Global Topology of 3D Symmetric Tensor Fields.

There have been recent advances in the analysis and visualization of 3D symmetric tensor fields, with a focus on the robust extraction of tensor field topology. However, topological features such as degenerate curves and neutral surfaces do not live in isolation. Instead, they intriguingly interact with each other. In this paper, we introduce the notion of topological graph for 3D symmetric tensor fields to facilitate global topological analysis of such fields. The nodes of the graph include degenerate curves and regions bounded by neutral surfaces in the domain. The edges in the graph denote the adjacency information between the regions and degenerate curves. In addition, we observe that a degenerate curve can be a loop and even a knot and that two degenerate curves (whether in the same region or not) can form a link. We provide a definition and theoretical analysis of individual degenerate curves in order to help understand why knots and links may occur. Moreover, we differentiate between wedges and trisectors, thus making the analysis more detailed about degenerate curves. We incorporate this information into the topological graph. Such a graph can not only reveal the global structure in a 3D symmetric tensor field but also allow two symmetric tensor fields to be compared. We demonstrate our approach by applying it to solid mechanics and material science data sets.

Feature Curves and Surfaces of 3D Asymmetric Tensor Fields.

3D asymmetric tensor fields have found many applications in science and engineering domains, such as fluid dynamics and solid mechanics. 3D asymmetric tensors can have complex eigenvalues, which makes their analysis and visualization more challenging than 3D symmetric tensors. Existing research in tensor field visualization focuses on 2D asymmetric tensor fields and 3D symmetric tensor fields. In this paper, we address the analysis and visualization of 3D asymmetric tensor fields. We introduce six topological surfaces and one topological curve, which lead to an eigenvalue space based on the tensor mode that we define. In addition, we identify several non-topological feature surfaces that are nonetheless physically important. Included in our analysis are the realizations that triple degenerate tensors are structurally stable and form curves, unlike the case for 3D symmetric tensors fields. Furthermore, there are two different ways of measuring the relative strengths of rotation and angular deformation in the tensor fields, unlike the case for 2D asymmetric tensor fields. We extract these feature surfaces using the A-patches algorithm. However, since three of our feature surfaces are quadratic, we develop a method to extract quadratic surfaces at any given accuracy. To facilitate the analysis of eigenvector fields, we visualize a hyperstreamline as a tree stem with the other two eigenvectors represented as thorns in the real domain or the dual-eigenvectors as leaves in the complex domain. To demonstrate the effectiveness of our analysis and visualization, we apply our approach to datasets from solid mechanics and fluid dynamics.

Structural investigation of ternary PdRuM (M = Pt, Rh, or Ir) nanoparticles using first-principles calculations.

We perform first-principles calculations and Monte Carlo sampling to investigate the structures of ternary PdRuM (M = Pt, Rh, or Ir) nanoparticles (NPs) with respect to three different spherical shapes. The morphologies include hexagonal close-packed (hcp), truncated-octahedral (fcc), and icosahedral (Ih, fcc) shapes with 57, 55, and 55 atoms, respectively. The calculations show that the atomic position is dominant in determining the stability of the ternary NPs. For bare ternary NPs, Pd and Ru atoms favor a location on the vertex sites and the core, respectively, which can be understood by the surface energy of the corresponding slab models. For single-crystalline NPs, the binary shell could be either a solid solution or a segregation alloy depending on composition and morphology. However, polycrystalline Ih NPs only form segregated binary shells surrounding the Ru core. Such configurations tend to minimize the surface lattice to gain more energy from the d orbital of the transition metals. In addition to the bare NPs, we study the oxidized ternary NPs. The results show that the Ru atoms penetrate outwards from the core to the surface reducing the oxidation formation energy. Furthermore, oxygen adsorption facilitates Pt, Pd, and Pd penetration into the PdRuPt, PdRuRh, and PdRuIr NPs, respectively. Most of the oxide shells are a solid solution, except for the PdRuRh NP with an Ih shape, which is found to be in a segregation shell. The free energy calculation reveals that the pure hcp NPs are thermodynamically unstable under oxygen-rich conditions. This work clearly demonstrates the structural trends of small ternary NPs and their oxidation, unveiling that the structural trends can be understood by the surface formation energy and the interplay between adsorbent and adsorbing oxygen atoms.

Micrography QR Codes.

