Multidimensional persistence in biomolecular data

Persistent homology has emerged as a popular technique for the topological simplification of big data, including biomolecular data. Multidimensional persistence bears considerable promise to bridge the gap between geometry and topology. However, its practical and robust construction has been a challenge. We introduce two families of multidimensional persistence, namely pseudomultidimensional persistence and multiscale multidimensional persistence. The former is generated via the repeated applications of persistent homology filtration to high‐dimensional data, such as results from molecular dynamics or partial differential equations. The latter is constructed via isotropic and anisotropic scales that create new simiplicial complexes and associated topological spaces. The utility, robustness, and efficiency of the proposed topological methods are demonstrated via protein folding, protein flexibility analysis, the topological denoising of cryoelectron microscopy data, and the scale dependence of nanoparticles. Topological transition between partial folded and unfolded proteins has been observed in multidimensional persistence. The separation between noise topological signatures and molecular topological fingerprints is achieved by the Laplace–Beltrami flow. The multiscale multidimensional persistent homology reveals relative local features in Betti‐0 invariants and the relatively global characteristics of Betti‐1 and Betti‐2 invariants. © 2015 Wiley Periodicals, Inc.     

Symmetry calculation for molecules and transition states

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three‐dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label‐stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules. © 2014 Wiley Periodicals, Inc.     

Experimental Charge Density Evidence for Pnicogen Bonding in a Crystal of Ammonium Chloride

Chemical binding in crystalline ammonium chloride, a simple inorganic salt with an unexpectedly complex bonding pattern, was studied by using a topological analysis of electron density function derived from high‐resolution X‐ray diffraction. Supported by periodic quantum chemical calculations, it provided experimental evidence for weak σ‐hole bonds (1.5 kcal mol^?1) that involve ammonium cations in a crystal. Our results show this type of supramolecular interaction to be more numerous than has been found to date by using gas‐phase calculations or statistical analysis of CSD.     

Electron Density Analysis of Hyperconjugation

Hyperconjugation is analyzed through the electron density of orbitals responsible for hyperconjugative interactions, which cannot be detected by means of conventional electron‐density‐based calculations. This interaction is detected through the π electron density topology, by excluding σ electron density from the total. As the presence of the hyperconjugation phenomenon in carbocation systems is well understood, several carbocations are benchmarked, and the results show that the positive carbon atom establishes a hyperconjugative critical point with the adjacent methyl group(s). Also, π localization and delocalization indices are employed to support the conclusions made by the topological analysis.     

Evolution of polarization singularities accompanied by avoided crossing in plasmonic system

The evolution of polarization singularities supported in a one-dimensional periodic plasmonic system is studied. The lateral inversion symmetry of the system, which breaks the in-plane inversion symmetry and up-down mirror symmetry simultaneously, yields abundant polarization states. A complete evolution process with geometry for the polarization states is traced. In the evolution, circularly polarized points (C points) can stem from 3 different processes. In addition to the previously reported processes occurring in an isolated band, a new type of C point appearing in two bands simultaneously due to the avoided band crossing, is observed. Unlike the dielectric system with a similar structure which only supports at-$\varGamma$ bound states in the continuum (BICs), accidental BICs off the $\varGamma$ point are realized in this plasmonic system. This work provides a new scheme of polarization manipulation for the plasmonic systems.     

Majorana zero modes induced by skyrmion lattice

One-dimensional s-wave superconductor with spin-orbit coupling is a platform for the realization of Majorana zero modes. The spin-exchange with the magnetic skyrmion lattice can induce spin-orbit coupling in a s-wave superconductor system and the effects are different from the constant spin-orbit coupling. The strength of the effective spin-orbit coupling as well as the rich topoloigcal phase diagram are directly connected to the radius of the skyrmion lattice R. We obtain the rich topological phase diagram of this system with different skyrmion lattice radii by numerically evaluating the spectrum of the system under the periodic boundary condition, and we also find the Majorana zero modes under the open boundary condition to verify the bulk-edge correspondence.     

Topological hinge modes in Dirac semimetals

Dirac semimetals (DSMs) are an important class of topological states of matter. Here, focusing on DSMs of band inversion type, we investigate their boundary modes from the effective model perspective. We show that in order to properly capture the boundary modes, k-cubic terms must be included in the effective model, which would drive an evolution of surface degeneracy manifold from a nodal line to a nodal point. Sizable k-cubic terms are also needed for better exposing the topological hinge modes in the spectrum. Using first-principles calculations, we demonstrate that this feature and the topological hinge modes can be clearly exhibited in β-CuI. We extend the discussion to magnetic DSMs and show that the time-reversal symmetry breaking can gap out the surface bands and hence is beneficial for the experimental detection of hinge modes. Furthermore, we show that magnetic DSMs serve as a parent state for realizing multiple other higher-order topological phases, including higher-order Weyl-point/nodal-line semimetals and higher-order topological insulators.     

Scaling Up DNA Origami Lattice Assembly

The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm² is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm² areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm², this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.     

Nematodynamics and structures in junctions of cylindrical micropores

ABSTRACT

We explore equilibrium structures and flow-driven deformations of nematic liquid crystals confined to 3D junctions of cylindrical micropores with homeotropic surface anchoring. The topological state of the nematic ordering field in such basic unit of porous networks is controlled by nematic orientation profiles in individual pores, anchoring frustration along the edges of joining pores and coupling to the material flow field. We numerically investigate formation of the flow-aligned configurations in single cylindrical pores and pore junctions. Depending on the arrangement of inlet and outlet flows in the junction, we demonstrate existence of numerous stationary nematic configurations, characterised by specific bulk defects and surface disclinations along joining edges. Observed bulk defects are nonsingular escaped structures, disclinations in the form of loops or disclination lines pinned to the joining edges of the pores. Furthermore, we show examples of defect dynamics during the flow-induced topological transformations.     

内部算子生成的直觉I-Fuzzy拓扑空间

在直觉I-fuzzy拓扑空间中定义了内部度,并研究了它的一些性质,接着给出了直觉I-fuzzy拓扑空间内部算子的概念,最后得到了从拓扑的直觉I-Fuzzy内部算子I出发,得到一个直觉I-fuzzy拓扑r,再利用r定义的内部算子恰好回到了I等结论.