@inproceedings{6628, abstract = {Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space.}, author = {Vegter, Gert and Wintraecken, Mathijs}, booktitle = {The 31st Canadian Conference in Computational Geometry}, location = {Edmonton, Canada}, pages = {275--279}, title = {{The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds}}, year = {2019}, } @article{6631, abstract = {The spatiotemporal organization of cell divisions constitutes an integral part in the development of multicellular organisms, and mis-regulation of cell divisions can lead to severe developmental defects. Cell divisions have an important morphogenetic function in development by regulating growth and shape acquisition of developing tissues, and, conversely, tissue morphogenesis is known to affect both the rate and orientation of cell divisions. Moreover, cell divisions are associated with an extensive reorganization of the cytoskeleton and adhesion apparatus in the dividing cells that in turn can affect large-scale tissue rheological properties. Thus, the interplay between cell divisions and tissue morphogenesis plays a key role in embryo and tissue morphogenesis.}, author = {Godard, Benoit G and Heisenberg, Carl-Philipp J}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, pages = {114--120}, publisher = {Elsevier}, title = {{Cell division and tissue mechanics}}, doi = {10.1016/j.ceb.2019.05.007}, volume = {60}, year = {2019}, } @article{6632, abstract = {We consider a two-component Bose gas in two dimensions at a low temperature with short-range repulsive interaction. In the coexistence phase where both components are superfluid, interspecies interactions induce a nondissipative drag between the two superfluid flows (Andreev-Bashkin effect). We show that this behavior leads to a modification of the usual Berezinskii-Kosterlitz-Thouless (BKT) transition in two dimensions. We extend the renormalization of the superfluid densities at finite temperature using the renormalization-group approach and find that the vortices of one component have a large influence on the superfluid properties of the other, mediated by the nondissipative drag. The extended BKT flow equations indicate that the occurrence of the vortex unbinding transition in one of the components can induce the breakdown of superfluidity also in the other, leading to a locking phenomenon for the critical temperatures of the two gases.}, author = {Karle, Volker and Defenu, Nicolò and Enss, Tilman}, issn = {2469-9934}, journal = {Physical Review A}, number = {6}, publisher = {American Physical Society}, title = {{Coupled superfluidity of binary Bose mixtures in two dimensions}}, doi = {10.1103/PhysRevA.99.063627}, volume = {99}, year = {2019}, } @article{6634, abstract = {In this paper we prove several new results around Gromov's waist theorem. We give a simple proof of Vaaler's theorem on sections of the unit cube using the Borsuk-Ulam-Crofton technique, consider waists of real and complex projective spaces, flat tori, convex bodies in Euclidean space; and establish waist-type results in terms of the Hausdorff measure.}, author = {Akopyan, Arseniy and Hubard, Alfredo and Karasev, Roman}, journal = {Topological Methods in Nonlinear Analysis}, number = {2}, pages = {457--490}, publisher = {Akademicka Platforma Czasopism}, title = {{Lower and upper bounds for the waists of different spaces}}, doi = {10.12775/TMNA.2019.008}, volume = {53}, year = {2019}, } @article{6637, abstract = {The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.}, author = {Trubenova, Barbora and Krejca, Martin and Lehre, Per Kristian and Kötzing, Timo}, journal = {Evolution}, number = {7}, pages = {1356--1374}, publisher = {Wiley}, title = {{Surfing on the seascape: Adaptation in a changing environment}}, doi = {10.1111/evo.13784}, volume = {73}, year = {2019}, } @article{6638, abstract = {The crossing number of a graph G is the least number of crossings over all possible drawings of G. We present a structural characterization of graphs with crossing number one.}, author = {Silva, André and Arroyo Guevara, Alan M and Richter, Bruce and Lee, Orlando}, issn = {0012-365X}, journal = {Discrete Mathematics}, number = {11}, pages = {3201--3207}, publisher = {Elsevier}, title = {{Graphs with at most one crossing}}, doi = {10.1016/j.disc.2019.06.031}, volume = {342}, year = {2019}, } @inproceedings{6642, abstract = {We present a thermodynamically based approach to the design of models for viscoelastic fluids with stress diffusion effect. In particular, we show how to add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus, FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that the resulting models with the added stress diffusion term are thermodynamically consistent in the sense that they obey the first and the second law of thermodynamics. We point out the potential applications of the provided thermodynamical background in the study of flows of fluids described by the proposed models.