optical/electrical properties, extra-high carrier mobility, excellent air stability, etc. So far, ultrathin PdSe₂ is mainly achieved via mechanical exfoliation from its bulk counterpart, and the direct synthesis is still challenging. Herein, the synthesis of ultrathin 2D PdSe₂ on conductive Au foil substrates via a facile chemical vapor deposition route is reported. Intriguingly, an anisotropic growth behavior is detected from the evolution of ribboned flakes with large length/width ratios, which is well explained from the orthorhombic symmetry of PdSe₂ . A unique even-layered growth mode from 2 to 20 layers is also confirmed by the perfect combination of onsite scanning tunneling microscopy characterizations, through deliberately scratching the flake edge to expose both even and odd layers. This even-layered, ribboned 2D material is expected to serve as a perfect platform for exploring unique physical properties, and for developing high-performance electronic and optoelectronic devices.

Layer-Dependent Electronic Structure of Atomically Resolved Two-Dimensional Gallium Selenide Telluride

Alloying two-dimensional (2D) semiconductors provides a powerful method to tune their physical properties, especially those relevant to optoelectronic applications. However, as the crystal structure becomes more complex, it becomes increasingly difficult to accurately correlate response characteristics to detailed atomic structure. We investigate, via annular dark-field scanning transmission electron microscopy, electron energy loss spectroscopy, and second harmonic generation, the layered III-VI alloy GaSe_0.5Te_0.5 as a function of layer number. The local atomic structure and stacking sequence for different layers is explicitly determined. We complement the measurements with first-principles calculations of the total energy and electronic band structure of GaSe_0.5Te_0.5 for different crystal structures and layer number. The electronic band gap as well as the π and π + σ plasmons are found to be sensitive to layer number.

Atomic-Approach to Predict the Energetically Favored Composition Region and to Characterize the Short-, Medium-, and Extended-Range Structures of the Ti-Nb-Al Ternary Metallic Glasses

Ab initio calculations were conducted to assist the construction of the n-body potential of the Ti-Nb-Al ternary metal system. Applying the constructed Ti-Nb-Al interatomic potential, molecular dynamics and Monte Carlo simulations were performed to predict a quadrilateral composition region, within which metallic glass was energetically favored to be formed. In addition, the amorphous driving force of those predicted possible glassy alloys was derived and an optimized composition around Ti₁₅Nb₄₅Al₄₀ was pinpointed, implying that this alloy was easier to be obtained. The atomic structure of Ti-Nb-Al metallic glasses was identified by short-, medium-, and extended-range analysis/calculations, and their hierarchical structures were responsible to the formation ability and unique properties in many aspects.

Role of Surface Morphology on Exciton Recombination in Single Quantum Dot-in-Rods Revealed by Optical and Atomic Structure Correlation

The physical structure of colloidal quantum dot (QD) nanostructures strongly influences their optical and electronic behavior. A fundamental understanding of this interplay between structure and function is crucial to fully tailor the performance of QDs and their assemblies. Here, by directly correlating the atomic and chemical structure of single CdSe-CdS quantum dot-in-rods with time-resolved fluorescence measurements on the same structures, we identify morphological irregularities at their surfaces that moderate photoluminescence efficiencies. We find that two nonradiative exciton recombination mechanisms are triggered by these imperfections: charging and trap-assisted nonradiative processes. Furthermore, we show that the proximity of the surface defects to the CdSe core of the core-shell structures influences whether the charging or trap-assisted nonradiative channel dominates exciton recombination. Our results extend to other QD nanostructures and emphasize surface roughness as a crucial parameter when designing colloidal QDs with specific excitonic fates.

