New topological structures of Skyrme theory: baryon number and monopole number

Energy Technology Data Exchange (ETDEWEB)

Cho, Y.M. [Chinese Academy of Science, Institute of Modern Physics, Lanzhou (China); Konkuk University, Seoul (Korea, Republic of); Seoul National University, School of Physics and Astronomy, Seoul (Korea, Republic of); Kimm, Kyoungtae [Seoul National University, Faculty of Liberal Education, Seoul (Korea, Republic of); Yoon, J.H. [Konkuk University, Department of Physics, Seoul (Korea, Republic of); Zhang, Pengming [Chinese Academy of Science, Institute of Modern Physics, Lanzhou (China)

2017-02-15

Based on the observation that the skyrmion in Skyrme theory can be viewed as a dressed monopole, we show that the skyrmions have two independent topology, the baryon topology π{sub 3}(S{sup 3}) and the monopole topology π{sub 2}(S{sup 2}). With this we propose to classify the skyrmions by two topological numbers (m, n), the monopole number m and the shell (radial) number n. In this scheme the popular (non spherically symmetric) skyrmions are classified as the (m, 1) skyrmions but the spherically symmetric skyrmions are classified as the (1, n) skyrmions, and the baryon number B is given by B = mn. Moreover, we show that the vacuum of the Skyrme theory has the structure of the vacuum of the Sine-Gordon theory and QCD combined together, which can also be classified by two topological numbers (p, q). This puts the Skyrme theory in a totally new perspective. (orig.)

Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera.

Science.gov (United States)

Afkhami, Michelle E; Luke Mahler, D; Burns, Jean H; Weber, Marjorie G; Wojciechowski, Martin F; Sprent, Janet; Strauss, Sharon Y

2018-02-01

How species interactions shape global biodiversity and influence diversification is a central - but also data-hungry - question in evolutionary ecology. Microbially based mutualisms are widespread and could cause diversification by ameliorating stress and thus allowing organisms to colonize and adapt to otherwise unsuitable habitats. Yet the role of these interactions in generating species diversity has received limited attention, especially across large taxonomic groups. In the massive angiosperm family Leguminosae, plants often associate with root-nodulating bacteria that ameliorate nutrient stress by fixing atmospheric nitrogen. These symbioses are ecologically-important interactions, influencing community assembly, diversity, and succession, contributing ~100-290 million tons of N annually to natural ecosystems, and enhancing growth of agronomically-important forage and crop plants worldwide. In recent work attempting to determine whether mutualism with N-fixing bacteria led to increased diversification across legumes, we were unable to definitively resolve the relationship between diversification and nodulation. We did, however, succeed in compiling a very large searchable, analysis-ready database of nodulation data for 749 legume genera (98% of Leguminosae genera; LPWG 2017), which, along with associated phylogenetic information, will provide a valuable resource for future work addressing this question and others. For each legume genus, we provide information about the species richness, frequency of nodulation, subfamily association, and topological correspondence with an additional data set of 100 phylogenetic trees curated for database compatibility. We found 386 legume genera were confirmed nodulators (i.e., all species examined for nodulation nodulated), 116 were non-nodulating, four were variable (i.e., containing both confirmed nodulators and confirmed non-nodulators), and 243 had not been examined for nodulation in published studies. Interestingly

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae).

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McCann, Jamie; Schneeweiss, Gerald M; Stuessy, Tod F; Villaseñor, Jose L; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae.

Directory of Open Access Journals (Sweden)

Jamie McCann

Full Text Available Chromosome number change (polyploidy and dysploidy plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods, branch length model (phylograms versus chronograms and phylogenetic uncertainty (topological and branch length uncertainty on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively with no prevailing direction.

Phylogenetic constraints do not explain the rarity of nitrogen-fixing trees in late-successional temperate forests.

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Menge, Duncan N L; DeNoyer, Jeanne L; Lichstein, Jeremy W

2010-08-06

Symbiotic nitrogen (N)-fixing trees are rare in late-successional temperate forests, even though these forests are often N limited. Two hypotheses could explain this paradox. The 'phylogenetic constraints hypothesis' states that no late-successional tree taxa in temperate forests belong to clades that are predisposed to N fixation. Conversely, the 'selective constraints hypothesis' states that such taxa are present, but N-fixing symbioses would lower their fitness. Here we test the phylogenetic constraints hypothesis. Using U.S. forest inventory data, we derived successional indices related to shade tolerance and stand age for N-fixing trees, non-fixing trees in the 'potentially N-fixing clade' (smallest angiosperm clade that includes all N fixers), and non-fixing trees outside this clade. We then used phylogenetically independent contrasts (PICs) to test for associations between these successional indices and N fixation. Four results stand out from our analysis of U.S. trees. First, N fixers are less shade-tolerant than non-fixers both inside and outside of the potentially N-fixing clade. Second, N fixers tend to occur in younger stands in a given geographical region than non-fixers both inside and outside of the potentially N-fixing clade. Third, the potentially N-fixing clade contains numerous late-successional non-fixers. Fourth, although the N fixation trait is evolutionarily conserved, the successional traits are relatively labile. These results suggest that selective constraints, not phylogenetic constraints, explain the rarity of late-successional N-fixing trees in temperate forests. Because N-fixing trees could overcome N limitation to net primary production if they were abundant, this study helps to understand the maintenance of N limitation in temperate forests, and therefore the capacity of this biome to sequester carbon.

New approaches to phylogenetic tree search and their application to large numbers of protein alignments.

Science.gov (United States)

Whelan, Simon

2007-10-01

Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies, including molecular systematics, phylogenetics, and comparative genomics. Finding the optimal tree relating a set of sequences using score-based (optimality criterion) methods, such as maximum likelihood and maximum parsimony, may require all possible trees to be considered, which is not feasible even for modest numbers of sequences. In practice, trees are estimated using heuristics that represent a trade-off between topological accuracy and speed. I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds. The heuristics function by allowing the efficient exploration of large numbers of trees through novel hill-climbing and resampling strategies. These heuristics, and other computational approximations, are implemented for maximum likelihood estimation of trees in the program Leaphy, and its performance is compared to other popular phylogenetic programs. Trees are estimated from 4059 different protein alignments using a selection of phylogenetic programs and the likelihoods of the tree estimates are compared. Trees estimated using Leaphy are found to have equal to or better likelihoods than trees estimated using other phylogenetic programs in 4004 (98.6%) families and provide a unique best tree that no other program found in 1102 (27.1%) families. The improvement is particularly marked for larger families (80 to 100 sequences), where Leaphy finds a unique best tree in 81.7% of families.

The relationship between the number of loci and the statistical support for the topology of UPGMA trees obtained from genetic distance data.

Science.gov (United States)

Highton, R

1993-12-01

An analysis of the relationship between the number of loci utilized in an electrophoretic study of genetic relationships and the statistical support for the topology of UPGMA trees is reported for two published data sets. These are Highton and Larson (Syst. Zool.28:579-599, 1979), an analysis of the relationships of 28 species of plethodonine salamanders, and Hedges (Syst. Zool., 35:1-21, 1986), a similar study of 30 taxa of Holarctic hylid frogs. As the number of loci increases, the statistical support for the topology at each node in UPGMA trees was determined by both the bootstrap and jackknife methods. The results show that the bootstrap and jackknife probabilities supporting the topology at some nodes of UPGMA trees increase as the number of loci utilized in a study is increased, as expected for nodes that have groupings that reflect phylogenetic relationships. The pattern of increase varies and is especially rapid in the case of groups with no close relatives. At nodes that likely do not represent correct phylogenetic relationships, the bootstrap probabilities do not increase and often decline with the addition of more loci.

YBYRÁ facilitates comparison of large phylogenetic trees.

Science.gov (United States)

Machado, Denis Jacob

2015-07-01

The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

Directory of Open Access Journals (Sweden)

Kodner Robin B

2010-10-01

Full Text Available Abstract Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.

The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.

Science.gov (United States)

Soria-Carrasco, Víctor; Talavera, Gerard; Igea, Javier; Castresana, Jose

2007-11-01

We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is applied to the two trees. We thus obtain the minimum branch length distance or K tree score. Two trees with very different relative branch lengths get a high K score whereas two trees that follow a similar among-lineage rate variation get a low score, regardless of the overall rates in both trees. There are several applications of the K tree score, two of which are explained here in more detail. First, this score allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also with respect to the reproduction of a given branch length variation. In a second example, we show how the K score allows the selection of orthologous genes by choosing those that better follow the overall shape of a given reference tree. http://molevol.ibmb.csic.es/Ktreedist.html

Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees.

Science.gov (United States)

Baste, Julien; Paul, Christophe; Sau, Ignasi; Scornavacca, Celine

2017-04-01

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species X; these relationships are often depicted via a phylogenetic tree-a tree having its leaves labeled bijectively by elements of X and without degree-2 nodes-called the "species tree." One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g., DNA sequences originating from some species in X), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping-but not identical-sets of labels, is called "supertree." In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed parameter tractable in the number of input trees k, by using their expressibility in monadic second-order logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on k of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time [Formula: see text], where n is the total size of the input.

Topological methods in Euclidean spaces

CERN Document Server

Naber, Gregory L

2000-01-01

Extensive development of a number of topics central to topology, including elementary combinatorial techniques, Sperner's Lemma, the Brouwer Fixed Point Theorem, homotopy theory and the fundamental group, simplicial homology theory, the Hopf Trace Theorem, the Lefschetz Fixed Point Theorem, the Stone-Weierstrass Theorem, and Morse functions. Includes new section of solutions to selected problems.

Rényi entropies and topological quantum numbers in 2D gapped Dirac materials

International Nuclear Information System (INIS)

Bolívar, Juan Carlos; Romera, Elvira

2017-01-01

New topological quantum numbers are introduced by analyzing complexity measures and relative Rényi entropies in silicene in the presence of perpendicular electric and magnetic fields. These topological quantum numbers characterize the topological insulator and band insulator phases in silicene. In addition, we have found that, these information measures reach extremum values at the charge neutrality points. These results are valid for other 2D gapped Dirac materials analogous to silicene with a buckled honeycomb structure and a significant spin-orbit coupling. - Highlights: • Topological quantum numbers (Chern-like numbers) by Rényi entropies in silicene. • These topological numbers characterize silicene topological and band insulator phases. • These information measures reach extremum values at the charge neutrality points. • These results are valid for other 2D gapped Dirac materials analogous to silicene.

Topological quantum numbers in nonrelativistic physics

CERN Document Server

Thouless, David James

1998-01-01

Topological quantum numbers are distinguished from quantum numbers based on symmetry because they are insensitive to the imperfections of the systems in which they are observed. They have become very important in precision measurements in recent years, and provide the best measurements of voltage and electrical resistance. This book describes the theory of such quantum numbers, starting with Dirac's argument for the quantization of electric charge, and continuing with discussions on the helium superfluids, flux quantization and the Josephson effect in superconductors, the quantum Hall effect,

Spatially balanced topological interaction grants optimal cohesion in flocking models.

Science.gov (United States)

Camperi, Marcelo; Cavagna, Andrea; Giardina, Irene; Parisi, Giorgio; Silvestri, Edmondo

2012-12-06

Models of self-propelled particles (SPPs) are an indispensable tool to investigate collective animal behaviour. Originally, SPP models were proposed with metric interactions, where each individual coordinates with neighbours within a fixed metric radius. However, recent experiments on bird flocks indicate that interactions are topological: each individual interacts with a fixed number of neighbours, irrespective of their distance. It has been argued that topological interactions are more robust than metric ones against external perturbations, a significant evolutionary advantage for systems under constant predatory pressure. Here, we test this hypothesis by comparing the stability of metric versus topological SPP models in three dimensions. We show that topological models are more stable than metric ones. We also show that a significantly better stability is achieved when neighbours are selected according to a spatially balanced topological rule, namely when interacting neighbours are evenly distributed in angle around the focal individual. Finally, we find that the minimal number of interacting neighbours needed to achieve fully stable cohesion in a spatially balanced model is compatible with the value observed in field experiments on starling flocks.

A topological derivative method for topology optimization

DEFF Research Database (Denmark)

Norato, J.; Bendsøe, Martin P.; Haber, RB

2007-01-01

resource constraint. A smooth and consistent projection of the region bounded by the level set onto the fictitious analysis domain simplifies the response analysis and enhances the convergence of the optimization algorithm. Moreover, the projection supports the reintroduction of solid material in void......We propose a fictitious domain method for topology optimization in which a level set of the topological derivative field for the cost function identifies the boundary of the optimal design. We describe a fixed-point iteration scheme that implements this optimality criterion subject to a volumetric...... regions, a critical requirement for robust topology optimization. We present several numerical examples that demonstrate compliance minimization of fixed-volume, linearly elastic structures....

Topological Fixed Point Theory and Applications : Conference held at the Nankai Institute of Mathematics

CERN Document Server

1989-01-01

This selection of papers from the Beijing conference gives a cross-section of the current trends in the field of fixed point theory as seen by topologists and analysts. Apart from one survey article, they are all original research articles, on topics including equivariant theory, extensions of Nielsen theory, periodic orbits of discrete and continuous dynamical systems, and new invariants and techniques in topological approaches to analytic problems.

AFLPMax: a user-friendly application for computing the optimal number of amplified fragment length polymorphism markers needed in phylogenetic reconstruction.

Science.gov (United States)

García-Pereira, M J; Quesada, H; Caballero, A; Carvajal-Rodríguez, A

2012-05-01

Amplified fragment length polymorphisms (AFLPs) are widely used for phylogenetic inference especially in non-model species. Frequently, trees obtained with other nuclear or mitochondrial markers or with morphological information need additional resolution, increased branch support, or independent data sources (i.e. unlinked loci). In such cases, the use of AFLPs is a quick and cheap option. Computer simulation has shown that dominant AFLP markers lead to less accurate tree topologies than bi-allelic codominant markers such as SNPs, but this difference becomes negligible for shallow trees when using AFLP data sets that include a sufficiently large number of characters. Thus, determining how many AFLP characters are required to recover a given phylogeny is a key issue regarding the appropriateness of AFLPs for phylogenetic reconstruction. Here, we present a user-friendly, java-based graphical interface, AFLPMax, which executes an automatic pipeline of different programs providing the user with the optimal number of AFLP characters needed to recover a given phylogeny with high accuracy and support. Executables for Windows, linux and MacOS X operating systems, source code and user manual are available from: http://webs.uvigo.es/acraaj/AFLPMax.htm. © 2012 Blackwell Publishing Ltd.