}, author = {Dostalík, Mark and Pruša, Vít and Skrivan, Tomas}, booktitle = {AIP Conference Proceedings}, location = {Zlin, Czech Republic}, publisher = {AIP Publishing}, title = {{On diffusive variants of some classical viscoelastic rate-type models}}, doi = {10.1063/1.5109493}, volume = {2107}, year = {2019}, } @inproceedings{6646, abstract = {We demonstrate robust retention of valley coherence and its control via polariton pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity exciton polaritons at room temperature.}, author = {Khatoniar, Mandeep and Yama, Nicholas and Ghazaryan, Areg and Guddala, Sriram and Ghaemi, Pouyan and Menon, Vinod}, booktitle = {CLEO: Applications and Technology}, isbn = {9781943580576}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Room temperature control of valley coherence in bilayer WS2 exciton polaritons}}, doi = {10.1364/cleo_at.2019.jtu2a.52}, year = {2019}, } @inproceedings{6647, abstract = {The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2.}, author = {Fulek, Radoslav and Gärtner, Bernd and Kupavskii, Andrey and Valtr, Pavel and Wagner, Uli}, booktitle = {35th International Symposium on Computational Geometry}, isbn = {9783959771047}, issn = {1868-8969}, location = {Portland, OR, United States}, pages = {38:1--38:13}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The crossing Tverberg theorem}}, doi = {10.4230/LIPICS.SOCG.2019.38}, volume = {129}, year = {2019}, } @inproceedings{6648, abstract = {Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.}, author = {Edelsbrunner, Herbert and Virk, Ziga and Wagner, Hubert}, booktitle = {35th International Symposium on Computational Geometry}, isbn = {9783959771047}, location = {Portland, OR, United States}, pages = {31:1--31:14}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Topological data analysis in information space}}, doi = {10.4230/LIPICS.SOCG.2019.31}, volume = {129}, year = {2019}, } @article{6650, abstract = {We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry.}, author = {Alderighi, Thomas and Malomo, Luigi and Giorgi, Daniela and Bickel, Bernd and Cignoni, Paolo and Pietroni, Nico}, issn = {0730-0301}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Volume-aware design of composite molds}}, doi = {10.1145/3306346.3322981}, volume = {38}, year = {2019}, } @article{6657, abstract = {In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as "gold" and "green" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising.}, author = {Danowski, Patrick}, issn = {1022-2588}, journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, number = {1}, pages = {59--65}, publisher = {Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, title = {{An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors}}, doi = {10.31263/voebm.v72i1.2276}, volume = {72}, year = {2019}, } @article{6658, abstract = {New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. }, author = {Raices, Julia and Otto, Paulo and Vibranovski, Maria}, issn = { 1549-5469}, journal = {Genome Research}, number = {7}, pages = {1115--1122}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Haploid selection drives new gene male germline expression}}, doi = {10.1101/gr.238824.118}, volume = {29}, year = {2019}, } @article{6659, abstract = {Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research.}, author = {Zenmyo, Naoki and Tokumaru, Hiroki and Uchinomiya, Shohei and Fuchida, Hirokazu and Tabata, Shigekazu and Hamachi, Itaru and Shigemoto, Ryuichi and Ojida, Akio}, issn = {0009-2673}, journal = {Bulletin of the Chemical Society of Japan}, number = {5}, pages = {995--1000}, publisher = {Bulletin of the Chemical Society of Japan}, title = {{Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins}}, doi = {10.1246/bcsj.20190034}, volume = {92}, year = {2019}, } @article{6660, abstract = {Commercially available full-color 3D printing allows for detailed control of material deposition in a volume, but an exact reproduction of a target surface appearance is hampered by the strong subsurface scattering that causes nontrivial volumetric cross-talk at the print surface. Previous work showed how an iterative optimization scheme based on accumulating absorptive materials at the surface can be used to find a volumetric distribution of print materials that closely approximates a given target appearance. In this work, we first revisit the assumption that pushing the absorptive materials to the surface results in minimal volumetric