Amyloid from a histochemical perspective. A review of the structure, properties and types of amyloid, and a proposed staining mechanism for Congo red staining

Amyloid is a diverse group of unrelated peptides or proteins that have positive functionality or are associated with various pathologies. Despite vast differences, all amyloids share several features that together uniquely define the group. 1) All amyloids possess a characteristic cross-ß pattern with X-ray diffraction typical of ß-sheet secondary protein structures. 2) All amyloids are birefringent and dichroic under polarizing microscopy after staining with Congo red, which indicates a crystalline-like (ordered) structure. 3) All amyloids cause a spectral shift in the peak wavelength of Congo red with conventional light microscopy due to perturbation of π electrons of the dye. 4) All amyloids show heightened intensity of fluorescence with Congo red, which suggests an unusual degree of packing of the dye onto the substrate. The ß portion of amyloid molecules, the only logical substrate for specific Congo red staining under histochemical conditions, consists of a stack of ß-sheets laminated by hydrophilic and hydrophobic interactions between adjacent pairs. Only the first and last ß-sheets are accessible to dyes. Each sheet is composed of numerous identical peptides running across the width of the sheet and arranged in parallel with side chains in register over the length of the fibril. Two sets of grooves are bordered by side chains. X grooves run perpendicular to the long axis of the fibril; these grooves are short (the width of the sheet) and number in the hundreds or thousands. Y grooves are parallel with the long axis. Each groove runs the entire length of the fibril, but there are very few of them. While Congo red is capable of ionic bonding with proteins via two sulfonic acid groups, physical constraints on the staining solution preclude ionic interactions. Hydrogen bonding between dye amine groups and peptide carbonyls is the most likely primary bonding mechanism, because all ß-sheets possess backbone carbonyls. Various amino acid residues may form secondary bonds to the dye via any of three van der Waals forces. It is possible that Congo red binds within the Y grooves, but that would not produce the characteristic staining features that are the diagnostic hallmarks of amyloid. Binding in the X grooves would produce a tightly packed series of dye molecules over the entire length of the fibril. This would account for the signature staining of amyloid by Congo red: dichroic birefringence, enhanced intensity of fluorescence and a shift in visible absorption wavelength.

Creating Zipper-Like van der Waals Gap Discontinuity in Low-Temperature-Processed Nanostructured PbBi2n Te1+3n : Enhanced Phonon Scattering and Improved Thermoelectric Performance

Nanoengineered materials can embody distinct atomic structures which deviate from that of the bulk-grain counterpart and induce significantly modified electronic structures and physical/chemical properties. The phonon structure and thermal properties, which can also be potentially modulated by the modified atomic structure in nanostructured materials, however, are seldom investigated. Employed here is a mild approach to fabricate nanostructured PbBi_2n Te_1+3n using a solution-synthesized PbTe-Bi₂ Te₃ nano-heterostructure as a precursor. The as-obtained monoliths have unprecedented atomic structure, differing from that of the bulk counterpart, especially the zipper-like van der Waals gap discontinuity and the random arrangement of septuple-quintuple layers. These structural motifs break the lattice periodicity and coherence of phonon transport, leading to ultralow thermal conductivity and excellent thermoelectric z T.

Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae

Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3.6 Å. The ligated exon is held in the active site through RNA-RNA contacts. Three bases at the 3' end of the 5' exon remain anchored to loop I of U5 small nuclear RNA, and the conserved AG nucleotides of the 3'-splice site (3'SS) are specifically recognized by the invariant adenine of the branch point sequence, the guanine base at the 5' end of the 5'SS, and an adenine base of U6 snRNA. The 3'SS is stabilized through an interaction with the 1585-loop of Prp8. The P complex structure provides a view on splice junction formation critical for understanding the complete splicing cycle.

A Structural View of αB-crystallin Assembly and Amyloid Aggregation

The major len protein αB-crystallin (αB) is an intracellular chaperone. It belongs to the family of small heat shock proteins (sHsps) which plays a critical role in maintaining protein homeostasis and preventing protein aggregation, especially under stress conditions. Dysfunction of αB is closely related to cataract, and many neurodegenerative diseases including Alzheimer's, Parkinson's, and Creutzfeldt-Jakob disease. Due to the extremely heterogeneous and polydispersed nature of αB, it remains unclear how αB self-assemblies and prevents its client proteins from aggregation. In this minireview, we summarize the structural studies of αB in self-assembly, chaperoning client proteins and amyloid aggregation. We also mention the recent progress in identification of small molecules preventing αB aggregation for potential cataract treatment. This review highlights the polymorphic structures of αB under different conditions and its wide-spectrum chaperone activities, and sheds light on understanding the complex relationship among αB, client proteins and the related diseases.