Reynolds number effects on mixing due to topological chaos.

Science.gov (United States)

Smith, Spencer A; Warrier, Sangeeta

2016-03-01

Topological chaos has emerged as a powerful tool to investigate fluid mixing. While this theory can guarantee a lower bound on the stretching rate of certain material lines, it does not indicate what fraction of the fluid actually participates in this minimally mandated mixing. Indeed, the area in which effective mixing takes place depends on physical parameters such as the Reynolds number. To help clarify this dependency, we numerically simulate the effects of a batch stirring device on a 2D incompressible Newtonian fluid in the laminar regime. In particular, we calculate the finite time Lyapunov exponent (FTLE) field for three different stirring protocols, one topologically complex (pseudo-Anosov) and two simple (finite-order), over a range of viscosities. After extracting appropriate measures indicative of both the amount of mixing and the area of effective mixing from the FTLE field, we see a clearly defined Reynolds number range in which the relative efficacy of the pseudo-Anosov protocol over the finite-order protocols justifies the application of topological chaos. More unexpectedly, we see that while the measures of effective mixing area increase with increasing Reynolds number for the finite-order protocols, they actually exhibit non-monotonic behavior for the pseudo-Anosov protocol.

Quantum numbers and band topology of nanotubes

Energy Technology Data Exchange (ETDEWEB)

Damnjanovic, M [Faculty of Physics, University of Belgrade, POB 368, 11001 Belgrade (Yugoslavia); Milosevic, I [Faculty of Physics, University of Belgrade, POB 368, 11001 Belgrade (Yugoslavia); Vukovic, T [Faculty of Physics, University of Belgrade, POB 368, 11001 Belgrade (Yugoslavia); Maultzsch, J [Institut fuer Festkoerper Physik, Technische Universitaet Berlin, Hardenbergstr. 36, 10623 Berlin (Germany)

2003-05-30

Nanotubes as well as polymers and quasi-1D subsystems of 3D crystals have line group symmetry. This allows two types of quantum numbers: roto-translational and helical. The roto-translational quantum numbers are linear and total angular (not conserved) momenta, while the helical quantum numbers are helical and complementary angular momenta. Their mutual relations determine some topological properties of energy bands, such as systematic band sticking or van Hove singularities related to parities. The importance of these conclusions is illustrated by the optical absorption in carbon nanotubes: parity may prevent absorption peaks at van Hove singularities.

Quantum numbers and band topology of nanotubes

International Nuclear Information System (INIS)

Damnjanovic, M; Milosevic, I; Vukovic, T; Maultzsch, J

2003-01-01

Nanotubes as well as polymers and quasi-1D subsystems of 3D crystals have line group symmetry. This allows two types of quantum numbers: roto-translational and helical. The roto-translational quantum numbers are linear and total angular (not conserved) momenta, while the helical quantum numbers are helical and complementary angular momenta. Their mutual relations determine some topological properties of energy bands, such as systematic band sticking or van Hove singularities related to parities. The importance of these conclusions is illustrated by the optical absorption in carbon nanotubes: parity may prevent absorption peaks at van Hove singularities

Quantum numbers and band topology of nanotubes

CERN Document Server

Damnjanovic, M; Vukovic, T; Maultzsch, J

2003-01-01

Nanotubes as well as polymers and quasi-1D subsystems of 3D crystals have line group symmetry. This allows two types of quantum numbers: roto-translational and helical. The roto-translational quantum numbers are linear and total angular (not conserved) momenta, while the helical quantum numbers are helical and complementary angular momenta. Their mutual relations determine some topological properties of energy bands, such as systematic band sticking or van Hove singularities related to parities. The importance of these conclusions is illustrated by the optical absorption in carbon nanotubes: parity may prevent absorption peaks at van Hove singularities.

Gauge-fixing ambiguity and monopole number

International Nuclear Information System (INIS)

Hioki, S.; Miyamura, O.

1991-01-01

Gauge-fixing ambiguities of lattice SU(2) QCD are studied in the maximally abelian and unitary gauges. In the former, we find local maxima of a gauge-fixing function which may correspond to Gribov copies. There is a definite anti-correlation between the number of monopoles and the value of the function. Errors of measured quantities coming from the ambiguity are found to be less than inherent dispersion in the ensemble average. No ambiguity is found in the unitary gauges. (orig.)

Phylogenetic trees in bioinformatics

Energy Technology Data Exchange (ETDEWEB)

Burr, Tom L [Los Alamos National Laboratory

2008-01-01

Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

Fermionic Approach to Weighted Hurwitz Numbers and Topological Recursion

Science.gov (United States)

Alexandrov, A.; Chapuy, G.; Eynard, B.; Harnad, J.

2017-12-01

A fermionic representation is given for all the quantities entering in the generating function approach to weighted Hurwitz numbers and topological recursion. This includes: KP and 2D Toda {τ} -functions of hypergeometric type, which serve as generating functions for weighted single and double Hurwitz numbers; the Baker function, which is expanded in an adapted basis obtained by applying the same dressing transformation to all vacuum basis elements; the multipair correlators and the multicurrent correlators. Multiplicative recursion relations and a linear differential system are deduced for the adapted bases and their duals, and a Christoffel-Darboux type formula is derived for the pair correlator. The quantum and classical spectral curves linking this theory with the topological recursion program are derived, as well as the generalized cut-and-join equations. The results are detailed for four special cases: the simple single and double Hurwitz numbers, the weakly monotone case, corresponding to signed enumeration of coverings, the strongly monotone case, corresponding to Belyi curves and the simplest version of quantum weighted Hurwitz numbers.

Fermionic Approach to Weighted Hurwitz Numbers and Topological Recursion

Science.gov (United States)

Alexandrov, A.; Chapuy, G.; Eynard, B.; Harnad, J.

2018-06-01

A fermionic representation is given for all the quantities entering in the generating function approach to weighted Hurwitz numbers and topological recursion. This includes: KP and 2 D Toda {τ} -functions of hypergeometric type, which serve as generating functions for weighted single and double Hurwitz numbers; the Baker function, which is expanded in an adapted basis obtained by applying the same dressing transformation to all vacuum basis elements; the multipair correlators and the multicurrent correlators. Multiplicative recursion relations and a linear differential system are deduced for the adapted bases and their duals, and a Christoffel-Darboux type formula is derived for the pair correlator. The quantum and classical spectral curves linking this theory with the topological recursion program are derived, as well as the generalized cut-and-join equations. The results are detailed for four special cases: the simple single and double Hurwitz numbers, the weakly monotone case, corresponding to signed enumeration of coverings, the strongly monotone case, corresponding to Belyi curves and the simplest version of quantum weighted Hurwitz numbers.

Scaling behavior of knotted random polygons and self-avoiding polygons: Topological swelling with enhanced exponent.

Science.gov (United States)

Uehara, Erica; Deguchi, Tetsuo

2017-12-07

We show that the average size of self-avoiding polygons (SAPs) with a fixed knot is much larger than that of no topological constraint if the excluded volume is small and the number of segments is large. We call it topological swelling. We argue an "enhancement" of the scaling exponent for random polygons with a fixed knot. We study them systematically through SAP consisting of hard cylindrical segments with various different values of the radius of segments. Here we mean by the average size the mean-square radius of gyration. Furthermore, we show numerically that the topological balance length of a composite knot is given by the sum of those of all constituent prime knots. Here we define the topological balance length of a knot by such a number of segments that topological entropic repulsions are balanced with the knot complexity in the average size. The additivity suggests the local knot picture.

Solving equations by topological methods

Directory of Open Access Journals (Sweden)

Lech Górniewicz

2005-01-01

Full Text Available In this paper we survey most important results from topological fixed point theory which can be directly applied to differential equations. Some new formulations are presented. We believe that our article will be useful for analysts applying topological fixed point theory in nonlinear analysis and in differential equations.

Anomalous quantum numbers and topological properties of field theories

International Nuclear Information System (INIS)

Polychronakos, A.P.

1987-01-01

We examine the connection between anomalous quantum numbers, symmetry breaking patterns and topological properties of some field theories. The main results are the following: In three dimensions the vacuum in the presence of abelian magnetic field configurations behaves like a superconductor. Its quantum numbers are exactly calculable and are connected with the Atiyah-Patodi-Singer index theorem. Boundary conditions, however, play a nontrivial role in this case. Local conditions were found to be physically preferable than the usual global ones. Due to topological reasons, only theories for which the gauge invariant photon mass in three dimensions obeys a quantization condition can support states of nonzero magnetic flux. For similar reasons, this mass induces anomalous angular momentum quantum numbers to the states of the theory. Parity invariance and global flavor symmetry were shown to be incompatible in such theories. In the presence of mass less flavored fermions, parity will always break for an odd number of fermion flavors, while for even fermion flavors it may not break but only at the expense of maximally breaking the flavor symmetry. Finally, a connection between these theories and the quantum Hall effect was indicated

Sampling strategies for improving tree accuracy and phylogenetic analyses: a case study in ciliate protists, with notes on the genus Paramecium.

Science.gov (United States)

Yi, Zhenzhen; Strüder-Kypke, Michaela; Hu, Xiaozhong; Lin, Xiaofeng; Song, Weibo

2014-02-01

In order to assess how dataset-selection for multi-gene analyses affects the accuracy of inferred phylogenetic trees in ciliates, we chose five genes and the genus Paramecium, one of the most widely used model protist genera, and compared tree topologies of the single- and multi-gene analyses. Our empirical study shows that: (1) Using multiple genes improves phylogenetic accuracy, even when their one-gene topologies are in conflict with each other. (2) The impact of missing data on phylogenetic accuracy is ambiguous: resolution power and topological similarity, but not number of represented taxa, are the most important criteria of a dataset for inclusion in concatenated analyses. (3) As an example, we tested the three classification models of the genus Paramecium with a multi-gene based approach, and only the monophyly of the subgenus Paramecium is supported. Copyright © 2013 Elsevier Inc. All rights reserved.

Topological Gravity on $(D,N)-$Shift Superspace Formulation

OpenAIRE

Lourenco, José A.; Neto, José A. Helayël; Spalenza, Wesley

2017-01-01

In this contribution, we re-assess the subject of topological gravity by following the Shift Supersymmetry formalism. The gauge-fixing of the theory goes under the Batallin-Vilkovisky (BV) prescription based on a diagram that contains both ghost and anti-ghost superfields, associated to the super-vielbein and the super-Lorentz connection. We extend the formulation of the topological gravity action to an arbitrary number of dimensions of the shift superspace by adopting a formulation based on ...

A measure of the denseness of a phylogenetic network. [by sequenced proteins from extant species

Science.gov (United States)

Holmquist, R.

1978-01-01

An objective measure of phylogenetic denseness is developed to examine various phylogenetic criteria: alpha- and beta-hemoglobin, myoglobin, cytochrome c, and the parvalbumin family. Attention is given to the number of nucleotide replacements separating homologous sequences, and to the topology of the network (in other words, to the qualitative nature of the network as defined by how closely the studied species are related). Applications include quantitative comparisons of species origin, relation, and rates of evolution.

L lines, C points and Chern numbers: understanding band structure topology using polarization fields

Science.gov (United States)

Fösel, Thomas; Peano, Vittorio; Marquardt, Florian

2017-11-01

Topology has appeared in different physical contexts. The most prominent application is topologically protected edge transport in condensed matter physics. The Chern number, the topological invariant of gapped Bloch Hamiltonians, is an important quantity in this field. Another example of topology, in polarization physics, are polarization singularities, called L lines and C points. By establishing a connection between these two theories, we develop a novel technique to visualize and potentially measure the Chern number: it can be expressed either as the winding of the polarization azimuth along L lines in reciprocal space, or in terms of the handedness and the index of the C points. For mechanical systems, this is directly connected to the visible motion patterns.

PDF fit in the fixed-flavour-number scheme

International Nuclear Information System (INIS)

Alekhin, S.; Bluemlein, J.; Moch, S.

2012-02-01

We discuss the heavy-quark contribution to deep inelastic scattering in the scheme with n f =3;4;5 fixed flavors. Based on the recent ABM11 PDF analysis of world data for deep-inelastic scattering and fixed-target data for the Drell-Yan process with the running-mass definition for heavy quarks we show that fixed flavor number scheme is sufficient for describing the deep-inelastic-scattering data in the entire kinematic range. We compare with other PDF sets and comment on the implications for measuring the strong coupling constant α s (M Z ).

Application of fixed point theory to chaotic attractors of forced oscillators

International Nuclear Information System (INIS)

Stewart, H.B.

1990-11-01

A review of the structure of chaotic attractors of periodically forced second order nonlinear oscillators suggests that the theory of fixed points of transformations gives information about the fundamental topological structure of attractors. First a simple extension of the Levinson index formula is proved. Then numerical evidence is used to formulate plausible conjectures about absorbing regions containing chaotic attractors in forced oscillators. Applying the Levinson formula suggests a fundamental relation between the number of fixed points or periodic points in a section of the chaotic attractor on the one hand, and a topological invariant of an absorbing region on the other hand. (author)

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees.

Science.gov (United States)

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

Tumourigenesis is a mutation accumulation process, which is likely to start with a mutated founder cell. The evolutionary nature of tumor development makes phylogenetic models suitable for inferring tumor evolution through genetic variation data. Copy number variation (CNV) is the major genetic marker of the genome with more genes, disease loci, and functional elements involved. Fluorescence in situ hybridization (FISH) accurately measures multiple gene copy number of hundreds of single cells. We propose an improved binary differential evolution algorithm, BDEP, to infer tumor phylogenetic tree based on FISH platform. The topology analysis of tumor progression tree shows that the pathway of tumor subcell expansion varies greatly during different stages of tumor formation. And the classification experiment shows that tree-based features are better than data-based features in distinguishing tumor. The constructed phylogenetic trees have great performance in characterizing tumor development process, which outperforms other similar algorithms.

The relative contribution of band number to phylogenetic accuracy in AFLP data sets.

