Adjacent Domains Research Articles

Nano-crystal domains in Co-based fcc(111) epitaxial magnetic junctions and their impact on tunnel magnetoresistance

Nano-crystal domain structures formed in a MgO barrier and their effects on tunnel magnetoresistance (TMR) in epitaxial fcc-Co90Fe10 (CoFe)(111)/MgO(111)/CoFe(111) magnetic tunnel junctions (MTJs) have been systematically studied using scanning transmission electron microscopy and first-principles calculations. These domains are widely distributed in the (111)-textured MgO layer, being different from conventional bcc-CoFe/MgO(001)-based MTJs. The (111)-texture is formed by extension of {111} planes through several adjacent MgO domains. Three types of orientation relationships (ORs) between CoFe and MgO are identified, including cube-on-cube type (Type-1), twin-like type (Type-2), and unexpected type (Type-3). Crystallographic analysis indicated that Type-2 OR is a variant of Type-1 OR, triggered by different stacking orders of MgO(111) planes, while Type-3 OR is formed by a 30° in-plane rotation of MgO lattice relative to Type-1 OR. Due to the large in-plane lattice mismatch (19.6%) between Co(111) and MgO(111) in Type-1 and Type-2 ORs, Type-3 OR (mismatch 3.4%) can be stabilized. First-principles calculations uncovered that the theoretical TMR ratio of the MgO(111) MTJ with Type-3 OR is ∼2 orders of magnitude smaller than that with Type-1 and Type-2 ORs. The small contribution of Type-3 OR to the transport reasonably interprets why the experimental TMR ratio (∼37%) is much lower than the theoretical value (∼2100%) in the Co/MgO/Co(111) MTJ. This study has revealed the nano-crystal domain formation unique to the fcc-CoFe/MgO(111) MTJs, indicating that controlling the nano-crystal domains (e.g., lattice optimization by atomic doping) can be a guiding principle to develop MgO(111)-based epitaxial MTJs and related heterostructure devices.

Ferroelastic twin domain patterns and polar domain walls of BiVO4 thin films via phase-field simulations

Polar domain walls in centrosymmetric ferroelastics (e.g., BiVO4 films) give rise to inhomogeneity and offer promises for solar energy conversion applications via expediting charge-carrier separation. However, the origin of polar domain walls and the relationship between them and spontaneous strain from structural phase transition remain elusive at the mesoscale in BiVO4 films. Here, from the perspective of phenomenological thermodynamics, the relationship between four variants of monoclinic (M) phase and the corresponding lattice parameters during the tetragonal-monoclinic (T-M) phase transition is revealed. Using phase-field simulations, it suggests that the formation of four variants of ferroelastic twin domains arises from spontaneous strain from T-M phase transition. Moreover, it is demonstrated that (i) polar domain walls in BiVO4 films originate from the flexoelectric effect induced by strain gradient across the domain walls during phase transition process; (ii) shear strain gradient dominates the contribution to the polarization vectors at the domain walls; (iii) 180° head-to-head or tail-to-tail in-plane polarization configurations emerge at the adjacent domain walls. The stability of several types of ferroelastic domain walls is also analyzed from the point of view of total free energy. These results not only provide a fundamental understanding of the origin of polar domain walls and the formation mechanisms of ferroelastic twin patterns, but also stimulate potential applications of polar domain walls of non-polar BiVO4 films in energy conversion.

Progress on the Pharmacological Targeting of Janus Pseudokinases.

The Janus kinases (JAKs) are key components of the JAK-STAT signaling pathway and are involved in myriad physiological processes. Though they are the molecular targets of many FDA-approved drugs, these drugs manifest adverse effects due in part to their inhibition of the requisite JAK kinase activity. However, the JAKs uniquely possess an integrated pseudokinase domain (JH2) that regulates the adjacent kinase domain (JH1). The therapeutic targeting of JH2 domains has been less thoroughly explored and may present an avenue to modulate the JAKs without the adverse effects associated with targeting the adjacent JH1 domain. The potential of this strategy was recently demonstrated with the FDA approval of the TYK2 JH2 ligand deucravacitinib for treating plaque psoriasis. In this light, the structure and targetability of the JAK pseudokinases are discussed, in conjunction with the state of development of ligands that bind to these domains.

