Domain Structure Research Articles

Fracture behaviors and crack propagation anisotropy in multi-ions modified bismuth titanate ferroelectrics

Bismuth titanate (BIT) is widely considered a promising lead-free piezoelectric material for advanced high-temperature applications. Despite significant advances in high-performance BIT ferroelectrics, there remains little understanding of mechanical properties including fracture failure and crack propagation behaviors, hindering the optimization of stability and reliability for next-generation high-temperature ferroelectrics. In this work, we investigated mechanical fracture and crack propagation behaviors of a type of high-performance bismuth titanate-based ceramic (Bi3.96Ce0.04Ti3–2xWxNbxO12, BCTWN) with different doping contents and electric poling states. High-resolution transmission electron microscopy (HRTEM) and electron backscatter diffraction (EBSD) results reveal that the BCTWN ceramics possess a single ferroelectric phase and exhibit layered crystal structures characterized by periodic fringe features. In addition, the striped domain structures are observed on the surface of plate-like grains. Mechanical measurements indicate that fracture behaviors of BCTWN ceramics are significantly affected by doping contents. The ceramics with the largest grain size present inferior microstructure with more defects, endowing the lowest bending strength and fracture toughness. For the samples with different poling states, strong anisotropy in crack propagation and fracture toughness is observed, attributed to the different domain switching mechanisms driven by local incompatible stress fields, which is experimentally validated by the intriguing evolutions of striped domain structures around crack tips. This work advances our understanding of the fracture and crack propagation mechanisms of BIT-based ceramics and provides insight into tailoring the mechanical behaviors through doping and poling strategies.

Josephson coupling across magnetic topological insulator MnBi2Te4

Topological superconductors hosting Majorana zero modes are of great interest for both fundamental physics and potential quantum computing applications. In this work, we investigate the transport properties of the intrinsic magnetic topological insulator MnBi2Te4 (MBT). In normal transport measurements, we observe the presence of chiral edge channels, though with deviations from perfect quantization due to factors such as non-uniform thickness, domain structures, and the presence of quasi-helical edge states. Subsequently, we fabricate superconducting junctions using niobium leads on MBT exfoliated flakes, which show an onset of supercurrent with clear Josephson coupling. The interference patterns in the superconducting junctions reveal interesting asymmetries, suggesting changes in the magnetic ordering of the MBT flakes under small applied magnetic fields. Moreover, the modulation of the critical current by magnetic field reveals a SQUID-like pattern, suggesting the presence of supercurrent through the quasi-helical edge states.

Micro-electromechanical system-based cryogenic and heating in situ transmission electron microscopy for investigating phase transitions and domain evolution in single-crystal BaTiO3

Investigating phase transitions between ferroelectric states is crucial for understanding the nucleation, dynamics, and kinetics of domains, both before and after transformation. Here, we assess all phase transitions and domain evolutions in single-crystal BaTiO3 by implementing microelectromechanical systems (MEMS)-based in situ cryogenic (cryo-) and heating transmission electron microscopy (TEM) by continuously varying sample temperatures from -175 °C to 200 °C. Every possible phase-cubic, tetragonal, orthorhombic, and rhombohedral - was identified. An ultra-stable imaging condition was achieved with a mean drift speed of 1.52 nm/min, providing unique opportunities for atomic resolution in situ scanning TEM with a wide temperature range. Furthermore, domain nucleation and evolution across phase transitions were investigated using complementary dielectric measurements, optical microscopy, and a phenomenological model. This study underscores the effectiveness and utility of MEMS-based in situ cryo-/heating TEM in revealing phase transitions and domain structures in ferroelectric materials.