Science.gov (United States)

García-Pereira, M J; Caballero, A; Quesada, H

2011-11-01

We examined the effect of increasing the number of sampled amplified fragment length polymorphism (AFLP) bands to reconstruct an accurate and well-supported AFLP-based phylogeny. In silico AFLP was performed using simulated DNA sequences evolving along balanced and unbalanced model trees with recent, uniform and ancient radiations and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.05 substitutions per site. Trees were estimated by minimum evolution (ME) and maximum parsimony (MP) methods from both DNA sequences and virtual AFLP fingerprints. The comparison of the true tree with the estimated AFLP trees suggests that moderate numbers of AFLP bands are necessary to recover the correct topology with high bootstrap support values (i.e. >70%). Fewer numbers of bands are necessary for shorter tree lengths and for balanced than for unbalanced tree topologies. However, branch length estimation was rather unreliable and did not improve substantially after a certain number of bands were sampled. These results hold for different levels of genome coverage and number of taxa analysed. In silico AFLP using bacterial genomic DNA sequences recovered a well-supported tree topology that mirrored an empirical phylogeny based on a set of 31 orthologous gene sequences when as few as 263 AFLP bands were scored. These results suggest that AFLPs may be an efficient alternative to traditional DNA sequencing for accurate topology reconstruction of shallow trees when not very short ancestral branches exist. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

PDF fit in the fixed-flavour-number scheme

Energy Technology Data Exchange (ETDEWEB)

Alekhin, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Institute for High Energy Physics, Moscow (Russian Federation); Bluemlein, J.; Moch, S. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany)

2012-02-15

We discuss the heavy-quark contribution to deep inelastic scattering in the scheme with n{sub f}=3;4;5 fixed flavors. Based on the recent ABM11 PDF analysis of world data for deep-inelastic scattering and fixed-target data for the Drell-Yan process with the running-mass definition for heavy quarks we show that fixed flavor number scheme is sufficient for describing the deep-inelastic-scattering data in the entire kinematic range. We compare with other PDF sets and comment on the implications for measuring the strong coupling constant {alpha}{sub s}(M{sub Z}).

Custom Topology Generation for Network-on-Chip

DEFF Research Database (Denmark)

Stuart, Matthias Bo; Sparsø, Jens

2007-01-01

This paper compares simulated annealing and tabu search for generating custom topologies for applications with periodic behaviour executing on a network-on-chip. The approach differs from previous work by starting from a fixed mapping of IP-cores to routers and performing design space exploration...... around an initial topology. The tabu search has been modified from its normally encountered form to allow easier escaping from local minima. A number of synthetic benchmarks are used for tuning the parameters of both heuristics and for testing the quality of the solutions each heuristic produces...

Aberrant topology of striatum's connectivity is associated with the number of episodes in depression.

Science.gov (United States)

Meng, Chun; Brandl, Felix; Tahmasian, Masoud; Shao, Junming; Manoliu, Andrei; Scherr, Martin; Schwerthöffer, Dirk; Bäuml, Josef; Förstl, Hans; Zimmer, Claus; Wohlschläger, Afra M; Riedl, Valentin; Sorg, Christian

2014-02-01

In major depressive disorder, depressive episodes reoccur in ∼60% of cases; however, neural mechanisms of depressive relapse are poorly understood. Depressive episodes are characterized by aberrant topology of the brain's intrinsic functional connectivity network, and the number of episodes is one of the most important predictors for depressive relapse. In this study we hypothesized that specific changes of the topology of intrinsic connectivity interact with the course of episodes in recurrent depressive disorder. To address this hypothesis, we investigated which changes of connectivity topology are associated with the number of episodes in patients, independently of current symptoms and disease duration. Fifty subjects were recruited including 25 depressive patients (two to 10 episodes) and 25 gender- and age-matched control subjects. Resting-state functional magnetic resonance imaging, Harvard-Oxford brain atlas, wavelet-transformation of atlas-shaped regional time-series, and their pairwise Pearson's correlation were used to define individual connectivity matrices. Matrices were analysed by graph-based methods, resulting in outcome measures that were used as surrogates of intrinsic network topology. Topological scores were subsequently compared across groups, and, for patients only, related with the number of depressive episodes and current symptoms by partial correlation analysis. Concerning the whole brain connectivity network of patients, small-world topology was preserved but global efficiency was reduced and global betweenness-centrality increased. Aberrant nodal efficiency and centrality of regional connectivity was found in the dorsal striatum, inferior frontal and orbitofrontal cortex as well as in the occipital and somatosensory cortex. Inferior frontal changes were associated with current symptoms, whereas aberrant right putamen network topology was associated with the number of episodes. Results were controlled for effects of total grey matter

Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?

Science.gov (United States)

Gambette, Philippe; van Iersel, Leo; Kelk, Steven; Pardi, Fabio; Scornavacca, Celine

2016-09-01

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental questions that arise in this context is whether the evolution of a gene with one copy in all species can be explained by a given network. In mathematical terms, this is often translated in the following way: is a given phylogenetic tree contained in a given phylogenetic network? Recently this tree containment problem has been widely investigated from a computational perspective, but most studies have only focused on the topology of the phylogenies, ignoring a piece of information that, in the case of phylogenetic trees, is routinely inferred by evolutionary analyses: branch lengths. These measure the amount of change (e.g., nucleotide substitutions) that has occurred along each branch of the phylogeny. Here, we study a number of versions of the tree containment problem that explicitly account for branch lengths. We show that, although length information has the potential to locate more precisely a tree within a network, the problem is computationally hard in its most general form. On a positive note, for a number of special cases of biological relevance, we provide algorithms that solve this problem efficiently. This includes the case of networks of limited complexity, for which it is possible to recover, among the trees contained by the network with the same topology as the input tree, the closest one in terms of branch lengths.

Topology Optimization of Thermal Heat Sinks

DEFF Research Database (Denmark)

Klaas Haertel, Jan Hendrik; Engelbrecht, Kurt; Lazarov, Boyan Stefanov

2015-01-01

In this paper, topology optimization is applied to optimize the cooling performance of thermal heat sinks. The coupled two-dimensional thermofluid model of a heat sink cooled with forced convection and a density-based topology optimization including density filtering and projection are implemented...... in COMSOL Multiphysics. The optimization objective is to minimize the heat sink’s temperature for a prescribed pressure drop and fixed heat generation. To conduct the optimization, COMSOL’s Optimization Module with GCMMA as the optimization method is used. The implementation of this topology optimization...... approach in COMSOL Multiphysics is described in this paper and results for optimized two-dimensional heat sinks are presented. Furthermore, parameter studies regarding the effect of the prescribed pressure drop of the system on Reynolds number and realized heat sink temperature are presented and discussed....

Topological phases in frustrated synthetic ladders with an odd number of legs

Science.gov (United States)

Barbarino, Simone; Dalmonte, Marcello; Fazio, Rosario; Santoro, Giuseppe E.

2018-01-01

The realization of the Hofstadter model in a strongly anisotropic ladder geometry has now become possible in one-dimensional optical lattices with a synthetic dimension. In this work, we show how the Hofstadter Hamiltonian in such ladder configurations hosts a topological phase of matter which is radically different from its two-dimensional counterpart. This topological phase stems directly from the hybrid nature of the ladder geometry and is protected by a properly defined inversion symmetry. We start our analysis by considering the paradigmatic case of a three-leg ladder which supports a topological phase exhibiting the typical features of topological states in one dimension: robust fermionic edge modes, a degenerate entanglement spectrum, and a nonzero Zak phase; then, we generalize our findings—addressable in the state-of-the-art cold-atom experiments—to ladders with a higher number of legs.

Many-to-Many Multicast Routing Schemes under a Fixed Topology

Directory of Open Access Journals (Sweden)

Wei Ding

2013-01-01

Full Text Available Many-to-many multicast routing can be extensively applied in computer or communication networks supporting various continuous multimedia applications. The paper focuses on the case where all users share a common communication channel while each user is both a sender and a receiver of messages in multicasting as well as an end user. In this case, the multicast tree appears as a terminal Steiner tree (TeST. The problem of finding a TeST with a quality-of-service (QoS optimization is frequently NP-hard. However, we discover that it is a good idea to find a many-to-many multicast tree with QoS optimization under a fixed topology. In this paper, we are concerned with three kinds of QoS optimization objectives of multicast tree, that is, the minimum cost, minimum diameter, and maximum reliability. All of three optimization problems are distributed into two types, the centralized and decentralized version. This paper uses the dynamic programming method to devise an exact algorithm, respectively, for the centralized and decentralized versions of each optimization problem.

Topological classification and enumeration of RNA structures by genus

DEFF Research Database (Denmark)

Andersen, Joergen Ellegard; Penner, Robert C.; Reidys, Christian

2013-01-01

To an RNA pseudoknot structure is naturally associated a topological surface, which has its associated genus, and structures can thus be classified by the genus. Based on earlier work of Harer-Zagier, we compute the generating function for the number of those structures of fixed genus and minimum...

Symmetry protected topological charge in symmetry broken phase: Spin-Chern, spin-valley-Chern and mirror-Chern numbers

International Nuclear Information System (INIS)

Ezawa, Motohiko

2014-01-01

The Chern number is a genuine topological number. On the other hand, a symmetry protected topological (SPT) charge is a topological number only when a symmetry exists. We propose a formula for the SPT charge as a derivative of the Chern number in terms of the Green function in such a way that it is valid and related to the associated Hall current even when the symmetry is broken. We estimate the amount of deviation from the quantized value as a function of the strength of the broken symmetry. We present two examples. First, we consider Dirac electrons with the spin–orbit coupling on honeycomb lattice, where the SPT charges are given by the spin-Chern, valley-Chern and spin-valley-Chern numbers. Though the spin-Chern charge is not quantized in the presence of the Rashba coupling, the deviation is estimated to be 10 −7 in the case of silicene, a silicon cousin of graphene. Second, we analyze the effect of the mirror-symmetry breaking of the mirror-Chern number in a thin-film of topological crystalline insulator.

Topology of a dissipative spin: Dynamical Chern number, bath-induced nonadiabaticity, and a quantum dynamo effect

Science.gov (United States)

Henriet, Loïc; Sclocchi, Antonio; Orth, Peter P.; Le Hur, Karyn

2017-02-01

We analyze the topological deformations of the ground state manifold of a quantum spin-1/2 in a magnetic field H =H (sinθ cosϕ ,sinθ sinϕ ,cosθ ) induced by a coupling to an ohmic quantum dissipative environment at zero temperature. From Bethe ansatz results and a variational approach, we confirm that the Chern number associated with the geometry of the reduced spin ground state manifold is preserved in the delocalized phase for α <1 . We report a divergence of the Berry curvature at αc=1 for magnetic fields aligned along the equator θ =π /2 . This divergence is caused by the complete quenching of the transverse magnetic field by the bath associated with a gap closing that occurs at the localization Kosterlitz-Thouless quantum phase transition in this model. Recent experiments in quantum circuits have engineered nonequilibrium protocols to access topological properties from a measurement of a dynamical Chern number defined via the out-of-equilibrium spin expectation values. Applying a numerically exact stochastic Schrödinger approach we find that, for a fixed field sweep velocity θ (t )=v t , the bath induces a crossover from (quasi)adiabatic to nonadiabatic dynamical behavior when the spin bath coupling α increases. We also investigate the particular regime H /ωc≪v /H ≪1 with large bath cutoff frequency ωc, where the dynamical Chern number vanishes already at α =1 /2 . In this regime, the mapping to an interacting resonance level model enables us to analytically describe the behavior of the dynamical Chern number in the vicinity of α =1 /2 . We further provide an intuitive physical explanation of the bath-induced breakdown of adiabaticity in analogy to the Faraday effect in electromagnetism. We demonstrate that the driving of the spin leads to the production of a large number of bosonic excitations in the bath, which strongly affect the spin dynamics. Finally, we quantify the spin-bath entanglement and formulate an analogy with an effective

Spin Chern number and topological phase transition on the Lieb lattice with spin–orbit coupling

International Nuclear Information System (INIS)

Chen, Rui; Zhou, Bin

2017-01-01

We propose that quantum anomalous Hall effect may occur in the Lieb lattice, when Rashba spin–orbit coupling, spin-independent and spin-dependent staggered potentials are introduced into the lattice. It is found that spin Chern numbers of two degenerate flat bands change from 0 to ±2 due to Rashba spin–orbit coupling effect. The inclusion of Rashba spin–orbit coupling and two kinds of staggered potentials opens a gap between the two flat bands. The topological property of the gap is determined by the amplitudes of Rashba spin–orbit coupling and staggered potentials, and thus the topological phase transition from quantum anomalous Hall effect to normal insulator can occur. Finally, the topological phase transition from quantum spin Hall state to normal insulator is discussed when Rashba spin–orbit coupling and intrinsic spin–orbit coupling coexist in the Lieb lattice. - Highlights: • Spin Chern numbers of the bulk states on the Lieb lattice are calculated. • RSOC plays an important role on the topological phase transition on the Lieb lattice. • Quantum anomalous Hall effect can occur due to RSOC and staggered potentials. • Topological phase transition can occur when ISOC and RSOC coexist.

Rearrangement moves on rooted phylogenetic networks.

Science.gov (United States)

Gambette, Philippe; van Iersel, Leo; Jones, Mark; Lafond, Manuel; Pardi, Fabio; Scornavacca, Celine

2017-08-01

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for

Rearrangement moves on rooted phylogenetic networks.

Directory of Open Access Journals (Sweden)

Philippe Gambette

2017-08-01

Full Text Available Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide

Localifecation of variable-basis topological systems | Solovyov ...

African Journals Online (AJOL)

The paper provides another approach to the notion of variable-basis topological system generalizing the fixed-basis concept of S. Vickers, considers functorial relationships between the categories of modified variable-basis topological systems and variable-basis fuzzy topological spaces in the sense of S.E. Rodabaugh ...

Algebraic topology a primer

CERN Document Server

Deo, Satya

2018-01-01

This book presents the first concepts of the topics in algebraic topology such as the general simplicial complexes, simplicial homology theory, fundamental groups, covering spaces and singular homology theory in greater detail. Originally published in 2003, this book has become one of the seminal books. Now, in the completely revised and enlarged edition, the book discusses the rapidly developing field of algebraic topology. Targeted to undergraduate and graduate students of mathematics, the prerequisite for this book is minimal knowledge of linear algebra, group theory and topological spaces. The book discusses about the relevant concepts and ideas in a very lucid manner, providing suitable motivations and illustrations. All relevant topics are covered, including the classical theorems like the Brouwer’s fixed point theorem, Lefschetz fixed point theorem, Borsuk-Ulam theorem, Brouwer’s separation theorem and the theorem on invariance of the domain. Most of the exercises are elementary, but sometimes chal...