Endothelial protein C receptor binding induces conformational changes to severe malaria-associated group A PfEMP1

Severe Plasmodium falciparum malaria infections are caused by microvascular sequestration of parasites binding to the human endothelial protein C receptor (EPCR) via the multi-domain P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion ligands. Using cryogenic electron microscopy (Cryo-EM) and PfEMP1 sequence diversity analysis, we found that group A PfEMP1 CIDRα1 domains interact with the adjacent DBLα1 domain through central, conserved residues of the EPCR-binding site to adopt a compact conformation. Upon EPCR binding, the DBLα1 domain is displaced, and the EPCR-binding helix of CIDRα1 is turned, kinked, and twisted to reach a rearranged, stable EPCR-bound conformation. The unbound conformation and the required transition to the EPCR-bound conformation may represent a conformational masking mechanism of immune evasion for the PfEMP1 family.

Boundary bypass activity in the abdominal-B region of the Drosophila bithorax complex is position dependent and regulated.

Expression of Abdominal-B (Abd-B) in abdominal segments A5-A8 is controlled by four regulatory domains, iab-5-iab-8. Each domain has an initiator element (which sets the activity state), elements that maintain this state and tissue-specific enhancers. To ensure their functional autonomy, each domain is bracketed by boundary elements (Mcp, Fab-7, Fab-7 and Fab-8). In addition to blocking crosstalk between adjacent regulatory domains, the Fab boundaries must also have bypass activity so the relevant regulatory domains can 'jump over' intervening boundaries and activate the Abd-B promoter. In the studies reported here we have investigated the parameters governing bypass activity. We find that the bypass elements in the Fab-7 and Fab-8 boundaries must be located in the regulatory domain that is responsible for driving Abd-B expression. We suggest that bypass activity may also be subject to regulation.

Demand-driven Innovation and Spillover Effects on Adjacent Technological Domains: Evidence from Electric Vehicle Technologies

Demand-driven Innovation and Spillover Effects on Adjacent Technological Domains: Evidence from Electric Vehicle Technologies

Middle Triassic (Muschelkalk) transgression in the West Tethys: biostratigraphic evidence from Sardinia (Italy)

Stratigraphic and palaeontological analyses of the Middle Triassic (latest Anisian–Ladinian) in Muschelkalk facies are performed here to further unravel the palaeogeographic evolution of Sardinia in this time-frame. These shallow marine successions reveal a significant palaeontological record comprising facies and marker fossils (ammonoids, bivalves, conodonts, foraminifera etc.) reflecting a regional transgressive episode recorded throughout the West Mediterranean, after the Permian–Triassic biotic crisis. Particularly rich in the Nurra and Sarcidano-Gerrei areas, the facies/fossil record indicates the progressive westward settling of carbonate platforms, and consequently the development of new migration and irradiation routes for Sephardic faunas from the southeast (Palaeotethys) and Alpine faunas (Neotethys) from the northeast. Based on new findings and the revision of palaeontological associations previously reported, comparisons were made with associations of adjacent domains (Balearic Islands, Levantine area), thus refining their palaeoecological distribution and better framing Sardinia as a key area in the palaeogeographic evolution of the West Tethys during the Ladinian.

