@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 = {24699934}, 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{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}, journal = {Genome Research}, number = {7}, pages = {1115--1122}, publisher = {CSH 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 = {00092673}, 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{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}, } @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 Press}, title = {{Efficiency guarantees for parallel incremental algorithms under relaxed schedulers}}, doi = {10.1145/3323165.3323201}, year = {2019}, } @inproceedings{6676, abstract = {It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.}, author = {Alistarh, Dan-Adrian and Aspnes, James and Ellen, Faith and Gelashvili, Rati and Zhu, Leqi}, booktitle = {Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing}, isbn = {9781450367059}, location = {Phoenix, AZ, United States}, pages = {986--996}, publisher = {ACM Press}, title = {{Why extension-based proofs fail}}, doi = {10.1145/3313276.3316407}, year = {2019}, } @inproceedings{6677, abstract = {The Fiat-Shamir heuristic transforms a public-coin interactive proof into a non-interactive argument, by replacing the verifier with a cryptographic hash function that is applied to the protocol’s transcript. Constructing hash functions for which this transformation is sound is a central and long-standing open question in cryptography. We show that solving the END−OF−METERED−LINE problem is no easier than breaking the soundness of the Fiat-Shamir transformation when applied to the sumcheck protocol. In particular, if the transformed protocol is sound, then any hard problem in #P gives rise to a hard distribution in the class CLS, which is contained in PPAD. Our result opens up the possibility of sampling moderately-sized games for which it is hard to find a Nash equilibrium, by reducing the inversion of appropriately chosen one-way functions to #SAT. Our main technical contribution is a stateful incrementally verifiable procedure that, given a SAT instance over n variables, counts the number of satisfying assignments. This is accomplished via an exponential sequence of small steps, each computable in time poly(n). Incremental verifiability means that each intermediate state includes a sumcheck-based proof of its correctness, and the proof can be updated and verified in time poly(n).}, author = {Choudhuri, Arka Rai and Hubáček, Pavel and Kamath Hosdurg, Chethan and Pietrzak, Krzysztof Z and Rosen, Alon and Rothblum, Guy N.}, booktitle = {Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019}, isbn = {9781450367059}, location = {Phoenix, AZ, United States}, pages = {1103--1114}, publisher = {ACM Press}, title = {{Finding a Nash equilibrium is no easier than breaking Fiat-Shamir}}, doi = {10.1145/3313276.3316400}, year = {2019}, } @article{6680, abstract = {This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.}, author = {Sachdeva, Himani}, issn = {1558-5646}, journal = {Evolution}, number = {9}, pages = {1729--1745}, publisher = {Wiley}, title = {{Effect of partial selfing and polygenic selection on establishment in a new habitat}}, doi = {10.1111/evo.13812}, volume = {73}, year = {2019}, } @phdthesis{6681, abstract = {The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2. However, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2, we construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X). In the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space.}, author = {Zhechev, Stephan Y}, issn = {2663-337X}, pages = {104}, publisher = {Institute of Science and Technology Austria}, title = {{Algorithmic aspects of homotopy theory and embeddability}}, doi = {10.15479/AT:ISTA:6681}, year = {2019}, } @article{6710, abstract = {Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species.}, author = {Cossard, Guillaume and Toups, Melissa A and Pannell, John }, issn = {1095-8290}, journal = {Annals of botany}, number = {7}, pages = {1119--1131}, publisher = {Oxford University Press}, title = {{Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb}}, doi = {10.1093/aob/mcy183}, volume = {123}, year = {2019}, } @article{6713, abstract = {Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.}, author = {Castro, João Pl and Yancoskie, Michelle N. and Marchini, Marta and Belohlavy, Stefanie and Hiramatsu, Layla and Kučka, Marek and Beluch, William H. and Naumann, Ronald and Skuplik, Isabella and Cobb, John and Barton, Nicholas H and Rolian, Campbell and Chan, Yingguang Frank}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice}}, doi = {10.7554/eLife.42014}, volume = {8}, year = {2019}, }