Topological map of the Hofstadter butterfly: Fine structure of Chern numbers and Van Hove singularities

International Nuclear Information System (INIS)

Naumis, Gerardo G.

2016-01-01

The Hofstadter butterfly is a quantum fractal with a highly complex nested set of gaps, where each gap represents a quantum Hall state whose quantized conductivity is characterized by topological invariants known as the Chern numbers. Here we obtain simple rules to determine the Chern numbers at all scales in the butterfly fractal and lay out a very detailed topological map of the butterfly by using a method used to describe quasicrystals: the cut and projection method. Our study reveals the existence of a set of critical points that separates orderly patterns of both positive and negative Cherns that appear as a fine structure in the butterfly. This fine structure can be understood as a small tilting of the projection subspace in the cut and projection method and by using a Chern meeting formula. Finally, we prove that the critical points are identified with the Van Hove singularities that exist at every band center in the butterfly landscape. - Highlights: • Use a higher dimensional approach to build a topological map of the Hofstadter butterfly. • There is a fine structure of Chern numbers around each rational flux. • Van Hove singularities are limiting points for topological sequences of the fine flux.

Topological map of the Hofstadter butterfly: Fine structure of Chern numbers and Van Hove singularities

Energy Technology Data Exchange (ETDEWEB)

Naumis, Gerardo G., E-mail: naumis@fisica.unam.mx [Departamento de Física–Química, Instituto de Física, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 20-364, 01000 México, Distrito Federal (Mexico); Department of Physics and Astronomy, George Mason University, Fairfax, VA 22030 (United States); Escuela Superior de Física y Matemáticas, ESIA-Zacatenco, Instituto Politécnico Nacional, México D.F. (Mexico)

2016-04-29

The Hofstadter butterfly is a quantum fractal with a highly complex nested set of gaps, where each gap represents a quantum Hall state whose quantized conductivity is characterized by topological invariants known as the Chern numbers. Here we obtain simple rules to determine the Chern numbers at all scales in the butterfly fractal and lay out a very detailed topological map of the butterfly by using a method used to describe quasicrystals: the cut and projection method. Our study reveals the existence of a set of critical points that separates orderly patterns of both positive and negative Cherns that appear as a fine structure in the butterfly. This fine structure can be understood as a small tilting of the projection subspace in the cut and projection method and by using a Chern meeting formula. Finally, we prove that the critical points are identified with the Van Hove singularities that exist at every band center in the butterfly landscape. - Highlights: • Use a higher dimensional approach to build a topological map of the Hofstadter butterfly. • There is a fine structure of Chern numbers around each rational flux. • Van Hove singularities are limiting points for topological sequences of the fine flux.

Conservation of topological quantum numbers in energy bands

International Nuclear Information System (INIS)

Chang, L.N.; Liang, Y.

1988-01-01

Quantum systems described by parametrized Hamiltinians are studied in a general context. Within this context, the classification scheme of Avron-Seiler-Simon for non-degenerate energy bands is extended to cover general parameter spaces, whole their sum rule is generalized to cover cases with degenerate bands as well. Additive topological quantum numbers are defined, and these are shown to be conserved in energy band ''collisions''. The conservation laws dictate that when some invariants are non-vanishing, no energy gap can develop in a set of degenerate bands. This gives rise to a series of splitting rules

Complexity of generic biochemical circuits: topology versus strength of interactions

Science.gov (United States)

Tikhonov, Mikhail; Bialek, William

2016-12-01

The historical focus on network topology as a determinant of biological function is still largely maintained today, illustrated by the rise of structure-only approaches to network analysis. However, biochemical circuits and genetic regulatory networks are defined both by their topology and by a multitude of continuously adjustable parameters, such as the strength of interactions between nodes, also recognized as important. Here we present a class of simple perceptron-based Boolean models within which comparing the relative importance of topology versus interaction strengths becomes a quantitatively well-posed problem. We quantify the intuition that for generic networks, optimization of interaction strengths is a crucial ingredient of achieving high complexity, defined here as the number of fixed points the network can accommodate. We propose a new methodology for characterizing the relative role of parameter optimization for topologies of a given class.

Number magnitude to finger mapping is disembodied and topological.

Science.gov (United States)

Plaisier, Myrthe A; Smeets, Jeroen B J

2011-03-01

It has been shown that humans associate fingers with numbers because finger counting strategies interact with numerical judgements. At the same time, there is evidence that there is a relation between number magnitude and space as small to large numbers seem to be represented from left to right. In the present study, we investigated whether number magnitude to finger mapping is embodied (related to the order of fingers on the hand) or disembodied (spatial). We let healthy human volunteers name random numbers between 1 and 30, while simultaneously tapping a random finger. Either the hands were placed directly next to each other, 30 cm apart, or the hands were crossed such that the left hand was on the right side of the body mid-line. The results show that naming a smaller number than the previous one was associated with tapping a finger to the left of the previously tapped finger. This shows that there is a spatial (disembodied) mapping between number magnitude and fingers. Furthermore, we show that this mapping is topological rather than metrically scaled.

Effects of rooting via out-groups on in-group topology in phylogeny.

Science.gov (United States)

Ackerman, Margareta; Brown, Daniel G; Loker, David

2014-01-01

Users of phylogenetic methods require rooted trees, because the direction of time depends on the placement of the root. While phylogenetic trees are typically rooted by using an out-group, this mechanism is inappropriate when the addition of an out-group changes the in-group topology. We perform a formal analysis of phylogenetic algorithms under the inclusion of distant out-groups. It turns out that linkage-based algorithms (including UPGMA) and a class of bisecting methods do not modify the topology of the in-group when an out-group is included. By contrast, the popular neighbour joining algorithm fails this property in a strong sense: every data set can have its structure destroyed by some arbitrarily distant outlier. Furthermore, including multiple outliers can lead to an arbitrary topology on the in-group. The standard rooting approach that uses out-groups may be fundamentally unsuited for neighbour joining.

Measurement-only topological quantum computation without forced measurements

International Nuclear Information System (INIS)

Zheng, Huaixiu; Dua, Arpit; Jiang, Liang

2016-01-01

We investigate the measurement-only topological quantum computation (MOTQC) approach proposed by Bonderson et al (2008 Phys. Rev. Lett. 101 010501) where the braiding operation is shown to be equivalent to a series of topological charge ‘forced measurements’ of anyons. In a forced measurement, the charge measurement is forced to yield the desired outcome (e.g. charge 0) via repeatedly measuring charges in different bases. This is a probabilistic process with a certain success probability for each trial. In practice, the number of measurements needed will vary from run to run. We show that such an uncertainty associated with forced measurements can be removed by simulating the braiding operation using a fixed number of three measurements supplemented by a correction operator. Furthermore, we demonstrate that in practice we can avoid applying the correction operator in hardware by implementing it in software. Our findings greatly simplify the MOTQC proposal and only require the capability of performing charge measurements to implement topologically protected transformations generated by braiding exchanges without physically moving anyons. (paper)

Some fixed point theorems in fuzzy reflexive Banach spaces

International Nuclear Information System (INIS)

Sadeqi, I.; Solaty kia, F.

2009-01-01

In this paper, we first show that there are some gaps in the fixed point theorems for fuzzy non-expansive mappings which are proved by Bag and Samanta, in [Bag T, Samanta SK. Fixed point theorems on fuzzy normed linear spaces. Inf Sci 2006;176:2910-31; Bag T, Samanta SK. Some fixed point theorems in fuzzy normed linear spaces. Inform Sci 2007;177(3):3271-89]. By introducing the notion of fuzzy and α- fuzzy reflexive Banach spaces, we obtain some results which help us to establish the correct version of fuzzy fixed point theorems. Second, by applying Theorem 3.3 of Sadeqi and Solati kia [Sadeqi I, Solati kia F. Fuzzy normed linear space and it's topological structure. Chaos, Solitons and Fractals, in press] which says that any fuzzy normed linear space is also a topological vector space, we show that all topological version of fixed point theorems do hold in fuzzy normed linear spaces.

Real topological string amplitudes

Energy Technology Data Exchange (ETDEWEB)

Narain, K.S. [The Abdus Salam International Centre for Theoretical Physics (ICTP),Strada Costiera 11, Trieste, 34151 (Italy); Piazzalunga, N. [Simons Center for Geometry and Physics, State University of New York,Stony Brook, NY, 11794-3636 (United States); International School for Advanced Studies (SISSA) and INFN, Sez. di Trieste,via Bonomea 265, Trieste, 34136 (Italy); Tanzini, A. [International School for Advanced Studies (SISSA) and INFN, Sez. di Trieste,via Bonomea 265, Trieste, 34136 (Italy)

2017-03-15

We discuss the physical superstring correlation functions in type I theory (or equivalently type II with orientifold) that compute real topological string amplitudes. We consider the correlator corresponding to holomorphic derivative of the real topological amplitude G{sub χ}, at fixed worldsheet Euler characteristic χ. This corresponds in the low-energy effective action to N=2 Weyl multiplet, appropriately reduced to the orientifold invariant part, and raised to the power g{sup ′}=−χ+1. We show that the physical string correlator gives precisely the holomorphic derivative of topological amplitude. Finally, we apply this method to the standard closed oriented case as well, and prove a similar statement for the topological amplitude F{sub g}.

treespace: Statistical exploration of landscapes of phylogenetic trees.

Science.gov (United States)

Jombart, Thibaut; Kendall, Michelle; Almagro-Garcia, Jacob; Colijn, Caroline

2017-11-01

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low-dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group-specific consensus phylogenies. treespace also provides a user-friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results. © 2017 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets

Directory of Open Access Journals (Sweden)

Quagliariello Carla

2008-03-01

Full Text Available Abstract Background In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded amino acid residues. Sites undergoing RNA editing evolve at a higher rate than sites not modified by the process. As a result, editing sites strongly affect the evolution of plant mitochondrial genomes, representing an important source of sequence variability and potentially informative characters. To date no clear and convincing evidence has established whether or not editing sites really affect the topology of reconstructed phylogenetic trees. For this reason, we investigated here the effect of RNA editing on the tree building process of twenty different plant mitochondrial gene sequences and by means of computer simulations. Results Based on our simulation study we suggest that the editing ‘noise’ in tree topology inference is mainly manifested at the cDNA level. In particular, editing sites tend to confuse tree topologies when artificial genomic and cDNA sequences are generated shorter than 500 bp and with an editing percentage higher than 5.0%. Similar results have been also obtained with genuine plant mitochondrial genes. In this latter instance, indeed, the topology incongruence increases when the editing percentage goes up from about 3.0 to 14.0%. However, when the average gene length is higher than 1,000 bp (rps3, matR and atp1 no differences in the comparison between inferred genomic and cDNA topologies could be detected. Conclusions Our findings by the here reported in silico and in vivo computer simulation system seem to strongly suggest that editing sites contribute in the generation of misleading phylogenetic trees if the analyzed mitochondrial gene sequence is highly edited (higher than 3.0% and reduced in length (shorter than 500 bp. In the current lack of direct experimental evidence the results

The Topological Vertex

CERN Document Server

Aganagic, M; Marino, M; Vafa, C; Aganagic, Mina; Klemm, Albrecht; Marino, Marcos; Vafa, Cumrun

2005-01-01

We construct a cubic field theory which provides all genus amplitudes of the topological A-model for all non-compact Calabi-Yau toric threefolds. The topology of a given Feynman diagram encodes the topology of a fixed Calabi-Yau, with Schwinger parameters playing the role of Kahler classes of Calabi-Yau. We interpret this result as an operator computation of the amplitudes in the B-model mirror which is the Kodaira-Spencer quantum theory. The only degree of freedom of this theory is an unconventional chiral scalar on a Riemann surface. In this setup we identify the B-branes on the mirror Riemann surface as fermions related to the chiral boson by bosonization.

Integrated topology and shape optimization in structural design

Science.gov (United States)

Bremicker, M.; Chirehdast, M.; Kikuchi, N.; Papalambros, P. Y.

1990-01-01

Structural optimization procedures usually start from a given design topology and vary its proportions or boundary shapes to achieve optimality under various constraints. Two different categories of structural optimization are distinguished in the literature, namely sizing and shape optimization. A major restriction in both cases is that the design topology is considered fixed and given. Questions concerning the general layout of a design (such as whether a truss or a solid structure should be used) as well as more detailed topology features (e.g., the number and connectivities of bars in a truss or the number of holes in a solid) have to be resolved by design experience before formulating the structural optimization model. Design quality of an optimized structure still depends strongly on engineering intuition. This article presents a novel approach for initiating formal structural optimization at an earlier stage, where the design topology is rigorously generated in addition to selecting shape and size dimensions. A three-phase design process is discussed: an optimal initial topology is created by a homogenization method as a gray level image, which is then transformed to a realizable design using computer vision techniques; this design is then parameterized and treated in detail by sizing and shape optimization. A fully automated process is described for trusses. Optimization of two dimensional solid structures is also discussed. Several application-oriented examples illustrate the usefulness of the proposed methodology.

Topology

CERN Document Server

Hocking, John G

1988-01-01

""As textbook and reference work, this is a valuable addition to the topological literature."" - Mathematical ReviewsDesigned as a text for a one-year first course in topology, this authoritative volume offers an excellent general treatment of the main ideas of topology. It includes a large number and variety of topics from classical topology as well as newer areas of research activity.There are four set-theoretic chapters, followed by four primarily algebraic chapters. Chapter I covers the fundamentals of topological and metrical spaces, mappings, compactness, product spaces, the Tychonoff t

Inferring 'weak spots' in phylogenetic trees: application to mosasauroid nomenclature.

Science.gov (United States)

Madzia, Daniel; Cau, Andrea

2017-01-01

Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the 'weak spots' in the phylogeny of mosasauroids, we revise the nomenclature of the 'traditionally' recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.