Structure of a Rhs effector clade domain provides mechanistic insights into type VI secretion system toxin delivery

The type VI secretion system (T6SS) is a molecular machine utilised by many Gram-negative bacteria to deliver antibacterial toxins into adjacent cells. Here we present the structure of Tse15, a T6SS Rhs effector from the nosocomial pathogen Acinetobacter baumannii. Tse15 forms a triple layered β-cocoon Rhs domain with an N-terminal α-helical clade domain and an unfolded C-terminal toxin domain inside the Rhs cage. Tse15 is cleaved into three domains, through independent auto-cleavage events involving aspartyl protease activity for toxin self-cleavage and a nucleophilic glutamic acid for N-terminal clade cleavage. Proteomic analyses identified that significantly more peptides from the N-terminal clade and toxin domains were secreted than from the Rhs cage, suggesting toxin delivery often occurs without the cage. We propose the clade domain acts as an internal chaperone to mediate toxin tethering to the T6SS machinery. Conservation of the clade domain in other Gram-negative bacteria suggests this may be a common mechanism for delivery.

Effect of grain size and grain boundary on the energy storage performance of polycrystalline ferroelectrics

Dielectric capacitors based on polycrystalline ferroelectrics have attracted much attention due to their significant power density and fast charge–discharge speed. The energy storage performance of polycrystalline ferroelectrics is highly dependent on the grain size and grain boundary. Here, the effect of grain size and grain boundary on the domain structures and polarization–electric field (P–E) hysteresis loops of polycrystalline ferroelectrics are investigated by using a phase-field model based on the time dependent Ginzburg–Landau (TDGL) equation. It is found that the depolarization field in the grain boundary induces the vortex domain when the grain size is reduced or the grain boundary thickness increases in certain extent, resulting in slender P–E loops, which contributes to an improvement in the energy storage efficiency and density. However, as the grain size further decreases or the grain boundary thickness further increases, the energy storage density decreases, which is attributed to the concurrent reduction in both the remnant and saturation polarizations. This study provides a considerable insight for optimizing the energy storage performance by carefully adjusting the grain size and grain boundary thickness in polycrystalline ferroelectrics.

Impedimetric Characterization of NanA Structural Domains Activity on Sialoside-Containing Interfaces.

Streptococcus pneumoniae is a pathogenic bacterium that contains the surface-bound neuraminidase, NanA. NanA has two domains that interact with sialosides. It is hard to determine the contribution of each domain separately on catalysis or binding. In this work, we used biochemical methods to obtain the separated domains, applied electrochemical and surface analysis approaches, and determined the catalytic and binding preferences toward a surface-bound library of sialosides. Impedimetric studies on two different surfaces revealed that protein-surface interactions provide a tool for distinguishing the unique contribution of each domain at the interface affecting the substrate preference of the enzyme in different surroundings. We showed that each domain has a sialoside-specific affinity. Furthermore, while the interaction of the sialoside-covered surface with the carbohydrate-binding domain results in an increase in impedance and binding, the catalytic domain adheres to the surface at high concentrations but retains its catalytic activity at low concentrations.

Domain swapping: a mathematical model for quantitative assessment of structural effects.

The domain-swapping mechanism involves the exchange of structural elements within a secondary or supersecondary structure between two (ormore) proteins. The present paper proposes to interpret the domain-swapping mechanism using a model that assesses the structure of proteins (and complexes) based on building the structure of a common hydrophobic core in a micelle-like arrangement (a central hydrophobic core with a polar shell in contact with polar water), which has a considerable impact on the stabilisation of the domain structure built by domain swapping. Domains with a hydrophobicity system that is incompatible with the micelle-like structure have also been identified. This incompatibility is the form of structural codes related to biological function.

Knockdown of SlYTHDF2 Accelerates Dark-Induced Tomato Leaf Senescence by Affecting the ABA Pathway.

