Three-dimensional Topological Structure Research Articles

Tetramethacrylic benzylidene cyclopentanone dye for one- and two-photon photopolymerization

The crystalline one-component methacrylate containing photoinitiator 4MetBAC was synthesized and characterized by 1H NMR, 13C NMR, IR-, UV–Vis spectrum, and X-Ray analysis. The one- and two-photon absorption, photoluminescence, and electrochemical properties of 4MetBAC in solution were investigated. The polymerization of PETA was induced directly by 4MetBAC (2.5–11.5 mM) under irradiation with LED@380 (1PP) or focused beam of femtosecond laser with wavelength 780 nm (2PP). The polymer nanostructures with intricate architecture («sleepers-rails»-, «cell scaffold»- and cylindrical spiral structures) were fabricated by the DLW method. The polymerization threshold of the composition based on 4Met-BAC (11.5 mM) was 0.9 mW at the recording speed of 170 μm/s. The smallest stable structures with the linear fragment sizes of 72 ± 5 nm (less than λ/10) have been obtained by nanolithography. Due to the polymerizable groups, 4Met-BAC has the ability to link into the polymer networks. Experiments with human dermal fibroblasts and cells of the HEK 293 line have been demonstrated that the final polymers prepared by both one- and two-photon photopolymerization (cell scaffold) are biosafety. Hence we believe that the PETA composition based on one-component methacrylate-containing photoinitiator 4Met-BAC opens up wide capabilities for creating three-dimensional topological structures with high submicron resolution by the DLW method for optoelectronic and biological applications.

Observation of optical vortex knots and links associated with topological charge.

Knots and links, as three-dimensional topologies, have played a fundamental role in many physical fields. Despite knotted vortex loops having been shown to exist in the light field, the three-dimensional configuration of vortex loop is fixed due to their topological robustness, making the fields with different topologies independent of each other. In this work, we established the mapping between the torus knots/links and the integer topological charge of the optical vortex, and demonstrated the change of the intermediate state with fractional charges. Furthermore, we experimentally observed the transformation process of the three-dimensional topological structure by only changing the topological charge. Remarkably, we revealed two different reconnection mechanisms associated with the odd or even index of the torus topology. We hope these results may provide new insight for the study of singular optics and evolution in other physical fields.

Three-dimensional topological structures and formation processes of dislocations in Au nanowire under tension loading

Dislocation is an important microstructural configuration in most crystalline materials, but it is still difficult for experiments to detect its local atomic structures and formation processes. Molecular dynamics simulation provides a powerful tool to investigate the dislocation by means of some geometrical structural analysis methods, but most of these methods cannot accurately distinguish the nuances of local configurations. Herein, we propose a new microstructural analysis method of cluster-type-index method (CTIM). The three-dimensional (3D) topological structures and formation processes of dislocations during tensioning Au nanowire are illuminated by means of CTIM. It is found that the favourite local atomic structures in dislocations are the defective FCC clusters represented by the CTIM indexes (13, 3/1421 2/1431 2/1441 4/1541 2/1661). The vector analysis method based on the accumulation of lattice distortions cannot identified the aggregation of disordered atoms in the initial nucleation of dislocation. In the formation processes of dislocation atoms, three trajectories of T1: FCC→(13, 3/1421 2/1431 2/1441 4/1541 2/1661), T2: FCC→(12, 2/1311 1/1411 9/1421) and T3: FCC→(11, 4/1311 7/1421) are favorite. The dislocation atoms following the T1 trajectory are mainly located at the core of dislocations, while that following the T2 and T3 trajectories is at the front of dislocations. CTIM would provide an effective tool to investigate the defective structures and their interactions in nanocrystalline structures.

An integrated strategy for designing and fabricating triple-layer vascular graft with oriented microgrooves to promote endothelialization.