Thermodynamics of the topological Kondo model

Directory of Open Access Journals (Sweden)

Francesco Buccheri

2015-07-01

Full Text Available Using the thermodynamic Bethe ansatz, we investigate the topological Kondo model, which describes a set of one-dimensional external wires, pertinently coupled to a central region hosting a set of Majorana bound states. After a short review of the Bethe ansatz solution, we study the system at finite temperature and derive its free energy for arbitrary (even and odd number of external wires. We then analyse the ground state energy as a function of the number of external wires and of their couplings to the Majorana bound states. Then, we compute, both for small and large temperatures, the entropy of the Majorana degrees of freedom localized within the central region and connected to the external wires. Our exact computation of the impurity entropy provides evidence of the importance of fermion parity symmetry in the realization of the topological Kondo model. Finally, we also obtain the low-temperature behaviour of the specific heat of the Majorana bound states, which provides a signature of the non-Fermi-liquid nature of the strongly coupled fixed point.

Thermodynamics of the topological Kondo model

Energy Technology Data Exchange (ETDEWEB)

Buccheri, Francesco, E-mail: buccheri@iip.ufrn.br [International Institute of Physics, Universidade Federal do Rio Grande do Norte, 59078-400 Natal, RN (Brazil); Babujian, Hrachya [International Institute of Physics, Universidade Federal do Rio Grande do Norte, 59078-400 Natal, RN (Brazil); Yerevan Physics Institute, Alikhanian Brothers 2, Yerevan, 375036 (Armenia); Korepin, Vladimir E. [International Institute of Physics, Universidade Federal do Rio Grande do Norte, 59078-400 Natal, RN (Brazil); C. N. Yang Institute for Theoretical Physics, Stony Brook University, NY 11794 (United States); Sodano, Pasquale [International Institute of Physics, Universidade Federal do Rio Grande do Norte, 59078-400 Natal, RN (Brazil); Departemento de Fisíca Teorica e Experimental, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Trombettoni, Andrea [CNR-IOM DEMOCRITOS Simulation Center, Via Bonomea 265, I-34136 Trieste (Italy); SISSA and INFN, Sezione di Trieste, Via Bonomea 265, I-34136 Trieste (Italy)

2015-07-15

Using the thermodynamic Bethe ansatz, we investigate the topological Kondo model, which describes a set of one-dimensional external wires, pertinently coupled to a central region hosting a set of Majorana bound states. After a short review of the Bethe ansatz solution, we study the system at finite temperature and derive its free energy for arbitrary (even and odd) number of external wires. We then analyse the ground state energy as a function of the number of external wires and of their couplings to the Majorana bound states. Then, we compute, both for small and large temperatures, the entropy of the Majorana degrees of freedom localized within the central region and connected to the external wires. Our exact computation of the impurity entropy provides evidence of the importance of fermion parity symmetry in the realization of the topological Kondo model. Finally, we also obtain the low-temperature behaviour of the specific heat of the Majorana bound states, which provides a signature of the non-Fermi-liquid nature of the strongly coupled fixed point.

Polytomy identification in microbial phylogenetic reconstruction

Directory of Open Access Journals (Sweden)

Lin Guan

2011-12-01

Full Text Available Abstract Background A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies for simplicity, although polytomies (multifurcating branches may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach, "PolyPhy", which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties. Results PolyPhy employs a machine learning technique, BLR (Bayesian logistic regression classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features, 'LR' (Leaf rate, 'IntraR' (Intra-subset branch rate and 'InterR' (Inter-subset branch rate, all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure (balanced measure between precision and recall of 81% with about 0.9 area under the curve (AUC of ROC. Conclusions PolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http://digbio.missouri.edu/ComPhy/phyloTreeBiNonBi-1.0.zip.

Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.

Science.gov (United States)

Puigbò, Pere; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."

Topological hierarchy matters — topological matters with superlattices of defects

International Nuclear Information System (INIS)

He Jing; Kou Su-Peng

2016-01-01

Topological insulators/superconductors are new states of quantum matter with metallic edge/surface states. In this paper, we review the defects effect in these topological states and study new types of topological matters — topological hierarchy matters. We find that both topological defects (quantized vortices) and non topological defects (vacancies) can induce topological mid-gap states in the topological hierarchy matters after considering the superlattice of defects. These topological mid-gap states have nontrivial topological properties, including the nonzero Chern number and the gapless edge states. Effective tight-binding models are obtained to describe the topological mid-gap states in the topological hierarchy matters. (topical review)

Generation of linearly polarized orbital angular momentum modes in a side-hole ring fiber with tunable topology numbers.

Science.gov (United States)

Han, Ya; Liu, Yan-Ge; Huang, Wei; Wang, Zhi; Guo, Jun-Qi; Luo, Ming-Ming

2016-07-25

A refractive index (RI) tunable functional materials infiltrated side-hole ring fiber (SHRF) is proposed to generate 10 LP OAM states with 6 topology numbers. On the basis of perturbation theory, the basis of the SHRF is demonstrated to be the LP modes. After a fixed propagation distance of 0.03 m, 0.009 m and 0.012 m, the phase difference between the odd and even LP11x, LP21x,y, LP31x,y modes in the SHRF accumulate to ± π/2 respectively with na ranging from 1.412 to 1.44. Correspondingly, the output states are OAM ± 1x, OAM ± 2x,y, OAM ± 3x,y with a bandwidth of 380 nm, 100 nm and 80 nm respectively. The proposed fiber is easy to be fabricated with the mature fiber drawing technology and could facilitate the realization of all fiber based OAM system.

Topological Methods for Visualization

Energy Technology Data Exchange (ETDEWEB)

Berres, Anne Sabine [Los Alamos National Lab. (LANL), Los Alamos, NM (United Stat

2016-04-07

This slide presentation describes basic topological concepts, including topological spaces, homeomorphisms, homotopy, betti numbers. Scalar field topology explores finding topological features and scalar field visualization, and vector field topology explores finding topological features and vector field visualization.

Using tree diversity to compare phylogenetic heuristics.

Science.gov (United States)

Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

2009-04-29

Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

Impact of topology in foliated quantum Einstein gravity.

Science.gov (United States)

Houthoff, W B; Kurov, A; Saueressig, F

2017-01-01

We use a functional renormalization group equation tailored to the Arnowitt-Deser-Misner formulation of gravity to study the scale dependence of Newton's coupling and the cosmological constant on a background spacetime with topology [Formula: see text]. The resulting beta functions possess a non-trivial renormalization group fixed point, which may provide the high-energy completion of the theory through the asymptotic safety mechanism. The fixed point is robust with respect to changing the parametrization of the metric fluctuations and regulator scheme. The phase diagrams show that this fixed point is connected to a classical regime through a crossover. In addition the flow may exhibit a regime of "gravitational instability", modifying the theory in the deep infrared. Our work complements earlier studies of the gravitational renormalization group flow on a background topology [Formula: see text] (Biemans et al. Phys Rev D 95:086013, 2017, Biemans et al. arXiv:1702.06539, 2017) and establishes that the flow is essentially independent of the background topology.

Inferring Phylogenetic Networks Using PhyloNet.

Science.gov (United States)

Wen, Dingqiao; Yu, Yun; Zhu, Jiafan; Nakhleh, Luay

2018-07-01

PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or biallelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudolikelihood measure. PhyloNet summarizes the results of the various analyzes and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.

Electron polarizability of crystalline solids in quantizing magnetic fields and topological gap numbers

Czech Academy of Sciences Publication Activity Database

Středa, Pavel; Jonckheere, T.; Martin, T.

2008-01-01

Roč. 100, - (2008), 146804/1-146804/4 ISSN 0031-9007 R&D Projects: GA ČR GA202/05/0365 Institutional research plan: CEZ:AV0Z10100521 Keywords : electron polarizability * quantum Hall effect * topological numbers Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 7.180, year: 2008

On Determining if Tree-based Networks Contain Fixed Trees.

Science.gov (United States)

Anaya, Maria; Anipchenko-Ulaj, Olga; Ashfaq, Aisha; Chiu, Joyce; Kaiser, Mahedi; Ohsawa, Max Shoji; Owen, Megan; Pavlechko, Ella; St John, Katherine; Suleria, Shivam; Thompson, Keith; Yap, Corrine

2016-05-01

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is N based on T? We show that it is [Formula: see text]-hard to decide, by reduction from 3-Dimensional Matching (3DM) and further that the problem is fixed-parameter tractable.

New weighting methods for phylogenetic tree reconstruction using multiple loci.

Science.gov (United States)

Misawa, Kazuharu; Tajima, Fumio

2012-08-01

Efficient determination of evolutionary distances is important for the correct reconstruction of phylogenetic trees. The performance of the pooled distance required for reconstructing a phylogenetic tree can be improved by applying large weights to appropriate distances for reconstructing phylogenetic trees and small weights to inappropriate distances. We developed two weighting methods, the modified Tajima-Takezaki method and the modified least-squares method, for reconstructing phylogenetic trees from multiple loci. By computer simulations, we found that both of the new methods were more efficient in reconstructing correct topologies than the no-weight method. Hence, we reconstructed hominoid phylogenetic trees from mitochondrial DNA using our new methods, and found that the levels of bootstrap support were significantly increased by the modified Tajima-Takezaki and by the modified least-squares method.

A general action for topological quantum field theories

International Nuclear Information System (INIS)

Dayi, O.F.

1989-03-01

Topological field theories can be formulated by beginning from a higher dimensional action. The additional dimension is an unphysical time parameter and the action is the derivative of a functional W with respect to this variable. In the d = 4 case, it produces actions which are shown to give topological quantum field theory after gauge fixing. In d = 3 this action leads to the Hamiltonian, which yields the Floer groups if the additional parameter is treated as physical when W is the pure Chern-Simons action. This W can be used to define a topological quantum field theory in d = 3 by treating the additional parameter as unphysical. The BFV-BRST operator quantization of this theory yields to an enlarged system which has only first class constraints. This is not identical to the previously introduced d = 3 topological quantum field theory, even if it is shown that the latter theory also gives the theory which we began with, after a partial gauge fixing. (author). 18 refs

Topological twist in four dimensions, R-duality and hyperinstantons

International Nuclear Information System (INIS)

Anselmi, D.; Fre, P.

1993-01-01

In this paper we continue the programme of topologically twisting N=2 theories in D=4, focusing on the coupling of vector multiplets to N=2 supergravity. We show that in the minimal case, namely when the special gometry prepotential F(X) is a quadratic polynomial, the theory has a so far unknown on-shell U(1) symmetry, that we name R-duality. R-duality is a generalization of the chiral-dual on-shell symmetry of N=2 pure supergravity and of the R-symmetry of N=2 super Yang-Mills theory. Thanks to this, the theory can be topologically twisted and topologically shifted, precisely as pure N=2 supergravity, to yield a natural coupling of topological gravity to topological Yang-Mills theory. The gauge-fixing condition that emerges from the twisting is the self-duality condition on the gauge field strength and on the spin connection. Hence our theory reduces to intersection theory in the moduli-space of gauge instantons living in gravitational instanton backgrounds. We remark that, for deep properties of the parent N=2 theory, the topological Yang-Mills theory we obtain by taking the flat space limit of our gravity-coupled lagrangian is different from the Donaldson theory constructed by Witten. Whether this difference is substantial and what its geometrical implications may be is yet to be seen. We also discuss the topological twist of the hypermultiplets leading to topological quaternionic sigma-models. The instantons of these models, named by us hyperinstantons, correspond to a notion of triholomorphic mappings discussed in the paper. In all cases the new ghost number is the sum of the old ghost number plus the R-duality charge. The observables described by the theory are briefly discussed. In conclusion, the topological twist of the complete N=2 theory defines intersection theory in the moduli-space of gauge instantons plus gravitational instantons plus hyperinstantons. This is possibly a new subject for further mathematical investigation. (orig.)

Fixed Points on the Real numbers without the Equality Test

DEFF Research Database (Denmark)

Korovina, Margarita

2002-01-01

In this paper we present a study of definability properties of fixed points of effective operators on the real numbers without the equality test. In particular we prove that Gandy theorem holds for the reals without the equality test. This provides a useful tool for dealing with recursive...

Statistics of an ideal homogeneous Bose gas with a fixed number of particles

International Nuclear Information System (INIS)

Alekseev, Vladimir A

2001-01-01

The distribution function w 0 (n 0 ) of the number n 0 of particles is found for the condensate of an ideal gas of free bosons with a fixed total number N of particles. It is shown that above the critical temperature (T > T c ) this function has the usual form w 0 (n 0 ) = (1 - e μ )e μn 0 , where μ is the chemical potential in temperature units. In a narrow vicinity of the critical temperature |T/T c - 1| ≤ N -1/3 , this distribution changes and at T c acquires the form of a resonance. The width of the resonance depends on the shape of the volume occupied by the gas and it has exponential (but not the Gaussian) wings. As the temperature is lowered, the resonance maximum shifts to larger values of n 0 and its width tends to zero, which corresponds to the suppression of fluctuations. For N → ∞, this change occurs abruptly. The distribution function of the number of particles in excited states for the systems with a fixed and a variable number of particles (when only a mean number of particles is fixed) prove to be identical and have the usual form. (physical basis of quantum electronics)

Some remarks on the topology of hyperbolic actions of Rn on n-manifolds

Science.gov (United States)

Bouloc, Damien

2017-11-01

This paper contains some results on the topology of a nondegenerate action of Rn on a compact connected n-manifold M when the action is totally hyperbolic (i.e. its toric degree is zero). We study the R-action generated by a fixed vector of Rn, that provides some results on the number of hyperbolic domains and the number of fixed points of the action. We study with more details the case of the 2-sphere, in particular we investigate some combinatorial properties of the associated 4-valent graph embedded in S2. We also construct hyperbolic actions in dimension 3, on the sphere S3 and on the projective space RP3.

Analysis of Acorus calamus chloroplast genome and its phylogenetic implications.