Unpaired sonar image denoising with simultaneous contrastive learning

Implementing underwater sonar image denoising algorithms through unpaired clean and noisy images is feasible and meaningful, since compliant paired real underwater sonar data is nearly impractical. Nevertheless, acquiring high-performance denoising algorithm is challenging without pairs of data as learning objects. In addition, the wide domain gap between noisy and clean samples as well as the noise contained in underwater sonar images is significantly more complex than that involved in normal images. Therefore, directly utilizing current unpaired optimization algorithms (e.g. generative adversarial learning and circular consistency learning) in underwater sonar image denoising tasks is not sufficient to explore the essential connection from noisy inputs to clean outputs. In this paper, we propose a novel framework for unpaired sonar image denoising which probes the same features of unpaired samples through a dual contrast optimization approach in latent space, named as NCD-GAN. The designed algorithm is composed of two basic parts: Simultaneous Transition Structure (STS) and Separable Contrast Unit (SCU). Separately, STS adopts a cyclic structure of multi-domain transformation to generate valuable surface information, and mines potential feature distributions between different domains via the addition of bidirectional mappings. Meanwhile, SCU introduces additional constraints in layer domains to encourage closer background layers between adjacent domains, while increasing the distance between noise layers so as to better promote the removal of noise and assist in image restoration. Sufficient experiments confirm that our algorithm provides better performance than existing unpaired denoising algorithms on multiple publicly available sonar image datasets and exhibits excellent robustness in the processing of multiple noises. Compared to the latest denoising algorithms, there is at most a 26.43% improvement in the evaluation metrics. Furthermore, it gains a 22.75% mAP boost on the subsequent advanced visual tasks.

ACM Conference on Recommender Systems September 18--22, 2023 at Singapore

ACM Conference on Recommender Systems (RecSys) is the premier international forum for the presentation of new research results, systems and techniques in the broad field of recommender systems. RecSys 2023 will be held in Singapore and will bring together the major international research groups working on recommender systems, along with many of the world's leading companies active in e-commerce and other adjacent domains. It is a SIGCHI-sponsored conference, that will attract also several leading industry sponsors. The proceedings will be published by ACM as part of the ACM Digital Library.

Numerical analysis of finite element methods for the cardiac extracellular-membrane-intracellular model: Steklov–Poincaré operator and spatial error estimates

The extracellular-membrane-intracellular (EMI) model consists in a set of Poisson equations in two adjacent domains, coupled on interfaces with nonlinear transmission conditions involving a system of ODEs. The unusual coupling of PDEs and ODEs on the boundary makes the EMI models challenging to solve numerically. In this paper, we reformulate the problem on the interface using a Steklov–Poincaré operator. We then discretize the model in space using a finite element method (FEM). We prove the existence of a semi-discrete solution using a reformulation as an ODE system on the interface. We derive stability and error estimates for the FEM. Finally, we propose a manufactured solution and use it to perform numerical tests. The order of convergence of the numerical method agrees with what is expected on the basis of the theoretical analysis of the convergence.

Nodes of Ranvier in health and disease.

Action potential propagation along myelinated axons depends on the geometry of the myelin unit and the division of the underlying axon to specialized domains. The latter include the nodes of Ranvier (NOR), the paranodal junction (PNJ) flanking the nodes, and the adjacent juxtaparanodal region that is located below the compact myelin of the internode. Each of these domains contains a unique composition of axoglial adhesion molecules (CAMs) and cytoskeletal scaffolding proteins, which together direct the placement of specific ion channels at the nodal and juxtaparanodal axolemma. In the last decade it has become increasingly clear that antibodies to some of these axoglial CAMs cause immune-mediated neuropathies. In the current review we detail the molecular composition of the NOR and adjacent membrane domains, describe the function of different CAM complexes that mediate axon-glia interactions along the myelin unit, and discuss their involvement and the underlying mechanisms taking place in peripheral nerve pathologies. This growing group of pathologies represent a new type of neuropathies termed "nodopathies" or "paranodopathies" that are characterized by unique clinical and molecular features which together reflect the mechanisms underlying the molecular assembly and maintenance of this specialized membrane domain.