This paper presents a novel algorithm to generate micrography QR codes, a novel machine-readable graphic generated by embedding a QR code within a micrography image. The unique structure of micrography makes it incompatible with existing methods used to combine QR codes with natural or halftone images. We exploited the high-frequency nature of micrography in the design of a novel deformation model that enables the skillful warping of individual letters and adjustment of font weights to enable the embedding of a QR code within a micrography. The entire process is supervised by a set of visual quality metrics tailored specifically for micrography, in conjunction with a novel QR code quality measure aimed at striking a balance between visual fidelity and decoding robustness. The proposed QR code quality measure is based on probabilistic models learned from decoding experiments using popular decoders with synthetic QR codes to capture the various forms of distortion that result from image embedding. Experiment results demonstrate the efficacy of the proposed method in generating micrography QR codes of high quality from a wide variety of inputs. The ability to embed QR codes with multiple scales makes it possible to produce a wide range of diverse designs. Experiments and user studies were conducted to evaluate the proposed method from a qualitative as well as quantitative perspective.

Multi-Scale Topological Analysis of Asymmetric Tensor Fields on Surfaces.

Asymmetric tensor fields have found applications in many science and engineering domains, such as fluid dynamics. Recent advances in the visualization and analysis of 2D asymmetric tensor fields focus on pointwise analysis of the tensor field and effective visualization metaphors such as colors, glyphs, and hyperstreamlines. In this paper, we provide a novel multi-scale topological analysis framework for asymmetric tensor fields on surfaces. Our multi-scale framework is based on the notions of eigenvalue and eigenvector graphs. At the core of our framework are the identification of atomic operations that modify the graphs and the scale definition that guides the order in which the graphs are simplified to enable clarity and focus for the visualization of topological analysis on data of different sizes. We also provide efficient algorithms to realize these operations. Furthermore, we provide physical interpretation of these graphs. To demonstrate the utility of our system, we apply our multi-scale analysis to data in computational fluid dynamics.

First-Principles Investigation of the Structure and Properties of Au Nanoparticles Supported on ZnO.

We present a first-principles investigation of the structure, stability, and reactivity of Au nanoparticles (NPs) supported on ZnO. The morphologies of supported Au NPs are predicted using the formation energy of Au surfaces and the adhesion energy between Au and the dominant ZnO surfaces exposed on ZnO tetrapods. We show how Zn interstitials (a stable intrinsic defect in ZnO) are attracted toward the Au/ZnO interface and in the presence of oxygen can lead to the encapsulation of Au by ZnO, an effect that is observed experimentally. We find that O2 molecules absorb preferentially at the perimeter of the NP in contact with the ZnO support. These results provide atomistic insight into the structure of ZnO-supported Au NPs with relevance to CO oxidation.

Gold-nanoparticle-based fluorescent "turn-on" sensor for selective and sensitive detection of dimethoate.

A simple approach to fabricate a highly selective and sensitive dimethoate probe was developed based on Rhodamine B (RB)-functionalized gold nanoparticles (AuNPs). The quenching of RB fluorescence in the presence of AuNPs in the solution, mediated by fluorescence resonance energy transfer, was observed. In the presence of dimethoate, the fluorescence intensity of the RB-AuNP solution is gradually recovered when dimethoate molecules displace RB molecules on the surface of the AuNPs, which significantly increased the fluorescence intensity of RB. Fluorescence is proportional to the dimethoate concentration in the range of 0.005-1.0 ppm (R2 = 0.989), and the LOD was 0.004 ppm. The recoveries of dimethoate in water and fruit samples were 86-116% with a good RSD (< 9.3%). Because of its high sensitivity, excellent selectivity, and convenient fabrication process, this method is a promising candidate for dimethoate screening.

Exposure of mass-selected bimetallic Pt-Ti nanoalloys to oxygen explored using scanning transmission electron microscopy and density functional theory.

The response of nanoparticles to exposure to ambient conditions and especially oxidation is fundamental to the application of nanotechnology. Bimetallic platinum-titanium nanoparticles of selected mass, 30 kDa and 90 kDa, were produced using a magnetron sputtering gas condensation cluster source and deposited onto amorphous carbon TEM grids. The nanoparticles were analysed with a Cs-corrected Scanning Transmission Electron Microscope (STEM) in High Angle Annular Dark Field (HAADF) mode. It was observed that prior to full Ti oxidation, Pt atoms were dispersed within a Ti shell. However, after full oxidation by prolonged exposure to ambient conditions prior to STEM, the smaller size 30 kDa particles form a single Pt core and the larger size 90 kDa particles exhibit a multi-core structure. Electron beam annealing induced a single core morphology in the larger particles. First principles density functional theory (DFT) calculations were employed to calculate the lowest energy structure of the Pt-Ti nanoparticles with and without the presence of oxygen. It was demonstrated that, as the concentration of oxygen increases, the lowest energy structure changes from dispersed Pt to multiple Pt cores and finally a single Pt core, which is in good agreement with the experimental observations.