Science.gov (United States)

Goremykin, Vadim V; Holland, Barbara; Hirsch-Ernst, Karen I; Hellwig, Frank H

2005-09-01

Determining the phylogenetic relationships among the major lines of angiosperms is a long-standing problem, yet the uncertainty as to the phylogenetic affinity of these lines persists. While a number of studies have suggested that the ANITA (Amborella-Nymphaeales-Illiciales-Trimeniales-Aristolochiales) grade is basal within angiosperms, studies of complete chloroplast genome sequences also suggested an alternative tree, wherein the line leading to the grasses branches first among the angiosperms. To improve taxon sampling in the existing chloroplast genome data, we sequenced the chloroplast genome of the monocot Acorus calamus. We generated a concatenated alignment (89,436 positions for 15 taxa), encompassing almost all sequences usable for phylogeny reconstruction within spermatophytes. The data still contain support for both the ANITA-basal and grasses-basal hypotheses. Using simulations we can show that were the ANITA-basal hypothesis true, parsimony (and distance-based methods with many models) would be expected to fail to recover it. The self-evident explanation for this failure appears to be a long-branch attraction (LBA) between the clade of grasses and the out-group. However, this LBA cannot explain the discrepancies observed between tree topology recovered using the maximum likelihood (ML) method and the topologies recovered using the parsimony and distance-based methods when grasses are deleted. Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the ML tree, when according to the simulations they would be expected to, when the out-group (Pinus) is deleted, suggests that either the generating tree is not correct or the best symmetric model is misspecified (or both). We demonstrate that the tree recovered under ML is extremely sensitive to model specification and that the best symmetric model is misspecified. Hence, we remain agnostic regarding phylogenetic relationships among basal angiosperm lineages.

Impact of topology in foliated quantum Einstein gravity

Energy Technology Data Exchange (ETDEWEB)

Houthoff, W.B.; Saueressig, F. [Radboud University Nijmegen, Institute for Mathematics, Astrophysics and Particle Physics (IMAPP), Nijmegen (Netherlands); Kurov, A. [Radboud University Nijmegen, Institute for Mathematics, Astrophysics and Particle Physics (IMAPP), Nijmegen (Netherlands); Moscow State University, Department of Theoretical Physics, Moscow (Russian Federation)

2017-07-15

We use a functional renormalization group equation tailored to the Arnowitt-Deser-Misner formulation of gravity to study the scale dependence of Newton's coupling and the cosmological constant on a background spacetime with topology S{sup 1} x S{sup d}. The resulting beta functions possess a non-trivial renormalization group fixed point, which may provide the high-energy completion of the theory through the asymptotic safety mechanism. The fixed point is robust with respect to changing the parametrization of the metric fluctuations and regulator scheme. The phase diagrams show that this fixed point is connected to a classical regime through a crossover. In addition the flow may exhibit a regime of ''gravitational instability'', modifying the theory in the deep infrared. Our work complements earlier studies of the gravitational renormalization group flow on a background topology S{sup 1} x T{sup d} (Biemans et al. Phys Rev D 95:086013, 2017, Biemans et al. arXiv:1702.06539, 2017) and establishes that the flow is essentially independent of the background topology. (orig.)

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers.

Science.gov (United States)

Thuillard, Marc; Fraix-Burnet, Didier

2015-01-01

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters' approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.

Topological Structures on DMC Spaces †

Directory of Open Access Journals (Sweden)

Rajai Nasser

2018-05-01

Full Text Available Two channels are said to be equivalent if they are degraded from each other. The space of equivalent channels with input alphabet X and output alphabet Y can be naturally endowed with the quotient of the Euclidean topology by the equivalence relation. A topology on the space of equivalent channels with fixed input alphabet X and arbitrary but finite output alphabet is said to be natural if and only if it induces the quotient topology on the subspaces of equivalent channels sharing the same output alphabet. We show that every natural topology is σ -compact, separable and path-connected. The finest natural topology, which we call the strong topology, is shown to be compactly generated, sequential and T 4 . On the other hand, the strong topology is not first-countable anywhere, hence it is not metrizable. We introduce a metric distance on the space of equivalent channels which compares the noise levels between channels. The induced metric topology, which we call the noisiness topology, is shown to be natural. We also study topologies that are inherited from the space of meta-probability measures by identifying channels with their Blackwell measures.

Topological signatures of interstellar magnetic fields - I. Betti numbers and persistence diagrams

Science.gov (United States)

Makarenko, Irina; Shukurov, Anvar; Henderson, Robin; Rodrigues, Luiz F. S.; Bushby, Paul; Fletcher, Andrew

2018-04-01

The interstellar medium (ISM) is a magnetized system in which transonic or supersonic turbulence is driven by supernova explosions. This leads to the production of intermittent, filamentary structures in the ISM gas density, whilst the associated dynamo action also produces intermittent magnetic fields. The traditional theory of random functions, restricted to second-order statistical moments (or power spectra), does not adequately describe such systems. We apply topological data analysis (TDA), sensitive to all statistical moments and independent of the assumption of Gaussian statistics, to the gas density fluctuations in a magnetohydrodynamic simulation of the multiphase ISM. This simulation admits dynamo action, so produces physically realistic magnetic fields. The topology of the gas distribution, with and without magnetic fields, is quantified in terms of Betti numbers and persistence diagrams. Like the more standard correlation analysis, TDA shows that the ISM gas density is sensitive to the presence of magnetic fields. However, TDA gives us important additional information that cannot be obtained from correlation functions. In particular, the Betti numbers per correlation cell are shown to be physically informative. Magnetic fields make the ISM more homogeneous, reducing the abundance of both isolated gas clouds and cavities, with a stronger effect on the cavities. Remarkably, the modification of the gas distribution by magnetic fields is captured by the Betti numbers even in regions more than 300 pc from the mid-plane, where the magnetic field is weaker and correlation analysis fails to detect any signatures of magnetic effects.

Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not.

Science.gov (United States)

Hedge, Jessica; Wilson, Daniel J

2014-11-25

Phylogenetic inference in bacterial genomics is fundamental to understanding problems such as population history, antimicrobial resistance, and transmission dynamics. The field has been plagued by an apparent state of contradiction since the distorting effects of recombination on phylogeny were discovered more than a decade ago. Researchers persist with detailed phylogenetic analyses while simultaneously acknowledging that recombination seriously misleads inference of population dynamics and selection. Here we resolve this paradox by showing that phylogenetic tree topologies based on whole genomes robustly reconstruct the clonal frame topology but that branch lengths are badly skewed. Surprisingly, removing recombining sites can exacerbate branch length distortion caused by recombination. Phylogenetic tree reconstruction is a popular approach for understanding the relatedness of bacteria in a population from differences in their genome sequences. However, bacteria frequently exchange regions of their genomes by a process called homologous recombination, which violates a fundamental assumption of phylogenetic methods. Since many researchers continue to use phylogenetics for recombining bacteria, it is important to understand how recombination affects the conclusions drawn from these analyses. We find that whole-genome sequences afford great accuracy in reconstructing evolutionary relationships despite concerns surrounding the presence of recombination, but the branch lengths of the phylogenetic tree are indeed badly distorted. Surprisingly, methods to reduce the impact of recombination on branch lengths can exacerbate the problem. Copyright © 2014 Hedge and Wilson.

Foundations of combinatorial topology

CERN Document Server

Pontryagin, L S

2015-01-01

Hailed by The Mathematical Gazette as ""an extremely valuable addition to the literature of algebraic topology,"" this concise but rigorous introductory treatment focuses on applications to dimension theory and fixed-point theorems. The lucid text examines complexes and their Betti groups, including Euclidean space, application to dimension theory, and decomposition into components; invariance of the Betti groups, with consideration of the cone construction and barycentric subdivisions of a complex; and continuous mappings and fixed points. Proofs are presented in a complete, careful, and eleg

Integrative taxonomy of ciliates: Assessment of molecular phylogenetic content and morphological homology testing.

Science.gov (United States)

Vďačný, Peter

2017-10-01

The very diverse and comparatively complex morphology of ciliates has given rise to numerous taxonomic concepts. However, the information content of the utilized molecular markers has seldom been explored prior to phylogenetic analyses and taxonomic decisions. Likewise, robust testing of morphological homology statements and the apomorphic nature of diagnostic characters of ciliate taxa is rarely carried out. Four phylogenetic techniques that may help address these issues are reviewed. (1) Split spectrum analysis serves to determine the exact number and quality of nucleotide positions supporting individual nodes in phylogenetic trees and to discern long-branch artifacts that cause spurious phylogenies. (2) Network analysis can depict all possible evolutionary trajectories inferable from the dataset and locate and measure the conflict between them. (3) A priori likelihood mapping tests the suitability of data for reconstruction of a well resolved tree, visualizes the tree-likeness of quartets, and assesses the support of an internal branch of a given tree topology. (4) Reconstruction of ancestral morphologies can be applied for analyzing homology and apomorphy statements without circular reasoning. Since these phylogenetic tools are rarely used, their principles and interpretation are introduced and exemplified using various groups of ciliates. Finally, environmental sequencing data are discussed in this light. Copyright © 2017 The Author. Published by Elsevier GmbH.. All rights reserved.

Phylogenetic rooting using minimal ancestor deviation.

Science.gov (United States)

Tria, Fernando Domingues Kümmel; Landan, Giddy; Dagan, Tal

2017-06-19

Ancestor-descendent relations play a cardinal role in evolutionary theory. Those relations are determined by rooting phylogenetic trees. Existing rooting methods are hampered by evolutionary rate heterogeneity or the unavailability of auxiliary phylogenetic information. Here we present a rooting approach, the minimal ancestor deviation (MAD) method, which accommodates heterotachy by using all pairwise topological and metric information in unrooted trees. We demonstrate the performance of the method, in comparison to existing rooting methods, by the analysis of phylogenies from eukaryotes and prokaryotes. MAD correctly recovers the known root of eukaryotes and uncovers evidence for the origin of cyanobacteria in the ocean. MAD is more robust and consistent than existing methods, provides measures of the root inference quality and is applicable to any tree with branch lengths.

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers

Science.gov (United States)

Thuillard, Marc; Fraix-Burnet, Didier

2015-01-01

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters’ approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers. PMID:26508826

Entanglement from topology in Chern-Simons theory

Science.gov (United States)

Salton, Grant; Swingle, Brian; Walter, Michael

2017-05-01

The way in which geometry encodes entanglement is a topic of much recent interest in quantum many-body physics and the AdS/CFT duality. This relation is particularly pronounced in the case of topological quantum field theories, where topology alone determines the quantum states of the theory. In this work, we study the set of quantum states that can be prepared by the Euclidean path integral in three-dimensional Chern-Simons theory. Specifically, we consider arbitrary three-manifolds with a fixed number of torus boundaries in both Abelian U (1 ) and non-Abelian S O (3 ) Chern-Simons theory. For the Abelian theory, we find that the states that can be prepared coincide precisely with the set of stabilizer states from quantum information theory. This constrains the multipartite entanglement present in this theory, but it also reveals that stabilizer states can be described by topology. In particular, we find an explicit expression for the entanglement entropy of a many-torus subsystem using only a single replica, as well as a concrete formula for the number of GHZ states that can be distilled from a tripartite state prepared through path integration. For the non-Abelian theory, we find a notion of "state universality," namely that any state can be prepared to an arbitrarily good approximation. The manifolds we consider can also be viewed as toy models of multiboundary wormholes in AdS/CFT.

Molecular phylogenetic trees - On the validity of the Goodman-Moore augmentation algorithm

Science.gov (United States)

Holmquist, R.

1979-01-01

A response is made to the reply of Nei and Tateno (1979) to the letter of Holmquist (1978) supporting the validity of the augmentation algorithm of Moore (1977) in reconstructions of nucleotide substitutions by means of the maximum parsimony principle. It is argued that the overestimation of the augmented numbers of nucleotide substitutions (augmented distances) found by Tateno and Nei (1978) is due to an unrepresentative data sample and that it is only necessary that evolution be stochastically uniform in different regions of the phylogenetic network for the augmentation method to be useful. The importance of the average value of the true distance over all links is explained, and the relative variances of the true and augmented distances are calculated to be almost identical. The effects of topological changes in the phylogenetic tree on the augmented distance and the question of the correctness of ancestral sequences inferred by the method of parsimony are also clarified.

A quadratic kernel for computing the hybridization number of multiple trees

NARCIS (Netherlands)

L.J.J. van Iersel (Leo); S. Linz

2012-01-01

htmlabstractIt has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter tractable if an instance of the problem consists of

Topological effects on the mechanical properties of polymer knots

Science.gov (United States)

Zhao, Yani; Ferrari, Franco

2017-11-01

The mechanical properties of knotted polymer rings under stretching in a bad or good solvent are investigated by applying a force F to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer conformations is performed on a simple cubic lattice using the Wang-Landau algorithm. The specific energy, specific heat capacity, gyration radius and the force-elongation curves are computed for several knot topologies with lengths up to 120 lattice units. The common features of the mechanical and thermal behavior of stretched short polymer rings forming knots of a given topological type are analyzed as well as the differences arising due to topology and size effects. It is found that these systems admit three different phases depending on the values of the tensile force F and the temperature T. The transitions from one phase to the other are well characterized by the peaks of the specific heat capacity and by the data of the gyration radius and specific energy. At very low temperatures the force-elongation curves show that the stretching of a knot is a stepwise process, which becomes smooth at higher temperatures. Criteria for distinguishing topological and size effects are provided. It turns out from our study that the behavior of short polymer rings is strongly influenced by topological effects. In particular, the swelling and the swelling rate of knots are severely limited by the topological constraints. Several other properties that are affected by topology, like the decay of the specific energy at high tensile forces, are discussed. The fading out of the influences of topological origin with increasing knot lengths has been verified. Some anomalies detected in the plots of the specific heat capacity of very short and complex knots have been explained by the limitations in the number of accessible energy states due to the topological constraints.

Effects of rigid or adaptive confinement on colloidal self-assembly. Fixed vs. fluctuating number of confined particles

Energy Technology Data Exchange (ETDEWEB)

Pȩkalski, J.; Ciach, A. [Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warszawa (Poland); Almarza, N. G. [Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid (Spain)

2015-05-28

The effects of confinement on colloidal self-assembly in the case of fixed number of confined particles are studied in the one dimensional lattice model solved exactly in the grand canonical ensemble (GCE) in Pȩkalski et al. [J. Chem. Phys. 142, 014903 (2015)]. The model considers a pair interaction defined by a short-range attraction plus a longer-range repulsion. We consider thermodynamic states corresponding to self-assembly into clusters. Both fixed and adaptive boundaries are studied. For fixed boundaries, there are particular states in which, for equal average densities, the number of clusters in the GCE is larger than in the canonical ensemble. The dependence of pressure on density has a different form when the system size changes with fixed number of particles and when the number of particles changes with fixed size of the system. In the former case, the pressure has a nonmonotonic dependence on the system size. The anomalous increase of pressure for expanding system is accompanied by formation of a larger number of smaller clusters. In the case of elastic confining surfaces, we observe a bistability, i.e., two significantly different system sizes occur with almost the same probability. The mechanism of the bistability in the closed system is different to that of the case of permeable walls, where the two equilibrium system sizes correspond to a different number of particles.

