@inproceedings{12903, author = {Schlögl, Alois and Stadlbauer, Stephan}, booktitle = {AHPC16 - Austrian HPC Meeting 2016}, location = {Grundlsee, Austria}, pages = {37}, publisher = {VSC - Vienna Scientific Cluster}, title = {{High performance computing at IST Austria: Modelling the human hippocampus}}, year = {2016}, } @article{1291, abstract = {We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than d + 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for p > 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs (d = 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity.}, author = {Giuliani, Alessandro and Seiringer, Robert}, journal = {Communications in Mathematical Physics}, number = {3}, pages = {983 -- 1007}, publisher = {Springer}, title = {{Periodic striped ground states in Ising models with competing interactions}}, doi = {10.1007/s00220-016-2665-0}, volume = {347}, year = {2016}, } @article{1292, abstract = {We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds.}, author = {Durst, Sebastian and Kegel, Marc and Klukas, Mirko D}, journal = {Acta Mathematica Hungarica}, number = {2}, pages = {441 -- 455}, publisher = {Springer}, title = {{Computing the Thurston–Bennequin invariant in open books}}, doi = {10.1007/s10474-016-0648-4}, volume = {150}, year = {2016}, } @article{1293, abstract = {For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry.}, author = {Solus, Liam T and Uhler, Caroline and Yoshida, Ruriko}, journal = {Linear Algebra and Its Applications}, pages = {247 -- 275}, publisher = {Elsevier}, title = {{Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors}}, doi = {10.1016/j.laa.2016.07.026}, volume = {509}, year = {2016}, } @article{1295, abstract = {Voronoi diagrams and Delaunay triangulations have been extensively used to represent and compute geometric features of point configurations. We introduce a generalization to poset diagrams and poset complexes, which contain order-k and degree-k Voronoi diagrams and their duals as special cases. Extending a result of Aurenhammer from 1990, we show how to construct poset diagrams as weighted Voronoi diagrams of average balls.}, author = {Edelsbrunner, Herbert and Iglesias Ham, Mabel}, journal = {Electronic Notes in Discrete Mathematics}, pages = {169 -- 174}, publisher = {Elsevier}, title = {{Multiple covers with balls II: Weighted averages}}, doi = {10.1016/j.endm.2016.09.030}, volume = {54}, year = {2016}, } @article{1303, abstract = {In bright light, cone-photoreceptors are active and colour vision derives from a comparison of signals in cones with different visual pigments. This comparison begins in the retina, where certain retinal ganglion cells have 'colour-opponent' visual responses-excited by light of one colour and suppressed by another colour. In dim light, rod-photoreceptors are active, but colour vision is impossible because they all use the same visual pigment. Instead, the rod signals are thought to splice into retinal circuits at various points, in synergy with the cone signals. Here we report a new circuit for colour vision that challenges these expectations. A genetically identified type of mouse retinal ganglion cell called JAMB (J-RGC), was found to have colour-opponent responses, OFF to ultraviolet (UV) light and ON to green light. Although the mouse retina contains a green-sensitive cone, the ON response instead originates in rods. Rods and cones both contribute to the response over several decades of light intensity. Remarkably, the rod signal in this circuit is antagonistic to that from cones. For rodents, this UV-green channel may play a role in social communication, as suggested by spectral measurements from the environment. In the human retina, all of the components for this circuit exist as well, and its function can explain certain experiences of colour in dim lights, such as a 'blue shift' in twilight. The discovery of this genetically defined pathway will enable new targeted studies of colour processing in the brain.}, author = {Maximilian Jösch and Meister, Markus}, journal = {Nature}, number = {7598}, pages = {236 -- 239}, publisher = {Nature Publishing Group}, title = {{A neuronal circuit for colour vision based on rod-cone opponency}}, doi = {10.1038/nature17158}, volume = {532}, year = {2016}, } @misc{9704, abstract = {Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.