Acid-sensing ion channels are proton-activated, sodium-selective channels composed of three subunits, and are members of the superfamily of epithelial sodium channels, mechanosensitive and FMRF-amide ...peptide-gated ion channels. These ubiquitous eukaryotic ion channels have essential roles in biological activities as diverse as sodium homeostasis, taste and pain. Despite their crucial roles in biology and their unusual trimeric subunit stoichiometry, there is little knowledge of the structural and chemical principles underlying their ion channel architecture and ion-binding sites. Here we present the structure of a functional acid-sensing ion channel in a desensitized state at 3 A resolution, the location and composition of the approximately 8 A 'thick' desensitization gate, and the trigonal antiprism coordination of caesium ions bound in the extracellular vestibule. Comparison of the acid-sensing ion channel structure with the ATP-gated P2X(4) receptor reveals similarity in pore architecture and aqueous vestibules, suggesting that there are unanticipated yet common structural and mechanistic principles.
•The state of the art on energy absorption of graded structures and materials is reviewed.•Structures and materials with functionally graded properties exhibit much better ...crashworthiness.•Performances of graded structures can be further improved by optimized design.•Research directions on graded structures and materials are discussed.
In the past decades, there has been a constant aspiration for light-weight and highly efficient energy-absorbing structures and materials in vehicle and other industries. A large number of publications have shown that advanced configurations with functionally graded properties could collapse in a more controlled manner and have a remarkable energy-absorbing efficiency when compared with traditional uniform structures and materials. This paper mainly covers the state of the art of energy absorption of graded structures and materials, and discusses the effects of the graded properties on their crashworthiness. Those advanced energy-absorbing structures and materials include primarily thin-walled structures with variable diameter/width/wall thickness/strength, cellular materials with variable density and their filling structures, and other hybrid structures with multiple graded properties. It demonstrates that thin-walled structures and cellular materials could exhibit more efficient and effective energy-absorbing performance by introducing graded properties. Additionally, some advanced manufacturing and modeling technologies such as the 3D printing, multi-scale computation, etc. provide a much wider and more feasible conceptual design for graded structures and materials.
A microscale vibration analysis of micro-plates is developed based on a modified couple stress theory. The presence of the length scale parameter in this theory enables us to describe the size effect ...in micro-structures. A variational approach based on Hamilton’s principle is employed to obtain the governing equations of motion. To illustrate the new model, the free vibration analysis of a rectangular micro plate with two opposite edges simply supported and arbitrary boundary conditions along the other edges and a circular micro-plate are considered. The natural frequencies of micro-plates are presented for over a wide range of length scale parameters, different aspect ratios and various boundary conditions for both rectangular and circular micro-plates. The effect of length scale parameter on natural frequencies of micro-plates are discussed in details and the numerical results reveal that the intrinsic size dependence of material leads to increase the natural frequency.
► A new model is presented for vibration analysis of micro-plates using a modified couple stress theory. ► The model contains an internal material length scale parameter and can predict the size effect in micro-scale plates. ► The natural frequencies are presented for both rectangular and circular micro-plates.
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function, physico-chemical properties and mode of interaction with other proteins. ...Currently about 90% of structures in the Protein Data Bank are crystal structures, in which the correct quaternary structure is embedded in the crystal lattice among a number of crystal contacts. Computational methods are required to 1) classify all protein-protein contacts in crystal lattices as biologically relevant or crystal contacts and 2) provide an assessment of how the biologically relevant interfaces combine into a biological assembly. In our previous work we addressed the first problem with our EPPIC (Evolutionary Protein Protein Interface Classifier) method. Here, we present our solution to the second problem with a new method that combines the interface classification results with symmetry and topology considerations. The new algorithm enumerates all possible valid assemblies within the crystal using a graph representation of the lattice and predicts the most probable biological unit based on the pairwise interface scoring. Our method achieves 85% precision (ranging from 76% to 90% for different oligomeric types) on a new dataset of 1,481 biological assemblies with consensus of PDB annotations. Although almost the same precision is achieved by PISA, currently the most popular quaternary structure assignment method, we show that, due to the fundamentally different approach to the problem, the two methods are complementary and could be combined to improve biological assembly assignments. The software for the automatic assessment of protein assemblies (EPPIC version 3) has been made available through a web server at http://www.eppic-web.org.
Spin-orbit coupling links a particle's velocity to its quantum-mechanical spin, and is essential in numerous condensed matter phenomena, including topological insulators and Majorana fermions. In ...solid-state materials, spin-orbit coupling originates from the movement of electrons in a crystal's intrinsic electric field, which is uniquely prescribed in any given material. In contrast, for ultracold atomic systems, the engineered 'material parameters' are tunable: a variety of synthetic spin-orbit couplings can be engineered on demand using laser fields. Here we outline the current experimental and theoretical status of spin-orbit coupling in ultracold atomic systems, discussing unique features that enable physics impossible in any other known setting.
The quantized version of the anomalous Hall effect has been predicted to occur in magnetic topological insulators, but the experimental realization has been challenging. Here, we report the ...observation of the quantum anomalous Hall (QAH) effect in thin films of chromium-doped (Bi, Sb)₂ Te₃, a magnetic topological insulator. At zero magnetic field, the gate-tuned anomalous Hall resistance reaches the predicted quantized value of h/e², accompanied by a considerable drop in the longitudinal resistance. Under a strong magnetic field, the longitudinal resistance vanishes, whereas the Hall resistance remains at the quantized value. The realization of the QAH effect may lead to the development of low-power-consumption electronics.
Photonic Floquet topological insulators RECHTSMAN, Mikael C; ZEUNER, Julia M; PLOTNIK, Yonatan ...
Nature (London),
04/2013, Letnik:
496, Številka:
7444
Journal Article
Recenzirano
Odprti dostop
Topological insulators are a new phase of matter, with the striking property that conduction of electrons occurs only on their surfaces. In two dimensions, electrons on the surface of a topological ...insulator are not scattered despite defects and disorder, providing robustness akin to that of superconductors. Topological insulators are predicted to have wide-ranging applications in fault-tolerant quantum computing and spintronics. Substantial effort has been directed towards realizing topological insulators for electromagnetic waves. One-dimensional systems with topological edge states have been demonstrated, but these states are zero-dimensional and therefore exhibit no transport properties. Topological protection of microwaves has been observed using a mechanism similar to the quantum Hall effect, by placing a gyromagnetic photonic crystal in an external magnetic field. But because magnetic effects are very weak at optical frequencies, realizing photonic topological insulators with scatter-free edge states requires a fundamentally different mechanism-one that is free of magnetic fields. A number of proposals for photonic topological transport have been put forward recently. One suggested temporal modulation of a photonic crystal, thus breaking time-reversal symmetry and inducing one-way edge states. This is in the spirit of the proposed Floquet topological insulators, in which temporal variations in solid-state systems induce topological edge states. Here we propose and experimentally demonstrate a photonic topological insulator free of external fields and with scatter-free edge transport-a photonic lattice exhibiting topologically protected transport of visible light on the lattice edges. Our system is composed of an array of evanescently coupled helical waveguides arranged in a graphene-like honeycomb lattice. Paraxial diffraction of light is described by a Schrödinger equation where the propagation coordinate (z) acts as 'time'. Thus the helicity of the waveguides breaks z-reversal symmetry as proposed for Floquet topological insulators. This structure results in one-way edge states that are topologically protected from scattering.
Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large ...structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
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