Unrealistic phylogenetic trees may improve phylogenetic footprinting.

Science.gov (United States)

Nettling, Martin; Treutler, Hendrik; Cerquides, Jesus; Grosse, Ivo

2017-06-01

The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily. Here, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprinting using synthetic and real data. For synthetic data we find that the classification performance is highest when the substitution probability used for phylogenetic footprinting is similar to that used for data generation. For real data, however, we typically find that the classification performance of phylogenetic footprinting surprisingly increases with increasing substitution probabilities and is often highest for unrealistically high substitution probabilities close to one. This finding suggests that choosing realistic model assumptions might not always yield optimal predictions in general and that choosing unrealistically high substitution probabilities close to one might actually improve the classification performance of phylogenetic footprinting. The proposed PF is implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFoo. : martin.nettling@informatik.uni-halle.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Machine learning topological states

Science.gov (United States)

Deng, Dong-Ling; Li, Xiaopeng; Das Sarma, S.

2017-11-01

Artificial neural networks and machine learning have now reached a new era after several decades of improvement where applications are to explode in many fields of science, industry, and technology. Here, we use artificial neural networks to study an intriguing phenomenon in quantum physics—the topological phases of matter. We find that certain topological states, either symmetry-protected or with intrinsic topological order, can be represented with classical artificial neural networks. This is demonstrated by using three concrete spin systems, the one-dimensional (1D) symmetry-protected topological cluster state and the 2D and 3D toric code states with intrinsic topological orders. For all three cases, we show rigorously that the topological ground states can be represented by short-range neural networks in an exact and efficient fashion—the required number of hidden neurons is as small as the number of physical spins and the number of parameters scales only linearly with the system size. For the 2D toric-code model, we find that the proposed short-range neural networks can describe the excited states with Abelian anyons and their nontrivial mutual statistics as well. In addition, by using reinforcement learning we show that neural networks are capable of finding the topological ground states of nonintegrable Hamiltonians with strong interactions and studying their topological phase transitions. Our results demonstrate explicitly the exceptional power of neural networks in describing topological quantum states, and at the same time provide valuable guidance to machine learning of topological phases in generic lattice models.

The topological filtration of gamma-structures

DEFF Research Database (Denmark)

Li, Thomas; Reidys, Christian

2013-01-01

In this paper we study gamma-structures filtered by topological genus. gamma-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A gamma-structure is composed by specific building blocks, that have...... topological genus less than or equal to gamma, where composition means concatenation and nesting of such blocks. Our main results are the derivation of a new bivariate generating function for gamma-structures via symbolic methods, the singularity analysis of the solutions and a central limit theorem...... for the distribution of topological genus in gamma-structures of given length. In our derivation specific bivariate polynomials play a central role. Their coefficients count particular motifs of fixed topological genus and they are of relevance in the context of genus recursion and novel folding algorithms....

Geometrical meaning of winding number and its characterization of topological phases in one-dimensional chiral non-Hermitian systems

Science.gov (United States)

Yin, Chuanhao; Jiang, Hui; Li, Linhu; Lü, Rong; Chen, Shu

2018-05-01

We unveil the geometrical meaning of winding number and utilize it to characterize the topological phases in one-dimensional chiral non-Hermitian systems. While chiral symmetry ensures the winding number of Hermitian systems are integers, it can take half integers for non-Hermitian systems. We give a geometrical interpretation of the half integers by demonstrating that the winding number ν of a non-Hermitian system is equal to half of the summation of two winding numbers ν1 and ν2 associated with two exceptional points, respectively. The winding numbers ν1 and ν2 represent the times of the real part of the Hamiltonian in momentum space encircling the exceptional points and can only take integers. We further find that the difference of ν1 and ν2 is related to the second winding number or energy vorticity. By applying our scheme to a non-Hermitian Su-Schrieffer-Heeger model and an extended version of it, we show that the topologically different phases can be well characterized by winding numbers. Furthermore, we demonstrate that the existence of left and right zero-mode edge states is closely related to the winding number ν1 and ν2.

[Genome-wide identification, phylogenetic analysis and expression profiling of the WOX family genes in Solanum lycopersicum].

Science.gov (United States)

Li, Xiao-xu; Liu, Cheng; Li, Wei; Zhang, Zeng-lin; Gao, Xiao-ming; Zhou, Hui; Guo, Yong-feng

2016-05-01

Members of the plant-specific WOX transcription factor family have been reported to play important roles in cell to cell communication as well as other physiological and developmental processes. In this study, ten members of the WOX transcription factor family were identified in Solanum lycopersicum with HMMER. Neighbor-joining phylogenetic tree, maximum-likelihood tree and Bayesian-inference tree were constructed and similar topologies were shown using the protein sequences of the homeodomain. Phylogenetic study revealed that the 25 WOX family members from Arabidopsis and tomato fall into three clades and nine subfamilies. The patterns of exon-intron structures and organization of conserved domains in Arabidopsis and tomato were consistent based on the phylogenetic results. Transcriptome analysis showed that the expression patterns of SlWOXs were different in different tissue types. Gene Ontology (GO) analysis suggested that, as transcription factors, the SlWOX family members could be involved in a number of biological processes including cell to cell communication and tissue development. Our results are useful for future studies on WOX family members in tomato and other plant species.

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

Science.gov (United States)

Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

Network topology analysis.

Energy Technology Data Exchange (ETDEWEB)

Kalb, Jeffrey L.; Lee, David S.

2008-01-01

Emerging high-bandwidth, low-latency network technology has made network-based architectures both feasible and potentially desirable for use in satellite payload architectures. The selection of network topology is a critical component when developing these multi-node or multi-point architectures. This study examines network topologies and their effect on overall network performance. Numerous topologies were reviewed against a number of performance, reliability, and cost metrics. This document identifies a handful of good network topologies for satellite applications and the metrics used to justify them as such. Since often multiple topologies will meet the requirements of the satellite payload architecture under development, the choice of network topology is not easy, and in the end the choice of topology is influenced by both the design characteristics and requirements of the overall system and the experience of the developer.

Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets.

Science.gov (United States)

García-Pereira, María Jesús; Caballero, Armando; Quesada, Humberto

2010-05-01

Using in silico amplified fragment length polymorphism (AFLP) fingerprints, we explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unbalanced trees with recent, uniform and ancient radiations, and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.4 substitutions per site. The resulting sequences were used to emulate the AFLP procedure. Trees were estimated by maximum parsimony (MP), neighbor-joining (NJ), and minimum evolution (ME) methods from both DNA sequences and virtual AFLP fingerprints. The estimated trees were compared with the reference trees using a score that measures overall differences in both topology and relative branch length. As expected, the accuracy of AFLP-based phylogenies decreased dramatically in the more divergent data sets. Above a divergence of approximately 0.05, AFLP-based phylogenies were largely inaccurate irrespective of the distinct topology, radiation model, or phylogenetic method used. This value represents an upper bound of expected tree accuracy for data sets with a simple divergence history; AFLP data sets with a similar divergence but with unbalanced topologies and short ancestral branches produced much less accurate trees. The lack of homology of AFLP bands quickly increases with divergence and reaches its maximum value (100%) at a divergence of only 0.4. Low guanine-cytosine (GC) contents increase the number of nonhomologous bands in AFLP data sets and lead to less reliable trees. However, the effect of the lack of band homology on tree accuracy is surprisingly small relative to the negative impact due to the low information content of AFLP characters. Tree-building methods based on genetic distance displayed similar trends and outperformed parsimony

Pseudoperiodic topology

CERN Document Server

Arnold, Vladimir; Zorich, Anton

1999-01-01

This volume offers an account of the present state of the art in pseudoperiodic topology-a young branch of mathematics, born at the boundary between the ergodic theory of dynamical systems, topology, and number theory. Related topics include the theory of algorithms, convex integer polyhedra, Morse inequalities, real algebraic geometry, statistical physics, and algebraic number theory. The book contains many new results. Most of the articles contain brief surveys on the topics, making the volume accessible to a broad audience. From the Preface by V.I. Arnold: "The authors … have done much to s

Orbifold line topology and the cosmic microwave background

Energy Technology Data Exchange (ETDEWEB)

Rathaus, Ben; Ben-David, Assaf; Itzhaki, Nissan, E-mail: ben.rathaus@gmail.com, E-mail: bd.assaf@gmail.com, E-mail: nitzhaki@post.tau.ac.il [Raymond and Beverly Sackler Faculty of Exact Sciences, School of Physics and Astronomy, Tel-Aviv University, Ramat-Aviv, 69978 (Israel)

2013-10-01

We extend our study of a universe with a non-classical stringy topology, and consider an orbifold line topology, R × R{sup 2}/Z{sub p}. This topology has a fixed line and identifies each point in space with p−1 other points. An observable imprint of an orbifold line on the CMB is the appearance of up to (p−1)/2 pairs of matching circles. Searching the WMAP data for matching circles, we can rule out an orbifold line topology with p up to 10, except for p = 8. While the significance of the peak at p = 8 varies between data releases of WMAP, it does not appear in Planck data, enabling us to rule out p = 8 as well.

Analysis of Fixed Duty Cycle Hysteretic Flyback Converter for Firing Set Applications.

Energy Technology Data Exchange (ETDEWEB)

Love, Thomas Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-05-01

This paper analyzes several performance aspects of the fixed-duty-cycle, hysteretic flyback converter topology typically used in firing sets. Topologies with and without active pulse-by-pulse current limiting are considered, and closed-form expressions in terms of basic operating parameters are derived.

Recursive algorithms for phylogenetic tree counting.

Science.gov (United States)

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

Multi-planed unified switching topologies

Science.gov (United States)

Chen, Dong; Heidelberger, Philip; Sugawara, Yutaka

2017-07-04

An apparatus and method for extending the scalability and improving the partitionability of networks that contain all-to-all links for transporting packet traffic from a source endpoint to a destination endpoint with low per-endpoint (per-server) cost and a small number of hops. An all-to-all wiring in the baseline topology is decomposed into smaller all-to-all components in which each smaller all-to-all connection is replaced with star topology by using global switches. Stacking multiple copies of the star topology baseline network creates a multi-planed switching topology for transporting packet traffic. Point-to-point unified stacking method using global switch wiring methods connects multiple planes of a baseline topology by using the global switches to create a large network size with a low number of hops, i.e., low network latency. Grouped unified stacking method increases the scalability (network size) of a stacked topology.

Multiple sequence alignment accuracy and phylogenetic inference.

Science.gov (United States)

Ogden, T Heath; Rosenberg, Michael S

2006-04-01

Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

Science.gov (United States)

Chernomor, Olga; Minh, Bui Quang; von Haeseler, Arndt

2015-12-01

In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

The number of k-colorings of a graph on a fixed surface

DEFF Research Database (Denmark)

Thomassen, Carsten

2006-01-01

We prove that, for every fixed surface S, there exists a largest positive constant c such that every 5-colorable graph with n vertices on S has at least c center dot 2(n) distinct 5-colorings. This is best possible in the sense that, for each sufficiently large natural number n, there is a graph ...

Molecular phylogenetics, seed morphometrics, chromosome number evolution and systematics of European Elatine L. (Elatinaceae species

Directory of Open Access Journals (Sweden)

Gábor Sramkó

2016-12-01

Full Text Available The genus Elatine contains ca 25 species, all of which are small, herbaceous annuals distributed in ephemeral waters on both hemispheres. However, due to a high degree of morphological variability (as a consequence of their amphibious life-style, the taxonomy of this genus remains controversial. Thus, to fill this gap in knowledge, we present a detailed molecular phylogenetic study of this genus based on nuclear (rITS and plastid (accD-psaI, psbJ-petA, ycf6-psbM-trnD sequences using 27 samples from 13 species. On the basis of this phylogenetic analysis, we provide a solid phylogenetic background for the modern taxonomy of the European members of the genus. Traditionally accepted sections of this tree (i.e., Crypta and Elatinella were found to be monophyletic; only E. borchoni—found to be a basal member of the genus—has to be excluded from the latter lineage to achieve monophyly. A number of taxonomic conclusions can also be drawn: E. hexandra, a high-ploid species, is most likely a stabilised hybrid between the main sections; E. campylosperma merits full species status based on both molecular and morphological evidence; E. gussonei is a more widespread and genetically diverse species with two main lineages; and the presence of the Asian E. ambigua in the European flora is questionable. The main lineages recovered in this analysis are also supported by a number of synapomorphic morphological characters as well as uniform chromosome counts. Based on all the evidence presented here, two new subsections within Elatinella are described: subsection Hydropipera consisting of the temperate species of the section, and subsection Macropodae including the Mediterranean species of the section.

On effective theories of topological strings

International Nuclear Information System (INIS)

Elitzur, S.; Forge, A.; Rabinovici, E.

1992-01-01

We study the construction of effective target-space theories of topological string theories. The example of the CP1 topological sigma model is analysed in detail. An effective target-space theory whose correlation functions are defined by the sum over connected Riemann surfaces of all genera is found to be itself topological. The values of the couplings of this effective theory are expressed in terms of those of the world-sheet theory for a general CP1-like world-sheet model. Any model of this type can be obtained as an effective theory. The definition of the effective theory's expectation values as a sum over disconnected surfaces as well, is shown not to be compatible with those of a topological theory, at least as long as the connectivity of the target space is kept fixed. Dilaton-type couplings emerge in the full lagrangian realization of the moduli space of topological theories with n observables. En route, we encounter a nonperturbative duality, an equivalence of theories with different world-sheets and discuss the relation between the cosmological constant in these finite theories and the zero-point function. (orig.)

Finding Non-Zero Stable Fixed Points of the Weighted Kuramoto model is NP-hard

OpenAIRE

Taylor, Richard

2015-01-01

The Kuramoto model when considered over the full space of phase angles [$0,2\\pi$) can have multiple stable fixed points which form basins of attraction in the solution space. In this paper we illustrate the fundamentally complex relationship between the network topology and the solution space by showing that determining the possibility of multiple stable fixed points from the network topology is NP-hard for the weighted Kuramoto Model. In the case of the unweighted model this problem is shown...