N6-methyladenosine (m6A) is a widespread post-transcriptional modification in eukaryotic mRNAs. Proteins with the YTH structural domain act as m6A-binding proteins by recognizing the m6A modification and regulating mRNA through this recognition. In this study, SlYTHDF2, a prototypical m6A -binding protein gene in the YTH family was expressed in various tissues, and subcellular localization analyses indicated that the SlYTHDF2 protein was localized in the nucleus and cytoplasm. SlYTHDF2 knockout lines were obtained using CRISPR/Cas9 technology and showed the senesced leaves prematurely increased endogenous ABA accumulation compared with the wild type. Moreover, we found that dark promoted leaf senescence in SlYTHDF2 knockout lines and exogenous ABA further accelerated leaf senescence under dark conditions. The qRT-PCR analysis revealed significant alterations in the expression of genes associated with the ABA pathway. Relative to the wild type, the CR-slythdf2 plants exhibited reduced levels of photosynthetic pigments, higher accumulation of reactive oxygen species, and increased damage to cell membranes. Additionally, we discovered that SlYTHDF2 interacts with the chloroplast-binding protein SlRBCS3 through yeast two-hybrid and BiFC experiments. Overall, our data suggest the important role of SlYTHDF2 in regulating tomato leaf senescence.

Damage detection and localization in plate-like structures using sideband peak count (SPC) technique

This paper addresses the critical issue of detecting and localizing damage in plate-like structures, which are commonly encountered in aerospace, marine and other engineering applications. To address this challenge, the current study introduces the sideband peak count (SPC) technique as the foundation for diagnostic imaging for damage detection in plate structures. The proposed damage detection algorithm requires only a limited number of sensor responses, streamlining the detection process. It does not rely on a reference baseline, thereby enhancing its efficiency and accuracy. This approach enables rapid and precise identification of damage and its location within the plate structure. To validate the effectiveness and applicability of the proposed method, finite element simulation results are utilized. These results demonstrate the capability of the proposed technique to accurately detect and localize damage, providing a promising solution for enhancing the structural health monitoring of plate-like structures in various engineering domains.

Enhancing magnetostriction in FeAl alloys via crystal growth orientation tuning by a trace amount of Pt doping

Iron-based cubic alloy systems opened the door to the development of magnetostrictive materials with moderate magnetostriction, low cost, and good mechanical properties. At the as-cast state, the grain growth orientation of these alloy systems is close to random, which deteriorates magnetostriction. Doping with certain elements can tune the growth orientation to enhance magnetostriction. However, the driving force for the crystal growth along preferential orientation is still not clear. Here in this work, revealed by density functional theory (DFT) calculation, Pt doping can tune the crystal growth direction of FeAl along <100> crystal direction (same as easy magnetization direction), which can be utilized to realize 90° domain-switching and thus magnetostriction is enhanced greatly. These are confirmed by experimental results. The magnetostriction increases from 29 ppm to 80 ppm, representing a 176% enhancement through doping with 0.4 at.% Pt. The maze magnetic domain structures, observed by magnetic force microscope, are also preferentially <100> oriented and feature stripes. In consideration of the similarity between this study and our previous study on FeGa alloy (C. Zhou et al., 2020), it can be expected that our methods can be extended to other magnetostrictive materials and help develop polycrystals with desired orientations.

Genome-wide characterization and expression analysis of WRKY transcription factors reveals biotic stress response potential mechanisms in Panax notoginseng

WRKY transcription factors (TFs), among the largest families of transcriptional regulators, are essential players in defense responses in plants. Panax notoginseng, a traditional and precious herbal medicine in China, is widely cultivated due to its excellent medicinal and edible value. However, P. notoginseng is frequently affected by various diseases (like Black blot disease, Root rot disease and Viral diseases). Therefore, the present study aimed to identify and characterize PnWRKYs in the P. notoginseng genome, reveal their structural attributes, regulatory elements, and potential functions in defense responses. 68 PnWRKY TFs that have conserved domains and different physicochemical characteristics were identified in the genome. They can be divided into four groups according to phylogenetic relationships and conserved domain structures. Furthermore, Group II WRKY TFs can be classified into five subgroups (IIa, IIb, IIc, IId, and IIe) according to their zinc finger-like motif. The PnWRKY family expands mainly via segmental duplication. Additionally, the promoter regions of PnWRKYs contain many hormone-responsive and stress-responsive elements. Expression patterns under different hormones (salicylic acid, methyl jasmonate, and melatonin) and disease (root rot disease, black blot disease, and virus disease) treatment analysis highlighted their wide involvement in plant hormone-induced disease defense responses. These findings affirmed the potential functions of PnWRKY TFs in disease-mediated defense responses and provided valuable insights for future agricultural applications.