Antibody-induced uncoating of human rhinovirus B14

Rhinoviruses (RVs) are the major causes of common colds in humans. They have a nonenveloped, icosahedral capsid surrounding a positive-strand RNA genome. Here we report that the antigen-binding (Fab) fragment of a neutralizing antibody (C5) can trigger genome release from RV-B14 to form emptied particles and neutralize virus infection. Using cryo-electron microscopy, structures of the C5 Fab in complex with the full and emptied particles have been determined at 2.3 Å and 3.0 Å resolution, respectively. Each of the 60 Fab molecules binds primarily to a region on viral protein 3 (VP3). Binding of the C5 Fabs to RV-B14 results in significant conformational changes around holes in the capsid through which the viral RNA might exit. These results are so far the highest resolution view of an antibody-virus complex and elucidate a mechanism whereby antibodies neutralize RVs and related viruses by inducing virus uncoating.

In situ electrochemical high-energy X-ray diffraction using a capillary working electrode cell geometry

The ability to generate new electrochemically active materials for energy generation and storage with improved properties will likely be derived from an understanding of atomic-scale structure/function relationships during electrochemical events. Here, the design and implementation of a new capillary electrochemical cell designed specifically for in situ high-energy X-ray diffraction measurements is described. By increasing the amount of electrochemically active material in the X-ray path while implementing low-Z cell materials with anisotropic scattering profiles, an order of magnitude enhancement in diffracted X-ray signal over traditional cell geometries for multiple electrochemically active materials is demonstrated. This signal improvement is crucial for high-energy X-ray diffraction measurements and subsequent Fourier transformation into atomic pair distribution functions for atomic-scale structural analysis. As an example, clear structural changes in LiCoO₂ under reductive and oxidative conditions using the capillary cell are demonstrated, which agree with prior studies. Accurate modeling of the LiCoO₂ diffraction data using reverse Monte Carlo simulations further verifies accurate background subtraction and strong signal from the electrochemically active material, enabled by the capillary working electrode geometry.

The Relationship Between Atomic Structure and Strain Distribution of Misfit Dislocation Cores at Cubic Heteroepitaxial Interfaces

The atomic reconstruction of a misfit dislocation (MD) core causes change in the strain distribution around the core. Several MD cores at the AlSb/GaAs (001) cubic zincblende interface, including a symmetrical glide set Lomer dislocation (LD), a left-displaced glide set LD, a glide set LD with an atomic step, a symmetrical shuffle set LD, and a 60° dislocation pair, were studied using simulated projected potential and aberration-corrected transmission electron microscope images. Image deconvolution was also used to restore structure images from nonoptimum-defocus images. The corresponding biaxial strain maps, ε xx (in-plane) and ε yy (out-of-plane), were obtained by geometric phase analysis using the GaAs substrate as the reference lattice. The results show that atomic structure characteristics of MD cores can be revealed by the strain maps. The strain maps should be measured from optimum-defocus images or restored structure images. Furthermore, the ε xx strain map has been found more accurate than the ε yy strain map for MD cores, and the specimen thickness should be below the critical thickness due to the influence of dynamical scattering.

Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator

The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues. A single gate near the extracellular surface closes the channel. The regulatory domain, dephosphorylated, is located in the intracellular opening between the two nucleotide-binding domains (NBDs), preventing NBD dimerization and channel opening. The structure also reveals why many cystic-fibrosis-causing mutations would lead to defects either in folding, ion conduction, or gating and suggests new avenues for therapeutic intervention.