}, author = {Mcmahon, Dino and Natsopoulou, Myrsini and Doublet, Vincent and Fürst, Matthias and Weging, Silvio and Brown, Mark and Gogol Döring, Andreas and Paxton, Robert}, publisher = {Dryad}, title = {{Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss}}, doi = {10.5061/dryad.cq7t1}, year = {2016}, } @misc{9710, abstract = {Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.}, author = {Barton, Nicholas H}, publisher = {Dryad}, title = {{Data from: How does epistasis influence the response to selection?}}, doi = {10.5061/dryad.s5s7r}, year = {2016}, } @misc{9720, abstract = {Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.}, author = {Mcmahon, Dino and Fürst, Matthias and Caspar, Jesicca and Theodorou, Panagiotis and Brown, Mark and Paxton, Robert}, publisher = {Dryad}, title = {{Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees}}, doi = {10.5061/dryad.4b565}, year = {2016}, } @article{983, abstract = {The half-filled Landau level is expected to be approximately particle-hole symmetric, which requires an extension of the Halperin-Lee-Read (HLR) theory of the compressible state observed at this filling. Recent work indicates that, when particle-hole symmetry is preserved, the composite fermions experience a quantized π-Berry phase upon winding around the composite Fermi surface, analogous to Dirac fermions at the surface of a 3D topological insulator. In contrast, the effective low-energy theory of the composite fermion liquid originally proposed by HLR lacks particle-hole symmetry and has vanishing Berry phase. In this paper, we explain how thermoelectric transport measurements can be used to test the Dirac nature of the composite fermions by quantitatively extracting this Berry phase. First, we point out that longitudinal thermopower (Seebeck effect) is nonvanishing because of the unusual nature of particle-hole symmetry in this context and is not sensitive to the Berry phase. In contrast, we find that off-diagonal thermopower (Nernst effect) is directly related to the topological structure of the composite Fermi surface, vanishing for zero Berry phase and taking its maximal value for π Berry phase. In contrast, in purely electrical transport signatures, the Berry phase contributions appear as small corrections to a large background signal, making the Nernst effect a promising diagnostic of the Dirac nature of composite fermions.}, author = {Potter, Andrew C and Maksym Serbyn and Vishwanath, Ashvin K}, journal = {Physical Review X}, number = {3}, publisher = {American Physical Society}, title = {{Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level}}, doi = {10.1103/PhysRevX.6.031026}, volume = {6}, year = {2016}, } @article{984, abstract = {The entanglement spectrum of the reduced density matrix contains information beyond the von Neumann entropy and provides unique insights into exotic orders or critical behavior of quantum systems. Here, we show that strongly disordered systems in the many-body localized phase have power-law entanglement spectra, arising from the presence of extensively many local integrals of motion. The power-law entanglement spectrum distinguishes many-body localized systems from ergodic systems, as well as from ground states of gapped integrable models or free systems in the vicinity of scale-invariant critical points. We confirm our results using large-scale exact diagonalization. In addition, we develop a matrix-product state algorithm which allows us to access the eigenstates of large systems close to the localization transition, and discuss general implications of our results for variational studies of highly excited eigenstates in many-body localized systems.}, author = {Maksym Serbyn and Alexios Michailidis and Abanin, Dmitry A and Papić, Zlatko}, journal = {Physical Review Letters}, number = {16}, publisher = {American Physical Society}, title = {{Power-law entanglement spectrum in many-body localized phases}}, doi = {10.1103/PhysRevLett.117.160601}, volume = {117}, year = {2016}, } @article{985, abstract = {We report on magnetotransport studies of dual-gated, Bernal-stacked trilayer graphene (TLG) encapsulated in boron nitride crystals. We observe a quantum Hall effect staircase which indicates a complete lifting of the 12-fold degeneracy of the zeroth Landau level. As a function of perpendicular electric field, our data exhibit a sequence of phase transitions between all integer quantum Hall states in the filling factor interval -8<ν<0. We develop a theoretical model and argue that, in contrast to monolayer and bilayer graphene, the observed Landau level splittings and quantum Hall phase transitions can be understood within a single-particle picture, but imply the presence of a charge density imbalance between the inner and outer layers of TLG, even at charge neutrality and zero transverse electric field. Our results indicate the importance of a previously unaccounted band structure parameter which, together with a more accurate estimate of the other tight-binding parameters, results in a significantly improved determination of the electronic and Landau level structure of TLG.