Nanoscale View of Alignment and Domain Growth in a Hexagonal Columnar Liquid Crystal.

Highly ordered liquid crystalline (LC) phases have important potential for organic electronics. We studied the molecular alignment and domain structure in a columnar LC thin film with nanometer resolution during in situ heating using four-dimensional scanning transmission electron microscopy (4D STEM). The initial disordered vapor-deposited LC glass thin film rapidly ordered at its glass transition temperature into a hexagonal columnar phase with small (<10 nm), well-aligned, planar domains (columns oriented parallel to the surface). Upon further heating, the domains coarsen via bulk diffusion, then the film crystallizes, then finally transforms back to an LC phase at an even higher temperature. The LC phase at high temperature shows straight columns of molecules, which we attribute to structure inherited from the intermediate crystalline phase. Nanoscale 4D STEM offers direct insight into the mechanisms of domain reorganization, and intermediate crystallization is a potential approach to manipulate orientational order and texture at the nano- to mesoscale in LC thin films.

Structural analysis of microtubule binding by minus-end targeting protein Spiral2

Microtubules (MTs) are dynamic cytoskeletal polymers that play a critical role in determining cell polarity and shape. In plant cells, acentrosomal MTs are localized on the cell surface and are referred to as cortical MTs. Cortical MTs nucleate in the cell cortex and detach from nucleation sites. The released MT filaments perform treadmilling, with the plus-ends of MTs polymerizing and the minus-ends depolymerizing. Minus-end targeting proteins, -TIPs, include Spiral2, which regulates the minus-end dynamics of acentrosomal MTs. Spiral2 accumulates autonomously at MT minus-ends and inhibits filament shrinkage, but the mechanism by which Spiral2 specifically recognizes minus-ends of MTs remains unknown. Here we describe the crystal structure of Spiral2's N-terminal MT-binding domain. The structural properties of this domain resemble those of the HEAT repeat structure of the tumor overexpressed gene (TOG) domain, but the number of HEAT repeats is different and the conformation is highly arched. Gel filtration and co-sedimentation analyses demonstrate that the domain binds preferentially to MT filaments rather than the tubulin dimer, and that the tubulin-binding mode of Spiral2 via the basic surface is similar to that of the TOG domain. We constructed an in silico model of the Spiral2-tubulin complex to identify residues that potentially recognize tubulin. Mutational analysis revealed that the key residues inferred in the model are involved in microtubule recognition, and provide insight into the mechanism by which end-targeting proteins stabilize MT ends.

An analytical dynamic stiffness method for efficient broadband vibro-acoustic analysis of complex built-up structures

An analytical modelling technique is presented, combining the dynamic stiffness method (DSM) with the spectral DSM (SDSM) for the broadband vibro-acoustic analysis of complex built-up structures. In particular, the structures are modelled exactly by the DSM based on particular solutions tailored for general acoustic or distributed force excitations; whereas the acoustic cavities are modelled by the SDSM where the boundary conditions are described by modified Fourier series with a rapid convergence rate. The vibro-acoustic coupling along the interfaces between the structures and the cavities is achieved by applying the normal velocity continuity condition, leading to a coupling matrix in an analytical manner. Both structural and acoustic cavity elements are assembled directly to model complex vibro-acoustic systems and no extra element discretization is required for both structural and acoustic domains. Consequently, the proposed method uses very few degrees of freedom (DoFs) but describes the broadband vibro-acoustic behaviour highly accurately. It is demonstrated that the proposed method exhibits a predominant advantage over the finite element package COMSOL in terms of accuracy and computational efficiency. This approach also has the potential to serve as the benchmark for a wide range of vibro-acoustic problems.

Genome-Wide Identification of the Geranylgeranyl Pyrophosphate Synthase (GGPS) Gene Family Associated with Natural Rubber Synthesis in Taraxacum kok-saghyz L. Rodin.