Compared with native blood vessels and existing vascular grafts, design and manufacture of vascular grafts with a three-dimensional topological structure is a key to induce cells and tissue growth, which remains an essential issue in both tissue engineering and regenerative medicine. This study sought to develop a novel triple-layer vascular graft (TLVG) with oriented microgrooves to investigate the mechanical property and endothelialization. The TLVGs were composed of electrospun Poly-ε-caprolactone (PCL)/thermoplastic polyurethane (TPU) as the inner layer, albumen/sodium alginate (SA) hydrogel as the middle layer, and electrospun PCL/TPU as the outer layer. In detail, a cylindrical sacrificial template was designed and printed using polyvinyl alcohol (PVA), served as the electrospinning receiving platform to form the oriented microgrooves in the inner layer of TLVGs. The highly elastic albumen/SA hydrogel and PCL/TPU nanofibers were able to simulate the elastin in blood vessels. In addition, the introduction of the albumen/SA hydrogel layer not only solves the leakage problem of a porous vascular graft but also improves the wettability of the scaffolds. The physicochemical properties and biological characteristics of TLVGs were evaluated by tensile testing, Surface wettability test, Fourier transform-infrared spectroscopy (FTIR) measurement, Live-Dead cell staining assay, and CCK-8 assay. Especially, the oriented microgrooves on the inner surface of the TLVGs can promote human umbilical vein endothelial cells (HUVECs) directed growth and migration in favor of endothelialization. All results showed that the fabricated TLVGs with excellent physicochemical properties and biocompatibility has great potential in clinic application.

Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression

Expression of the Human Endogenous Retrovirus Type K (HERV-K), the youngest and most active HERV, has been associated with various cancers and neurodegenerative diseases. As in all retroviruses, a fraction of HERV-K transcripts is exported from the nucleus in unspliced or incompletely spliced forms to serve as templates for translation of viral proteins. In a fraction of HERV-K loci (Type 2 proviruses), nuclear export of the unspliced HERV-K mRNA appears to be mediated by a cis-acting signal on the mRNA, the RcRE, and the protein Rec—these are analogous to the RRE-Rev system in HIV-1. Interestingly, the HIV-1 Rev protein is able to mediate the nuclear export of the HERV-K RcRE, contributing to elevated HERV-K expression in HIV-infected patients. We aimed to understand the structural basis for HIV Rev-HERV-K RcRE recognition. We examined the conformation of the RcRE RNA in solution using small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM). We found that the 433-nt long RcRE can assume folded or extended conformations as observed by AFM. SAXS analysis of a truncated RcRE variant revealed an “A”-shaped topological structure similar to the one previously reported for the HIV-1 RRE. The effect of the overall topology was examined using several deletion variants. SAXS and biochemical analyses demonstrated that the “A” shape is necessary for efficient Rev-RcRE complex formation in vitro and nuclear export activity in cell culture. The findings provide insight into the mechanism of HERV-K expression and a structural explanation for HIV-1 Rev-mediated expression of HERV-K in HIV-infected patients. ImportanceExpression of the human endogenous retrovirus type K (HERV-K) has been associated with various cancers and autoimmune diseases. Nuclear export of both HIV-1 and HERV-K mRNAs is dependent on the interaction between a small viral protein (Rev in HIV-1 and Rec in HERV-K) and a region on the mRNA (RRE in HIV-1 and RcRE in HERV-K). HIV-1 Rev is able to mediate the nuclear export of RcRE-containing HERV-K mRNAs, which contributes to elevated production of HERV-K proteins in HIV-infected patients. We report the solution conformation of the RcRE RNA—the first three-dimensional topological structure for a HERV molecule—and find that the RcRE resembles the HIV-1 nuclear export signal, RRE. The finding reveals the structural basis for the increased HERV-K expression observed in HIV-infected patients. Elevated HERV expression, mediated by HIV infection or other stressors, can have various HERV-related biological consequences. The findings provide structural insight for regulation of HERV-K expression.

Dynamic Rearrangements of a Three-Dimensional Topological Structure of a Moving Domain Wall in Magnetic Film in the Presence of Random Perturbations

Using three-dimensional micromagnetic simulation, the dynamic processes occurring in a domain wall (DW) that moves under the influence of a constant magnetic field in a magnetically soft uniaxial film with planar anisotropy are studied. It is shown that the general picture of the dynamics of topological transformations taking place in DWs can significantly vary with the introduction of perturbing factors that randomly depend on the coordinates or time (spatially heterogeneous anisotropy; a magnetic field fluctuating in time). Moreover, the characteristic configurations of a vector magnetization field near the intrafilm vortex cores and singular (Bloch) points preserve their shape. The dependences of the energy and DW shifts on the time are determined for a wide range of film thickness values, temperatures, and magnetic field intensities. Imaging techniques based on calculating two types of topological charges are used when analyzing magnetization configurations.