}, author = {Campos, Leonardo C and Taychatanapat, Thiti and Maksym Serbyn and Surakitbovorn, Kawin N and Watanabe, Kenji and Taniguchi, Takashi and Abanin, Dmitry A and Jarillo-Herrero, Pablo}, journal = {Physical Review Letters}, number = {6}, publisher = {American Physical Society}, title = {{Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene}}, doi = {10.1103/PhysRevLett.117.066601}, volume = {117}, year = {2016}, } @article{986, abstract = {The many-body localization transition (MBLT) between ergodic and many-body localized phases in disordered interacting systems is a subject of much recent interest. The statistics of eigenenergies is known to be a powerful probe of crossovers between ergodic and integrable systems in simpler examples of quantum chaos. We consider the evolution of the spectral statistics across the MBLT, starting with mapping to a Brownian motion process that analytically relates the spectral properties to the statistics of matrix elements. We demonstrate that the flow from Wigner-Dyson to Poisson statistics is a two-stage process. First, a fractal enhancement of matrix elements upon approaching the MBLT from the delocalized side produces an effective power-law interaction between energy levels, and leads to a plasma model for level statistics. At the second stage, the gas of eigenvalues has local interactions and the level statistics belongs to a semi-Poisson universality class. We verify our findings numerically on the XXZ spin chain. We provide a microscopic understanding of the level statistics across the MBLT and discuss implications for the transition that are strong constraints on possible theories.}, author = {Maksym Serbyn and Moore, Joel E}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {4}, publisher = {American Physical Society}, title = {{Spectral statistics across the many-body localization transition}}, doi = {10.1103/PhysRevB.93.041424}, volume = {93}, year = {2016}, } @misc{9862, author = {Roux, Camille and Fraisse, Christelle and Romiguier, Jonathan and Anciaux, Youann and Galtier, Nicolas and Bierne, Nicolas}, publisher = {Public Library of Science}, title = {{Simulation study to test the robustness of ABC in face of recent times of divergence}}, doi = {10.1371/journal.pbio.2000234.s016}, year = {2016}, } @misc{9863, author = {Roux, Camille and Fraisse, Christelle and Romiguier, Jonathan and Anciaux, Youann and Galtier, Nicolas and Bierne, Nicolas}, publisher = {Public Library of Science}, title = {{Accessions of surveyed individuals, geographic locations and summary statistics}}, doi = {10.1371/journal.pbio.2000234.s017}, year = {2016}, } @misc{9864, abstract = {Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.}, author = {Fernandes Redondo, Rodrigo A and de Vladar, Harold and Włodarski, Tomasz and Bollback, Jonathan P}, publisher = {The Royal Society}, title = {{Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family}}, doi = {10.6084/m9.figshare.4315652.v1}, year = {2016}, } @misc{9866, author = {Zagórski, Marcin P and Burda, Zdzisław and Wacław, Bartłomiej}, publisher = {Public Library of Science}, title = {{ZIP-archived directory containing all data and computer programs}}, doi = {10.1371/journal.pcbi.1005218.s009}, year = {2016}, } @misc{9867, abstract = {In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German.}, author = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred}, publisher = {Public Library of Science}, title = {{Experimental game instructions}}, doi = {10.1371/journal.pone.0163867.s008}, year = {2016}, } @misc{9868, abstract = {The raw data file containing the experimental decisions of all our study subjects.}, author = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred}, publisher = {Public Library of Science}, title = {{Experimental data}}, doi = {10.1371/journal.pone.0163867.s009}, year = {2016}, } @misc{9869, abstract = {A lower bound on the error of a positional estimator with limited positional information is derived.}, author = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Error bound on an estimator of position}}, doi = {10.1371/journal.pone.0163628.s001}, year = {2016}, }