cross-talk. We design a full-fledged optimization on a small domain for this task and confirm this previously reported heuristic. Then, we extend the above approach that is critically limited to color reproduction on planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color texture reproduction on 3D prints by effectively compensating for internal light scattering within arbitrarily shaped objects. In addition, we propose a content-aware gamut mapping that significantly improves color reproduction for the pathological case of thin geometric features. Using a wide range of sample objects with complex textures and geometries, we demonstrate color reproduction whose fidelity is superior to state-of-the-art drivers for color 3D printers.}, author = {Sumin, Denis and Weyrich, Tim and Rittig, Tobias and Babaei, Vahid and Nindel, Thomas and Wilkie, Alexander and Didyk, Piotr and Bickel, Bernd and Křivánek, Jaroslav and Myszkowski, Karol}, issn = {0730-0301}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Geometry-aware scattering compensation for 3D printing}}, doi = {10.1145/3306346.3322992}, volume = {38}, year = {2019}, } @article{6662, abstract = {In phase retrieval, we want to recover an unknown signal 𝑥∈ℂ𝑑 from n quadratic measurements of the form 𝑦𝑖=|⟨𝑎𝑖,𝑥⟩|2+𝑤𝑖, where 𝑎𝑖∈ℂ𝑑 are known sensing vectors and 𝑤𝑖 is measurement noise. We ask the following weak recovery question: What is the minimum number of measurements n needed to produce an estimator 𝑥^(𝑦) that is positively correlated with the signal 𝑥? We consider the case of Gaussian vectors 𝑎𝑎𝑖. We prove that—in the high-dimensional limit—a sharp phase transition takes place, and we locate the threshold in the regime of vanishingly small noise. For 𝑛≤𝑑−𝑜(𝑑), no estimator can do significantly better than random and achieve a strictly positive correlation. For 𝑛≥𝑑+𝑜(𝑑), a simple spectral estimator achieves a positive correlation. Surprisingly, numerical simulations with the same spectral estimator demonstrate promising performance with realistic sensing matrices. Spectral methods are used to initialize non-convex optimization algorithms in phase retrieval, and our approach can boost the performance in this setting as well. Our impossibility result is based on classical information-theoretic arguments. The spectral algorithm computes the leading eigenvector of a weighted empirical covariance matrix. We obtain a sharp characterization of the spectral properties of this random matrix using tools from free probability and generalizing a recent result by Lu and Li. Both the upper bound and lower bound generalize beyond phase retrieval to measurements 𝑦𝑖 produced according to a generalized linear model. As a by-product of our analysis, we compare the threshold of the proposed spectral method with that of a message passing algorithm.}, author = {Mondelli, Marco and Montanari, Andrea}, issn = {1615-3383}, journal = {Foundations of Computational Mathematics}, number = {3}, pages = {703--773}, publisher = {Springer}, title = {{Fundamental limits of weak recovery with applications to phase retrieval}}, doi = {10.1007/s10208-018-9395-y}, volume = {19}, year = {2019}, } @article{6663, abstract = {Consider the problem of constructing a polar code of block length N for a given transmission channel W. Previous approaches require one to compute the reliability of the N synthetic channels and then use only those that are sufficiently reliable. However, we know from two independent works by Schürch and by Bardet et al. that the synthetic channels are partially ordered with respect to degradation. Hence, it is natural to ask whether the partial order can be exploited to reduce the computational burden of the construction problem. We show that, if we take advantage of the partial order, we can construct a polar code by computing the reliability of roughly a fraction 1/ log 3/2 N of the synthetic channels. In particular, we prove that N/ log 3/2 N is a lower bound on the number of synthetic channels to be considered and such a bound is tight up to a multiplicative factor log log N. This set of roughly N/ log 3/2 N synthetic channels is universal, in the sense that it allows one to construct polar codes for any W, and it can be identified by solving a maximum matching problem on a bipartite graph. Our proof technique consists of reducing the construction problem to the problem of computing the maximum cardinality of an antichain for a suitable partially ordered set. As such, this method is general, and it can be used to further improve the complexity of the construction problem, in case a refined partial order on the synthetic channels of polar codes is discovered.