The bromo-adjacent homology domains of PBRM1 associate with histone tails and contribute to PBAF-mediated gene regulation

A critical component of gene regulation is recognition of histones and their post-translational modifications by transcription-associated proteins or complexes. Although many histone-binding reader modules have been characterized, the bromo-adjacent homology (BAH) domain family of readers is still poorly characterized. A pre-eminent member of this family is PBRM1 (BAF180), a component of the PBAF chromatin-remodeling complex. PBRM1 contains two adjacent BAH domains of unknown histone-binding potential. We evaluated the tandem BAH domains for their capacity to associate with histones and to contribute to PBAF-mediated gene regulation. The BAH1 and BAH2 domains of human PBRM1 broadly interacted with histone tails, but they showed a preference for unmodified N-termini of histones H3 and H4. Molecular modeling and comparison of the BAH1 and BAH2 domains with other BAH readers pointed to a conserved binding mode via an extended open pocket and, in general, an aromatic cage for histone lysine binding. Point mutants that were predicted to disrupt the interaction between the BAH domains and histones reduced histone binding invitro and resulted in dysregulation of genes targeted by PBAF in cellulo. Although the BAH domains in PBRM1 were important for PBAF-mediated gene regulation, we found that overall chromatin targeting of PBRM1 was not dependent on BAH-histone interaction. Our findings identify a function of the PBRM1 BAH domains in PBAF activity that is likely mediated by histone tail interaction.

Switching Chirality in Arrays of Shape-Reconfigurable Spindle Microparticles.

The giant circular photo-galvanic effect is realized in chiral metals when illuminated by circularly polarized light. However, the structure itself is not switchable nor is the crystal chirality in the adjacent chiral domains. Here spindle-shaped liquid crystalline elastomer microparticles that can switch from prolate to spherical to oblate reversibly upon heating above the nematic to isotropic transition temperature are synthesized. When arranged in a honeycomb lattice, the continuous shape change of the microparticles leads to lattice reconfiguration, from a right-handed chiral state to an achiral one, then to a left-handed chiral state, without breaking the translational symmetry. Accordingly, the sign of rotation of the polarized light passing through the lattices changes as measured by time-domain terahertz spectroscopy. Further, it can locally alter the chirality in the adjacent domains using near-infrared light illumination. The reconfigurable chiral microarrays will allow us to explore non-trivial symmetry-protected transport modes of topological lattices at the light-matter interface. Specifically, the ability to controllably create chiral states at the boundary of the achiral/chiral domains will lead to rich structures emerging from the interplay of symmetry and topology.

Uniform Droplet Spraying of Magnesium Alloys: Modeling of Apollonian Fractal Structures on Micrograph Sections

A variety of advanced manufacturing processes have been developed based on the concept of rapid solidification processing (RSP), such as uniform droplet spraying (UDS) for the additive manufacturing of metals and alloys. This article introduces a morphological simulation of fractal dendric structures deposited by UDS of magnesium (Mg) alloys on two-dimensional (2D) planar sections. The fractal structure evolution is modeled as Apollonian packs of generalized ellipsoidal domains growing out of nuclei and dendrite arm fragments. The model employs descriptions of the dynamic thermal field based on superposed Green’s/Rosenthal functions with source images for initial/boundary effects, along with alloy phase diagrams and the classical solidification theory for nucleation and fragmentation rates. The initiation of grains is followed by their free and constrained growth by adjacent domains, represented via potential fields of level-set methods, for the effective mapping of the solidified topology and its metrics (grain size and fractal dimension of densely packed domains). The model is validated by comparing modeling results against micrographs of three UDS-deposited Mg–Zn–Y alloys. The further evolution of this real-time computational model and its application as a process observer for feedback control in 3D printing, as well as for off-line material design and optimization, is discussed.

Cyclic di-AMP traps proton-coupled K+ transporters of the KUP family in an inward-occluded conformation

Cyclic di-AMP is the only known essential second messenger in bacteria and archaea, regulating different proteins indispensable for numerous physiological processes. In particular, it controls various potassium and osmolyte transporters involved in osmoregulation. In Bacillus subtilis, the K+/H+ symporter KimA of the KUP family is inactivated by c-di-AMP. KimA sustains survival at potassium limitation at low external pH by mediating potassium ion uptake. However, at elevated intracellular K+ concentrations, further K+ accumulation would be toxic. In this study, we reveal the molecular basis of how c-di-AMP binding inhibits KimA. We report cryo-EM structures of KimA with bound c-di-AMP in detergent solution and reconstituted in amphipols. By combining structural data with functional assays and molecular dynamics simulations we reveal how c-di-AMP modulates transport. We show that an intracellular loop in the transmembrane domain interacts with c-di-AMP bound to the adjacent cytosolic domain. This reduces the mobility of transmembrane helices at the cytosolic side of the K+ binding site and therefore traps KimA in an inward-occluded conformation.