Long-range chiral exchange interaction in synthetic antiferromagnets.

The exchange interaction governs static and dynamic magnetism. This fundamental interaction comes in two flavours-symmetric and antisymmetric. The symmetric interaction leads to ferro- and antiferromagnetism, and the antisymmetric interaction has attracted significant interest owing to its major role in promoting topologically non-trivial spin textures that promise fast, energy-efficient devices. So far, the antisymmetric exchange interaction has been found to be rather short ranged and limited to a single magnetic layer. Here we report a long-range antisymmetric interlayer exchange interaction in perpendicularly magnetized synthetic antiferromagnets with parallel and antiparallel magnetization alignments. Asymmetric hysteresis loops under an in-plane field reveal a unidirectional and chiral nature of this interaction, which results in canted magnetic structures. We explain our results by considering spin-orbit coupling combined with reduced symmetry in multilayers. Our discovery of a long-range chiral interaction provides an additional handle to engineer magnetic structures and could enable three-dimensional topological structures.

Aggregation-induced Emission-active Hyperbranched Poly(tetrahydropyrimidine) s Synthesized from Multicomponent Tandem Polymerization

Hyperbranched polymer with highly branched three-dimensional topological structure, a large number of end groups, and multifaceted functionalities have gained much attention, while polymers with aggregation-induced emission (AIE) properties become a group of popular luminescent materials recently. The design and synthesis of AIE-active hyperbranched polymers, which combine the advantages of these two types of materials, are attractive but challenging. In this work, four hyperbranched poly(tetrahydropyrimidine)s were synthesized from the metal-free room temperature multicomponent tandem polymerization of diester group-activated internal alkyne, polyfunctional aromatic amines, and formaldehyde in methanol under the catalysis of acetic acid. Through different monomer combination and controlling the monomer loading order, hyperbranched polymers with various topological structures as well as sequences of different functional groups in the polymer backbone were obtained with high molecular weights (up to 3.0 × 104 g/mol) in high yields (up to 98%). The hyperbranched poly(tetrahydropyrimidine) emitted faintly in solution, while its luminescence was notably enhanced in the aggregated state, suggesting its typical aggregation-induced emission property. It is anticipated that the multicomponent polymerization may provide a synthetic platform for the construction of hyperbranched polyheterocycles with diverse structures and functionalities.

Electronic properties of defects inWeyl semimetal tantalum arsenide**Project supported by the National Natural Science Foundation of China (Grant Nos. 11635003, 11025524, and 11161130520), the National Basic Research Program of China (Grant No. 2010CB832903), and the European Commissions of 7th Framework Programme (FP7-PEOPLE-2010-IRSES) (Grant No. 269131).

The tantalum arsenide (TaAs) is a topological Weyl semimetal which is a class of materials of gapless with three-dimensional topological structure. In order to develop a comprehensive description of the topological properties of the Weyl semimetal, we use the density functional theory to study several defects of TaAs after H irradiation and report the electronic dispersion curves and the density of states of these defects. We find that various defects have different influences on the topological properties. Interstitial H atom can shift the Fermi level. Both Ta vacancy with a concentration of 1/64 and As vacancy with a concentration of 1/64 destruct a part of the Weyl points. The substitutional H atom on a Ta site could repair only a part of the Weyl points, while H atom on an As site could repair all the Weyl points.

Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering

Knowledge of RNA three-dimensional topological structures provides important insight into the relationship between RNA structural components and function. It is often likely that near-complete sets of biochemical and biophysical data containing structural restraints are not available, but one still wants to obtain knowledge about approximate topological folding of RNA. In this regard, general methods for determining such topological structures with minimum readily available restraints are lacking. Naked RNAs are difficult to crystallize and NMR spectroscopy is generally limited to small RNA fragments. By nature, sequence determines structure and all interactions that drive folding are self-contained within sequence. Nevertheless, there is little apparent correlation between primary sequences and three-dimensional folding unless supplemented with experimental or phylogenetic data. Thus, there is an acute need for a robust high-throughput method that can rapidly determine topological structures of RNAs guided by some experimental data. We present here a novel method (RS3D) that can assimilate the RNA secondary structure information, small-angle X-ray scattering data, and any readily available tertiary contact information to determine the topological fold of RNA. Conformations are firstly sampled at glob level where each glob represents a nucleotide. Best-ranked glob models can be further refined against solvent accessibility data, if available, and then converted to explicit all-atom coordinates for refinement against SAXS data using the Xplor-NIH program. RS3D is widely applicable to a variety of RNA folding architectures currently present in the structure database. Furthermore, we demonstrate applicability and feasibility of the program to derive low-resolution topological structures of relatively large multi-domain RNAs.

Topological structure determination of RNA using small-angle X-ray scattering

Knowledge of RNA three-dimensional topological structures provides important insight into the relationship between RNA structural components and function. It is often likely that near-complete sets of biochemical and biophysical data containing structural restraints are not available, but one still wants to obtain knowledge about approximate topological folding of RNA. In this regard, general methods for determining such topological structures with minimum readily available restraints are lacking. Naked RNAs are difficult to crystallize and NMR spectroscopy is generally limited to small RNA fragments. By nature, sequence determines structure and all interactions that drive folding are self-contained within sequence. Nevertheless, there is little apparent correlation between primary sequences and three-dimensional folding unless supplemented with experimental or phylogenetic data. Thus, there is an acute need for a robust high-throughput method that can rapidly determine topological structures of RNAs guided by some experimental data. We present here a novel method (RS3D) that can assimilate the RNA secondary structure information, small-angle X-ray scattering data, and any readily available tertiary contact information to determine the topological fold of RNA. Conformations are firstly sampled at glob level where each glob represents a nucleotide. Best-ranked glob models can be further refined against solvent accessibility data, if available, and then converted to explicit all-atom coordinates for refinement against SAXS data using the Xplor-NIH program. RS3D is widely applicable to a variety of RNA folding architectures currently present in the structure database. Furthermore, we demonstrate applicability and feasibility of the program to derive low-resolution topological structures of relatively large multi-domain RNAs.

Supramolecular hyperbranched polymers.

Supramolecular polymers with topological structures offer a new way for creating novel supramolecular polymer species and smart materials. As one special class of supramolecular topological polymers, supramolecular hyperbranched polymers (SHPs), combining the advantages of supramolecular polymers and hyperbranched polymers, have attracted interest due to their unique chemical and physical properties and potential application in many fields such as biochemistry, medicine, and materials science. SHPs exhibit the apparent merits of a reversible and tunable nature, three-dimensional topological structure, high solubility, and plenty of terminal groups. The positive cooperativity generated from the hyperbranched topological structure and supramolecular interactions may further endow SHPs with enhanced properties and functions. This feature article highlights the recent advances and future trends in SHPs depending on two different construction methodologies including a direct strategy and an indirect approach. Various hyperbranched architectures, responsive and functional features, self-assembly, and potential applications are comprehensively discussed.

Visualization and criticality of magnetotail field topology in a three-dimensional particle simulation

We present the temporal evolution of magnetic field topology in the magnetotail with a southward IMF in order to identify the magnetic reconnection. The magnetic field topology is uniquely determined by the eigenvalues of the critical points, if they are not degenerated. This is because the critical points, their number, and the rules between them characterize the whole magnetic field pattern. At the critical points, the magnetics become zero. The magnetic vector field curves and surfaces are both integrated out along the principal directions of certain classes of critical points including the Earth’s dipole magnetic field. The skeleton that includes the critical points, characteristic curves, and surfaces provides the three-dimensional topological structure of the reconnection. The change of the skeleton, i.e. the change of the topology, has revealed the occurrence of magnetic reconnection. Namely, three-dimensional “X-points” or the more-than-two critical points that are saddle and connected each other are unstable and can move, vanish, and generated.