Taraxacum kok-saghyz Rodin (TKS) is a recognized alternative source of natural rubber comparable to the rubber tree. The geranylgeranyl pyrophosphate synthase (GGPS) catalyzed the synthesis of geranylgeranyl pyrophosphate (GGPP), which is an important enzyme in the secondary metabolism pathway. In this study, we present the first analysis of the GGPS gene family in TKS, where a total of seven TkGGPS family members were identified. Their core motifs, conserved structural domains, gene structures, and cis-acting elements were described. In addition, two phylogenetic trees were constructed based on the Neighbor-Joining and Maximum-Likelihood methods, and the TkGGPSs were highly conserved and exhibited good collinearity with the other species. Transcriptome data showed that seven TkGGPS gene members were expressed in all the 12 tissues measured, and TkGGPS1, TkGGPS3, and TkGGPS6 were highly expressed in latex, suggesting that they may be associated with natural rubber synthesis. Meanwhile, quantitative real-time PCR (qRT-PCR) showed that the expression levels of the TkGGPS genes were regulated by the ethylene and methyl jasmonate (MeJA) pathways. Subcellular localization results indicated that all the TkGGPS proteins were also located in chloroplasts involved in photosynthesis in plants. This study will provide valuable insights into the selection of candidate genes for molecular breeding and natural rubber biosynthesis in TKS.

Structural mechanisms of SLF1 interactions with Histone H4 and RAD18 at the stalled replication fork.

DNA damage that obstructs the replication machinery poses a significant threat to genome stability. Replication-coupled repair mechanisms safeguard stalled replication forks by coordinating proteins involved in the DNA damage response (DDR) and replication. SLF1 (SMC5-SMC6 complex localization factor 1) is crucial for facilitating the recruitment of the SMC5/6 complex to damage sites through interactions with SLF2, RAD18,and nucleosomes. However, the structural mechanisms of SLF1's interactions are unclear. In this study, we determined the crystal structure of SLF1's ankyrin repeat domain bound to an unmethylated histone H4 tail, illustrating how SLF1 reads nascent nucleosomes. Using structure-based mutagenesis, we confirmed a phosphorylation-dependent interaction necessary for a stable complex between SLF1's tandem BRCA1 C-Terminal domain (tBRCT) and the phosphorylated C-terminal region (S442 and S444) of RAD18. We validated a functional role of conserved phosphate-binding residues inSLF1, and hydrophobic residues in RAD18 that areadjacent to phosphorylation sites, both of whichcontribute to the strong interaction. Interestingly, we discovered a DNA-binding property of this RAD18-binding interface, providing an additional domain of SLF1 to enhance binding to nucleosomes. Our results provide critical structural insights into SLF1's interactions with post-replicative chromatin and phosphorylation-dependent DDR signalling, enhancing our understanding of SMC5/6 recruitment and/or activity during replication-coupled DNA repair.

Genome-wide investigation and analysis of U-box E3 ubiquitin-protein ligase gene family in kiwifruit (Actinidia chinensis) in response to the yeast antagonist, Wickerhamomyces anomalus

ABSTRACT Although the ubiquitin ligase U-box protein family is a vital component of plant development and stress response, the exact role of kiwifruit U-box genes family is not known. The study identified 73 putative U-box genes from the kiwifruit genome. Chromosomal localisation, phylogenetic analysis, physicochemical properties, gene structure, motifs, and promoters of these genes were analysed. Distribution of Actinidia chinensis PUB (AcPUB) genes exhibited varying densities across 27 chromosomes. The study found that U-box clusters were classified into groups I–VII in phylogenetic analyses of a variety of plants, including kiwifruit, Arabidopsis thaliana, and rice, with most of the genes in kiwifruit being related to rice. The conserved motif analyses revealed that all the AcPUB genes have typical U-box structural domains. Analysis of the cis-acting elements suggested that AcPUBs expression may be responsive to several hormones and stresses. RNA-Seq analysis showed that six kiwifruit U-box genes were differentially expressed after induction by Wickerhamomyces anomalus, suggesting a potential involvement of these U-box genes in the kiwifruit's response to W. anomalus, which might include mechanisms related to resistance. Overall, our findings provide valuable insights into the function and structure of U-box genes that will help develop new genomic technologies and study plant resistance.