Texture weakening and ductility improvement of Mg-1.1Mn-0.5Al alloy via medium temperature-high reduction rolling: twinning variants selection and dynamic recrystallization mechanism

The weakening of basal texture is beneficial to improve the formability and mechanical properties of deformed magnesium alloys. In this paper, the microstructure and texture evolution of single pass rolled Mg-1.1Mn-0.5Al alloys with various reduction of 10%–60% at 200 °C were observed to reveal twin variants selection and mediated dynamic recrystallization (DRX) mechanism. The results showed that the type and volume fraction of activated twins were strongly related to rolling reduction. Primary {101¯2} tensile twins (TTWs), which were mainly activated in the 10% reduction rolled alloys, were not sufficient to induce recrystallization due to the absence of cumulative dislocation and lower plastic strain energy. In contrast, {101¯1}/ {101¯3} compression twins (CTWs) and {101¯1}−{101¯2}/ {101¯3}−{101¯2} double twins (DTWs) were preferred for recrystallization because of higher dislocation accumulation and stored strain energy. The occurrence of DRX was beneficial to absorb stored energy, relax stress concentration and weaken basal texture in adjacent domains. Due to the sufficient stress provided by massive basal slip dislocations, the type I and type II DTWs were more commonly observed than the type III and type IV variants, which involved much more dissociations of the mixed <c+a> dislocations in deformed magnesium alloys.

Melting domain size and recrystallization dynamics of ice revealed by time-resolved x-ray scattering

The phase transition between water and ice is ubiquitous and one of the most important phenomena in nature. Here, we performed time-resolved x-ray scattering experiments capturing the melting and recrystallization dynamics of ice. The ultrafast heating of ice I is induced by an IR laser pulse and probed with an intense x-ray pulse which provided us with direct structural information on different length scales. From the wide-angle x-ray scattering (WAXS) patterns, the molten fraction, as well as the corresponding temperature at each delay, were determined. The small-angle x-ray scattering (SAXS) patterns, together with the information extracted from the WAXS analysis, provided the time-dependent change of the size and the number of liquid domains. The results show partial melting (~13%) and superheating of ice occurring at around 20 ns. After 100 ns, the average size of the liquid domains grows from about 2.5 nm to 4.5 nm by the coalescence of approximately six adjacent domains. Subsequently, we capture the recrystallization of the liquid domains, which occurs on microsecond timescales due to the cooling by heat dissipation and results to a decrease of the average liquid domain size.

Replitrons: A major group of eukaryotic transposons encoding HUH endonuclease

HUH endonucleases of the Rep (replication protein) class mediate the replication of highly diverse plasmids and viral genomes across all domains of life. HUH transposases have independently evolved from Reps, giving rise to three major transposable element groups: the prokaryotic insertion sequences IS200/IS605 and IS91/ISCR, and the eukaryotic Helitrons. Here, I present Replitrons, a second group of eukaryotic transposons encoding Rep HUH endonuclease. Replitron transposases feature a Rep domain with one catalytic Tyr (Y1) and an adjacent domain that may function in oligomerization, contrasting with Helitron transposases that feature Rep with two Tyr (Y2) and a fused helicase domain (i.e., RepHel). Protein clustering found no link between Replitron transposases and described HUH transposases, and instead recovered a weak association with Reps of circular Rep-encoding single-stranded (CRESS) DNA viruses and their related plasmids (pCRESS). The predicted tertiary structure of the transposase of Replitron-1, the founding member of the group that is active in the green alga Chlamydomonas reinhardtii, closely resembles that of CRESS-DNA viruses and other HUH endonucleases. Replitrons are present in at least three eukaryotic supergroups and reach high copy numbers in nonseed plant genomes. Replitron DNA sequences feature short direct repeats at, or potentially near, their termini. Finally, I characterize copy-and-paste de novo insertions of Replitron-1 using long-read sequencing of C. reinhardtii experimental lines. These results support an ancient and evolutionarily independent origin of Replitrons, in line with other major groups of eukaryotic transposons. This work expands the known diversity of both transposons and HUH endonucleases in eukaryotes.

