Structural and optical properties of amorphous Si–Ge–Te thin films prepared by combinatorial sputtering

The lack of order in amorphous chalcogenides offers them novel properties but also adds increased challenges in the discovery and design of advanced functional materials. The amorphous compositions in the Si–Ge–Te system are of interest for many applications such as optical data storage, optical sensors and Ovonic threshold switches. But an extended exploration of this system is still missing. In this study, magnetron co-sputtering is used for the combinatorial synthesis of thin film libraries, outside the glass formation domain. Compositional, structural and optical properties are investigated and discussed in the framework of topological constraint theory. The materials in the library are classified as stressed-rigid amorphous networks. The bandgap is heavily influenced by the Te content while the near-IR refractive index dependence on Ge concentration shows a minimum, which could be exploited in applications. A transition from a disordered to a more ordered amorphous network at 60 at% Te, is observed. The thermal stability study shows that the formed crystalline phases are dictated by the concentration of Ge and Te. New amorphous compositions in the Si–Ge–Te system were found and their properties explored, thus enabling an informed and rapid material selection and design for applications.

Keeping it together: A phase-field version of path-connectedness and its implementation

We describe the implementation of a topological constraint in finite-element simulations of phase-field models, which ensures path-connectedness of preimages of intervals in the phase-field variable. The constraint takes the form of an energetic penalty for a suitable geodesic distance between all pairs of points in the domain. The main application of our method presented here is a discrete steepest descent of a phase-field version of a bending energy with spontaneous curvature and additional surface area penalty. This leads to disconnected surfaces without our topological constraint but connected surfaces with the constraint. Numerically, our constraint is treated by first transforming the double integral over all pairs of points in the domain to a weighted graph structure and then using Dijkstra’s algorithm to calculate the distance between discrete connected components.

Abstract 17379: Relationship Between Myocyte Branching and Location Within Myocardial Sheetlet

Introduction: Cardiomyocytes form a continuously branching syncytium that also form sheetlets four to six cells thick. Myocytes and sheetlets have essential structural and functional roles, but descriptions of their complex branching structure are limited. Herein, we characterize the branching structure of cardiomyocytes within a myocardial sheetlet segment. Hypothesis: Due to topological constraints, cardiomyocytes on the sheetlet surfaces branch within the fiber-sheetlet plane more than myocytes on the interior of the sheetlet. Methods: Rodent myocardium was stained for collagen and the left ventricular free wall was imaged using extended volume confocal microscopy (0.4 μm 3 voxel size), a and sheetlet portion segmented (146 х 214 х 339 μm 3 , approx. 5 by 10 by 3 cells). The centerline of each myocyte was tracked, with branch-points identified where the cell bodies of adjacent cardiomyocytes merge. This produced a connected network (Figure) with five cell-layers along the normal axis: lower surface, lower interior, middle interior, upper interior, and upper surface. Results: The cardiomyocyte branching frequency varied between cell-layers (Figure); the sheetlet-surface cell-layers branched within their own cell-layer more frequently than myocytes in the sheetlet interior (0.28 vs 0.11 branches per 100 μm). Cardiomyocytes on the sheetlet surface also branched less frequently with cardiomyocytes of a different cell-layer, compared with cardiomyocytes in the sheetlet interior (0.31 vs 0.67 branches per 100 μm). Cardiomyocytes in the middle interior cell-layer had the highest number of branches between cell-layers (0.86 per 100 μm), and the lowest number of branches within their own cell-layer (0.03 per 100 μm). Conclusion: Analysis of confocal images revealed differences in cardiomyocyte branching between cell-layers of a sheetlet segment, and confirmed that sheetlet boundaries provide a topological constraint for cardiomyocyte branching.

Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference

The empirical details of whole transcriptome sequencing and assembly have been thoroughly evaluated, but few studies have addressed how user-defined aspects of the assembly process may influence performance in phylogenomic analyses. Errors in transcriptome assembly could affect ortholog prediction, alignment quality, and phylogenetic signal. Here we investigate the impacts of transcriptome assembly quality in phylogenomic studies by constructing phylogenomic data matrices from alternative transcriptome assemblies representing high-quality and intentionally low-quality assembly outcomes. We leveraged a well-resolved topology for craniates to apply a topological constraint to our analyses, providing a way to quantify phylogenetic signal. Craniates are amply represented in publicly available raw RNA-seq repositories, allowing us to control for transcriptome tissue type as well. By studying the performance of phylogenomic datasets derived from these alternative high- and low-quality inputs in a controlled experiment, we show that high-quality transcriptomes produce richer phylogenomic datasets with partitions that have lower alignment ambiguity, less compositional bias, and stronger phylogenetic signal than low-quality transcriptome assemblies. Our findings demonstrate the importance of transcriptome assembly in phylogenomic analyses and suggest that a portion of the uncertainty observed in phylogenomic studies could be alleviated at the assembly stage.

Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.

Structure Dependence of Poisson’s Ratio in Cesium Silicate and Borate Glasses

In glass materials, Poisson’s ratio (ν) has been proposed to be correlated with a variety of features, including atomic packing density (Cg), liquid fragility (m), and network connectivity. To further investigate these correlations in oxide glasses, here, we study cesium borate and cesium silicate glasses with varying modifier/former ratio given the difference in network former coordination and because cesium results in relatively high ν compared to the smaller alkali modifiers. Within the binary glass series, we find positive correlations between ν on one hand and m and Cg on the other hand. The network former is found to greatly influence the correlation between ν and the number of bridging oxygens (nBO), with a negative correlation for silicate glasses and positive correlation for borate glasses. An analysis based on topological constraint theory shows that this difference cannot be explained by the effect of superstructural units on the network connectivity in lithium borate glasses. Considering a wider range of oxide glasses from the literature, we find that ν generally decreases with increasing network connectivity, but with notable exceptions for heavy alkali borate glasses and calcium alumino tectosilicate glasses.