Doxycycline potentiates antitumor effect of 5-aminolevulinic acid-mediated photodynamic therapy in malignant peripheral nerve sheath tumor cells.

Neurofibromatosis type 1 (NF1) is one of the most common neurocutaneous disorders. Some NF1 patients develop benign large plexiform neurofibroma(s) at birth, which can then transform into a malignant peripheral nerve sheath tumor (MPNST). There is no curative treatment for this rapidly progressive and easily metastatic neurofibrosarcoma. Photodynamic therapy (PDT) has been developed as an anti-cancer treatment, and 5-aminolevulinic (ALA) mediated PDT (ALA-PDT) has been used to treat cutaneous skin and oral neoplasms. Doxycycline, a tetracycline derivative, can substantially reduce the tumor burden in human and animal models, in addition to its antimicrobial effects. The purpose of this study was to evaluate the effect and to investigate the mechanism of action of combined doxycycline and ALA-PDT treatment of MPNST cells. An 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay showed that the combination of ALA-PDT and doxycycline significantly reduce MPNST survival rate, compared to cells treated with each therapy alone. Isobologram analysis showed that the combined treatment had a synergistic effect. The increased cytotoxic activity could be seen by an increase in cellular protoporphyrin IX (PpIX) accumulation. Furthermore, we found that the higher retention of PpIX was mainly due to increasing ALA uptake, rather than activity changes of the enzymes porphobilinogen deaminase and ferrochelatase. The combined treatment inhibited tumor growth in different tumor cell lines, but not in normal human Schwann cells or fibroblasts. Similarly, a synergistic interaction was also found in cells treated with ALA-PDT combined with minocycline, but not tetracycline. In summary, doxycycline can potentiate the effect of ALA-PDT to kill tumor cells. This increased potency allows for a dose reduction of doxycycline and photodynamic radiation, reducing the occurrence of toxic side effects in vivo.

Manga Vectorization and Manipulation with Procedural Simple Screentone.

Manga are a popular artistic form around the world, and artists use simple line drawing and screentone to create all kinds of interesting productions. Vectorization is helpful to digitally reproduce these elements for proper content and intention delivery on electronic devices. Therefore, this study aims at transforming scanned Manga to a vector representation for interactive manipulation and real-time rendering with arbitrary resolution. Our system first decomposes the patch into rough Manga elements including possible borders and shading regions using adaptive binarization and screentone detector. We classify detected screentone into simple and complex patterns: our system extracts simple screentone properties for refining screentone borders, estimating lighting, compensating missing strokes inside screentone regions, and later resolution independently rendering with our procedural shaders. Our system treats the others as complex screentone areas and vectorizes them with our proposed line tracer which aims at locating boundaries of all shading regions and polishing all shading borders with the curve-based Gaussian refiner. A user can lay down simple scribbles to cluster Manga elements intuitively for the formation of semantic components, and our system vectorizes these components into shading meshes along with embedded Bézier curves as a unified foundation for consistent manipulation including pattern manipulation, deformation, and lighting addition. Our system can real-time and resolution independently render the shading regions with our procedural shaders and drawing borders with the curve-based shader. For Manga manipulation, the proposed vector representation can be not only magnified without artifacts but also deformed easily to generate interesting results.

Real-time remote control of artificial cilia actuation using fingertip drawing for efficient micromixing.

Low-efficiency diffusion mechanism poses a significant barrier to the enhancement of micromixing efficiency in microfluidics. Actuating artificial cilia to increase the contact area of two flow streams during micromixing provides a promising alternative to enhance the mixing performance. Real-time adjustment of beating behavior in artificial cilia is necessary to accommodate various biological/chemical reagents with different hydrodynamic properties that are processed in a single microfluidic platform during micromixing. Equipping the microfluidic device with a self-troubleshooting feature for the end user, such as a bubble removal function during the process of multiple chemical solution injections, is also essential for robust micromixing. To meet these requirements, we initiated a new beating control concept by controlling the beating behavior of the artificial cilia through remote and simultaneous actuation of human fingertip drawing. A series of micromixing test cases under extreme flow conditions (Re < 10(-3)) was conducted in the designed micromixer with high mixing performance. Satisfactory micromixing efficiency was achieved even with a rapid beating trajectory of the artificial cilia actuated through the fingertip motion of end users. The analytical paradigm and results allow end users to troubleshoot technical difficulties encountered during micromixing operations.