}, author = {Mondelli, Marco and Hassani, Hamed and Urbanke, Rudiger}, journal = {IEEE}, number = {5}, pages = {2782--2791}, publisher = {IEEE}, title = {{Construction of polar codes with sublinear complexity}}, doi = {10.1109/tit.2018.2889667}, volume = {65}, year = {2019}, } @article{6671, abstract = {In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.}, author = {Boissonnat, Jean-Daniel and Lieutier, André and Wintraecken, Mathijs}, issn = {2367-1734}, journal = {Journal of Applied and Computational Topology}, number = {1-2}, pages = {29–58}, publisher = {Springer Nature}, title = {{The reach, metric distortion, geodesic convexity and the variation of tangent spaces}}, doi = {10.1007/s41468-019-00029-8}, volume = {3}, year = {2019}, } @article{6672, abstract = {The construction of anisotropic triangulations is desirable for various applications, such as the numerical solving of partial differential equations and the representation of surfaces in graphics. To solve this notoriously difficult problem in a practical way, we introduce the discrete Riemannian Voronoi diagram, a discrete structure that approximates the Riemannian Voronoi diagram. This structure has been implemented and was shown to lead to good triangulations in $\mathbb{R}^2$ and on surfaces embedded in $\mathbb{R}^3$ as detailed in our experimental companion paper. In this paper, we study theoretical aspects of our structure. Given a finite set of points $\mathcal{P}$ in a domain $\Omega$ equipped with a Riemannian metric, we compare the discrete Riemannian Voronoi diagram of $\mathcal{P}$ to its Riemannian Voronoi diagram. Both diagrams have dual structures called the discrete Riemannian Delaunay and the Riemannian Delaunay complex. We provide conditions that guarantee that these dual structures are identical. It then follows from previous results that the discrete Riemannian Delaunay complex can be embedded in $\Omega$ under sufficient conditions, leading to an anisotropic triangulation with curved simplices. Furthermore, we show that, under similar conditions, the simplices of this triangulation can be straightened.}, author = {Boissonnat, Jean-Daniel and Rouxel-Labbé, Mael and Wintraecken, Mathijs}, issn = {1095-7111}, journal = {SIAM Journal on Computing}, number = {3}, pages = {1046--1097}, publisher = {Society for Industrial & Applied Mathematics (SIAM)}, title = {{Anisotropic triangulations via discrete Riemannian Voronoi diagrams}}, doi = {10.1137/17m1152292}, volume = {48}, year = {2019}, } @inproceedings{6673, abstract = {Several classic problems in graph processing and computational geometry are solved via incremental algorithms, which split computation into a series of small tasks acting on shared state, which gets updated progressively. While the sequential variant of such algorithms usually specifies a fixed (but sometimes random) order in which the tasks should be performed, a standard approach to parallelizing such algorithms is to relax this constraint to allow for out-of-order parallel execution. This is the case for parallel implementations of Dijkstra's single-source shortest-paths (SSSP) algorithm, and for parallel Delaunay mesh triangulation. While many software frameworks parallelize incremental computation in this way, it is still not well understood whether this relaxed ordering approach can still provide any complexity guarantees. In this paper, we address this problem, and analyze the efficiency guarantees provided by a range of incremental algorithms when parallelized via relaxed schedulers. We show that, for algorithms such as Delaunay mesh triangulation and sorting by insertion, schedulers with a maximum relaxation factor of k in terms of the maximum priority inversion allowed will introduce a maximum amount of wasted work of O(łog n poly(k)), where n is the number of tasks to be executed. For SSSP, we show that the additional work is O(poly(k), dmax / wmin), where dmax is the maximum distance between two nodes, and wmin is the minimum such distance. In practical settings where n >> k, this suggests that the overheads of relaxation will be outweighed by the improved scalability of the relaxed scheduler. On the negative side, we provide lower bounds showing that certain algorithms will inherently incur a non-trivial amount of wasted work due to scheduler relaxation, even for relatively benign relaxed schedulers.}, author = {Alistarh, Dan-Adrian and Nadiradze, Giorgi and Koval, Nikita}, booktitle = {31st ACM Symposium on Parallelism in Algorithms and Architectures}, isbn = {9781450361842}, location = {Phoenix, AZ, United States}, pages = {145--154}, publisher = {ACM}, title = {{Efficiency guarantees for parallel incremental algorithms under relaxed schedulers}}, doi = {10.1145/3323165.3323201}, year = {2019}, }