ROS-mediated damage to the core domain of HIV integrase: A molecular dynamics simulation

Using molecular dynamics simulation with reactive force-field (ReaxFF), we study the reactive oxygen species (ROS)-mediated damage to the core domain of human immunodeficiency virus (HIV) integrase. Our results demonstrate that with the increase in the ROS concentration, the structure of the core domain of HIV is more severely damaged, including dehydrogenation, increasing oxygen-containing groups, shorting or damaging spirals, and breaking peptide bonds. We particularly note that ROS has a significantly higher capability to abstract H atoms from N atoms than C atoms. The effects of different species of ROS on dehydrogenation and shorting or damaging spirals are not prominent. In contrast, for increasing oxygen-containing groups and breaking peptide bonds, the effect of O is more remarkable than O3 and O3 is greater than ·OH. Moreover, carboxyl dehydrogenation and nitrogen dehydrogenation are more easily dehydrogenated, resulting in higher dehydrogenation ratios for polar amino acid residues. These meticulous findings deepen our understanding of the role of ROS in regulating the structure and function of the core domain of HIV integrase and provide valuable insights into the plasma treatment of acquired immune deficiency syndrome.

Cooling rate dependence of charge density wave phases in 1T-TaS2 studied by scanning tunneling microscopy and x-ray diffraction

The role of dynamics in the charge density wave (CDW) phases of 1T-TaS2, especially in accessing metastable phases, is still under scrutiny. We investigated cooling rate dependence on low-temperature CDW phases in this material by scanning tunneling microscopy and x-ray diffraction. In the majority of cases, we found the typical low temperature commensurate CDW and identified no other differences between samples that were fast cooled vs slow cooled from room temperature. In rare cases (1/18 STM experiments and 1/30 XRD experiments), we found a multi-domain structure in the low temperature CDW. The domain structure and metallic behavior revealed by STM and STS measurements of this phase are in excellent agreement with the previously reported metallic mosaic CDW phase.

A novel strategy for obtaining lead-based piezoelectric ceramics with giant piezoelectricity and high-temperature stability through the construction of “slush-like” polar states

Maintaining high piezoelectric response and piezoelectric temperature stability of lead-based piezoceramics is critical for applications under high-temperature environments. Unfortunately, the piezoelectric response of lead-based piezoceramics shows strong temperature dependence. Herein, an innovative strategy was proposed to solve this problem. The method consisted of constructing “slush-like” polar states by introducing localized heterostructures in the tetragonal phase structure to lower the energy barriers. The presence of the tetragonal phase stabilized the domain structure, providing excellent temperature stability, while the localized heterostructures also flattened the free energy landscape and enhanced the piezoelectric response. The strategy was implemented by using 0.11Pb(In0.5Nb0.5)O3-0.89Pb(Hf0.47Ti0.53)O3(PIN-PHT) piezoceramics doped with heterovalent ion Nb5+ to form a “slush-like” polar state with strong interactions inside the ceramics. The piezoelectric response and relaxor behavior of the ceramics were then investigated using piezoelectric force microscopy to reveal the mapping relationship between the complex ferroelectric domain structure and both the piezoelectric response and temperature stability. At Nb5+ doping amount of 0.8 mol%, the ceramics showed excellent comprehensive performances with d33 = 764 pC/N, Tc = 319.1 °C, εr = 3253.59, kp = 0.67, and tanδ = 0.0122. At an external ambient temperature of 300°C, the d33 of PIN-PHT-0.8Nb5+ remained high at 734 pC/N, with piezoelectric performance retention of 96.1%, showing excellent temperature stability. Overall, a new path was proposed for developing Pb-based piezoceramics with both good piezoelectric response and high-temperature stability, promising to broaden the temperature range of high-temperature piezoceramics for various applications.