Interdomain Linker of the Bioelecrocatalyst Cellobiose Dehydrogenase Governs the Electron Transfer.

Direct bioelectrocatalysis applied in biosensors, biofuel cells, and bioelectrosynthesis is based on an efficient electron transfer between enzymes and electrodes in the absence of redox mediators. Some oxidoreductases are capable of direct electron transfer (DET), while others achieve the enzyme to electrode electron transfer (ET) by employing an electron-transferring domain. Cellobiose dehydrogenase (CDH) is the most-studied multidomain bioelectrocatalyst and features a catalytic flavodehydrogenase domain and a mobile, electron-transferring cytochrome domain connected by a flexible linker. The ET to the physiological redox partner lytic polysaccharide monooxygenase or, ex vivo, electrodes depends on the flexibility of the electron transferring domain and its connecting linker, but the regulatory mechanism is little understood. Studying the linker sequences of currently characterized CDH classes we observed that the inner, mobile linker sequence is flanked by two outer linker regions that are in close contact with the adjacent domain. A function-based definition of the linker region in CDH is proposed and has been verified by rationally designed variants of Neurospora crassa CDH. The effect of linker length and its domain attachment on electron transfer rates has been determined by biochemical and electrochemical methods, while distances between the domains of CDH variants were computed. This study elucidates the regulatory mechanism of the interdomain linker on electron transfer by determining the minimum linker length, observing the effects of elongated linkers, and testing the covalent stabilization of a linker part to the flavodehydrogenase domain. The evolutionary guided, rational design of the interdomain linker provides a strategy to optimize electron transfer rates in multidomain enzymes and maximize their bioelectrocatalytic performance.

Sub-Millisecond Laser-Irradiation-Mediated Surface Restructure Boosts the CO Production Yield of Cobalt Oxide Supported Pd Nanoparticles.

The catalytic conversion of CO2 into valuable commodities has the potential to balance ongoing energy and environmental issues. To this end, the reverse water-gas shift (RWGS) reaction is a key process that converts CO2 into CO for various industrial processes. However, the competitive CO2 methanation reaction severely limits the CO production yield; therefore, a highly CO-selective catalyst is needed. To address this issue, we have developed a bimetallic nanocatalyst comprising Pd nanoparticles on the cobalt oxide support (denoted as CoPd) via a wet chemical reduction method. Furthermore, the as-prepared CoPd nanocatalyst was exposed to sub-millisecond laser irradiation with per-pulse energies of 1 mJ (denoted as CoPd-1) and 10 mJ (denoted as CoPd-10) for a fixed duration of 10 s to optimize the catalytic activity and selectivity. For the optimum case, the CoPd-10 nanocatalyst exhibited the highest CO production yield of ∼1667 μmol g-1catalyst, with a CO selectivity of ∼88% at a temperature of 573 K, which is a 41% improvement over pristine CoPd (~976 μmol g-1catalyst). The in-depth analysis of structural characterizations along with gas chromatography (GC) and electrochemical analysis suggested that such a high catalytic activity and selectivity of the CoPd-10 nanocatalyst originated from the sub-millisecond laser-irradiation-assisted facile surface restructure of cobalt oxide supported Pd nanoparticles, where atomic CoOx species were observed in the defect sites of the Pd nanoparticles. Such an atomic manipulation led to the formation of heteroatomic reaction sites, where atomic CoOx species and adjacent Pd domains, respectively, promoted the CO2 activation and H2 splitting steps. In addition, the cobalt oxide support helped to donate electrons to Pd, thereby enhancing its ability of H2 splitting. These results provide a strong foundation to use sub-millisecond laser irradiation for catalytic applications.