From topology to geometry

International Nuclear Information System (INIS)

Eberhart, M.

1996-01-01

A systematic study of the charge density topologies corresponding to a number of transition metal aluminides with the B2 structure indicates that unstable crystal structures are sometimes associated with uncharacteristic topologies. This observation invites the speculation that the distance to a topological instability might relate to a metals phase behavior. Following this speculation, a metric is imposed on the topological theory of Bader, producing a geometrical theory, where it is now possible to assign a distance from a calculated charge density topology to a topological instability. For the cubic transition metals, these distances are shown to correlate with single crystal elastic constants, where the metals that are furthest from an instability are observed to be the stiffest. (author). 16 refs., 1 tab., 9 figs

The coupling of Poisson sigma models to topological backgrounds

Energy Technology Data Exchange (ETDEWEB)

Rosa, Dario [School of Physics, Korea Institute for Advanced Study,Seoul 02455 (Korea, Republic of)

2016-12-13

We extend the coupling to the topological backgrounds, recently worked out for the 2-dimensional BF-model, to the most general Poisson sigma models. The coupling involves the choice of a Casimir function on the target manifold and modifies the BRST transformations. This in turn induces a change in the BRST cohomology of the resulting theory. The observables of the coupled theory are analyzed and their geometrical interpretation is given. We finally couple the theory to 2-dimensional topological gravity: this is the first step to study a topological string theory in propagation on a Poisson manifold. As an application, we show that the gauge-fixed vectorial supersymmetry of the Poisson sigma models has a natural explanation in terms of the theory coupled to topological gravity.

Tight Network Topology Dependent Bounds on Rounds of Communication

OpenAIRE

Chattopadhyay, Arkadev; Langberg, Michael; Li, Shi; Rudra, Atri

2016-01-01

We prove tight network topology dependent bounds on the round complexity of computing well studied $k$-party functions such as set disjointness and element distinctness. Unlike the usual case in the CONGEST model in distributed computing, we fix the function and then vary the underlying network topology. This complements the recent such results on total communication that have received some attention. We also present some applications to distributed graph computation problems. Our main contri...

Geometrical protection of topological magnetic solitons in microprocessed chiral magnets

Science.gov (United States)

Mito, Masaki; Ohsumi, Hiroyuki; Tsuruta, Kazuki; Kotani, Yoshinori; Nakamura, Tetsuya; Togawa, Yoshihiko; Shinozaki, Misako; Kato, Yusuke; Kishine, Jun-ichiro; Ohe, Jun-ichiro; Kousaka, Yusuke; Akimitsu, Jun; Inoue, Katsuya

2018-01-01

A chiral soliton lattice stabilized in a monoaxial chiral magnet CrNb3S6 is a magnetic superlattice consisting of magnetic kinks with a ferromagnetic background. The magnetic kinks are considered to be topological magnetic solitons (TMSs). Changes in the TMS number yield discretized responses in magnetization and electrical conductivity, and this effect is more prominent in smaller crystals. We demonstrate that, in microprocessed CrNb3S6 crystals, TMSs are geometrically protected through element-selected micromagnetometry using soft x-ray magnetic circular dichroism (MCD). A series of x-ray MCD data is supported by mean-field and micromagnetic analyses. By designing the microcrystal geometry, TMS numbers can be successfully changed and fixed over a wide range of magnetic fields.

Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family

Directory of Open Access Journals (Sweden)

Berger-Bächi Brigitte

2008-12-01

Full Text Available Abstract Background The bacterial cell wall is the target of many antibiotics and cell envelope constituents are critical to host-pathogen interactions. To combat resistance development and virulence, a detailed knowledge of the individual factors involved is essential. Members of the LytR-CpsA-Psr family of cell envelope-associated attenuators are relevant for β-lactam resistance, biofilm formation, and stress tolerance, and they are suggested to play a role in cell wall maintenance. However, their precise function is still unknown. This study addresses the occurrence as well as sequence-based characteristics of the LytR-CpsA-Psr proteins. Results A comprehensive list of LytR-CpsA-Psr proteins was established, and their phylogenetic distribution and clustering into subgroups was determined. LytR-CpsA-Psr proteins were present in all Gram-positive organisms, except for the cell wall-deficient Mollicutes and one strain of the Clostridiales. In contrast, the majority of Gram-negatives did not contain LytR-CpsA-Psr family members. Despite high sequence divergence, the LytR-CpsA-Psr domains of different subclusters shared a highly similar, predicted mixed a/β-structure, and conserved charged residues. PhoA fusion experiments, using MsrR of Staphylococcus aureus, confirmed membrane topology predictions and extracellular location of its LytR-CpsA-Psr domain. Conclusion The LytR-CpsA-Psr domain is unique to bacteria. The presence of diverse subgroups within the LytR-CpsA-Psr family might indicate functional differences, and could explain variations in phenotypes of respective mutants reported. The identified conserved structural elements and amino acids are likely to be important for the function of the domain and will help to guide future studies of the LytR-CpsA-Psr proteins.

Phylogenetic relationships in Asarum: Effect of data partitioning and a revised classification.

Science.gov (United States)

Sinn, Brandon T; Kelly, Lawrence M; Freudenstein, John V

2015-05-01

Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato (Aristolochiaceae) have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyzed additional molecular markers from the nuclear and plastid genomes, reevaluated the possibility of a derived loss of autonomous self-pollination, and investigated the topological effects of matrix-partitioning-scheme choice. We sequenced seven plastid regions and the nuclear ITS1-ITS2 region of 58 individuals representing all previously recognized Asarum s.l. segregate genera and the monotypic genus Saruma. Matrices were partitioned using common a priori partitioning schemes and PartitionFinder. Topologies that were recovered using a priori partitioning of matrices differed from those recovered using a PartitionFinder-selected scheme, and by analysis method. We recovered six monophyletic groups that we circumscribed into three subgenera and six sections. Putative fungal mimic characters served as synapomorphies only for subgenus Heterotropa. Subgenus Geotaenium, a new subgenus, was recovered as sister to the remainder of Asarum by ML analyses of highly partitioned datasets. Section Longistylis, also newly named, is sister to section Hexastylis. Our analyses do not unambiguously support a single origin for all fungal-mimicry characters. Topologies recovered through the analysis of PartitionFinder-optimized matrices can differ drastically from those inferred from a priori partitioned matrices, and by analytical method. We recommend that investigators evaluate the topological effects of matrix partitioning using multiple methods of phylogenetic reconstruction. © 2015 Botanical Society of America, Inc.

Routing in Networks with Random Topologies

Science.gov (United States)

Bambos, Nicholas

1997-01-01

We examine the problems of routing and server assignment in networks with random connectivities. In such a network the basic topology is fixed, but during each time slot and for each of tis input queues, each server (node) is either connected to or disconnected from each of its queues with some probability.

Fast Structural Search in Phylogenetic Databases

Directory of Open Access Journals (Sweden)

William H. Piel

2005-01-01

Full Text Available As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P . The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising

Cosmic Topology

Science.gov (United States)

Luminet, Jean-Pierre

2015-08-01

Cosmic Topology is the name given to the study of the overall shape of the universe, which involves both global topological features and more local geometrical properties such as curvature. Whether space is finite or infinite, simply-connected or multi-connected like a torus, smaller or greater than the portion of the universe that we can directly observe, are questions that refer to topology rather than curvature. A striking feature of some relativistic, multi-connected "small" universe models is to create multiples images of faraway cosmic sources. While the most recent cosmological data fit the simplest model of a zero-curvature, infinite space model, they are also consistent with compact topologies of the three homogeneous and isotropic geometries of constant curvature, such as, for instance, the spherical Poincaré Dodecahedral Space, the flat hypertorus or the hyperbolic Picard horn. After a "dark age" period, the field of Cosmic Topology has recently become one of the major concerns in cosmology, not only for theorists but also for observational astronomers, leaving open a number of unsolved issues.

On the Shapley Value of Unrooted Phylogenetic Trees.

Science.gov (United States)

Wicke, Kristina; Fischer, Mareike

2018-01-17

The Shapley value, a solution concept from cooperative game theory, has recently been considered for both unrooted and rooted phylogenetic trees. Here, we focus on the Shapley value of unrooted trees and first revisit the so-called split counts of a phylogenetic tree and the Shapley transformation matrix that allows for the calculation of the Shapley value from the edge lengths of a tree. We show that non-isomorphic trees may have permutation-equivalent Shapley transformation matrices and permutation-equivalent null spaces. This implies that estimating the split counts associated with a tree or the Shapley values of its leaves does not suffice to reconstruct the correct tree topology. We then turn to the use of the Shapley value as a prioritization criterion in biodiversity conservation and compare it to a greedy solution concept. Here, we show that for certain phylogenetic trees, the Shapley value may fail as a prioritization criterion, meaning that the diversity spanned by the top k species (ranked by their Shapley values) cannot approximate the total diversity of all n species.

Bayesian models for comparative analysis integrating phylogenetic uncertainty

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Villemereuil Pierre de

2012-06-01

Full Text Available Abstract Background Uncertainty in comparative analyses can come from at least two sources: a phylogenetic uncertainty in the tree topology or branch lengths, and b uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow and inflated significance in hypothesis testing (e.g. p-values will be too small. Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible

Bayesian models for comparative analysis integrating phylogenetic uncertainty

Science.gov (United States)

2012-01-01

Background Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for

Charges and Electromagnetic Radiation as Topological Excitations

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Manfried Faber

2017-01-01

Full Text Available We discuss a model with stable topological solitons in Minkowski space with only three degrees of freedom, the rotational angles of a spatial Dreibein. This model has four types of solitons differing in two topological quantum numbers which we identify with electric charge and spin. The vacuum has a two-dimensional degeneracy leading to two types of massless excitations, characterised by a topological quantum number which could have a physical equivalent in the photon number.

Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification.

Directory of Open Access Journals (Sweden)

Angela Stokes

Full Text Available The requirement for large amounts of good quality DNA for whole-genome applications prohibits their use for small, laser capture micro-dissected (LCM, and/or rare clinical samples, which are also often formalin-fixed and paraffin-embedded (FFPE. Whole-genome amplification of DNA from these samples could, potentially, overcome these limitations. However, little is known about the artefacts introduced by amplification of FFPE-derived DNA with regard to genotyping, and subsequent copy number and loss of heterozygosity (LOH analyses. Using a ligation adaptor amplification method, we present data from a total of 22 Affymetrix SNP 6.0 experiments, using matched paired amplified and non-amplified DNA from 10 LCM FFPE normal and dysplastic oral epithelial tissues, and an internal method control. An average of 76.5% of SNPs were called in both matched amplified and non-amplified DNA samples, and concordance was a promising 82.4%. Paired analysis for copy number, LOH, and both combined, showed that copy number changes were reduced in amplified DNA, but were 99.5% concordant when detected, amplifications were the changes most likely to be 'missed', only 30% of non-amplified LOH changes were identified in amplified pairs, and when copy number and LOH are combined ∼50% of gene changes detected in the unamplified DNA were also detected in the amplified DNA and within these changes, 86.5% were concordant for both copy number and LOH status. However, there are also changes introduced as ∼20% of changes in the amplified DNA are not detected in the non-amplified DNA. An integrative network biology approach revealed that changes in amplified DNA of dysplastic oral epithelium localize to topologically critical regions of the human protein-protein interaction network, suggesting their functional implication in the pathobiology of this disease. Taken together, our results support the use of amplification of FFPE-derived DNA, provided sufficient samples are used

Topological field theory: zero-modes and renormalization

International Nuclear Information System (INIS)

Ouvry, S.; Thompson, G.

1989-09-01

We address the issue of the non-triviality of the observables in various Topological Field Theories by means of the explicit introduction of the zero-modes into the BRST algebra. Supersymmetric quantum mechanics and Topological Yang-Mills theory are dealt with in detail. It is shown that due to the presence of fermionic zero-modes the BRST algebra may be dynamically broken leading to non trivial observables albeit the local cohomology being trivial. However the metric and coupling constant independence of the observables are still valid. A renormalization procedure is given that correctly incorporates the zero-modes. Particular attention is given to the conventional gauge fixing in Topological Yang-Mills theories, with emphasis on the geometrical character of the fields and their role in the non-triviality of the observables

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

Science.gov (United States)

Zhou, Xiaofan; Shen, Xing-Xing; Hittinger, Chris Todd

2018-01-01

Abstract The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets with hundreds to thousands of genes and up to 200 taxa with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation-based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the programs’ relative performance. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses. PMID:29177474

Modeling Internet Topology Dynamics

NARCIS (Netherlands)

Haddadi, H.; Uhlig, S.; Moore, A.; Mortier, R.; Rio, M.

Despite the large number of papers on network topology modeling and inference, there still exists ambiguity about the real nature of the Internet AS and router level topology. While recent findings have illustrated the inaccuracies in maps inferred from BGP peering and traceroute measurements,

Adaptive approach to global synchronization of directed networks with fast switching topologies

International Nuclear Information System (INIS)

Qin Buzhi; Lu Xinbiao

2010-01-01

Global synchronization of directed networks with switching topologies is investigated. It is found that if there exists at least one directed spanning tree in the network with the fixed time-average topology and the time-average topology is achieved sufficiently fast, the network will reach global synchronization for appreciate coupling strength. Furthermore, this appreciate coupling strength may be obtained by local adaptive approach. A sufficient condition about the global synchronization is given. Numerical simulations verify the effectiveness of the adaptive strategy.

Topological 2-dimensional quantum mechanics

International Nuclear Information System (INIS)

Dasnieres de Veigy, A.; Ouvry, S.

1992-12-01

A Chern-Simons Lagrangian is defined for a system of planar particles topologically interacting at a distance. The anyon model appears as a particular case where all the particles are identical. Exact N-body eigenstates are proposed and a perturbative algorithm is set up. The case where some particles are fixed on a lattice, is discussed, and curved manifolds are considered. (author) 14 refs

Topological Luttinger liquids from decorated domain walls

Science.gov (United States)

Parker, Daniel E.; Scaffidi, Thomas; Vasseur, Romain

2018-04-01

We introduce a systematic construction of a gapless symmetry-protected topological phase in one dimension by "decorating" the domain walls of Luttinger liquids. The resulting strongly interacting phases provide a concrete example of a gapless symmetry-protected topological (gSPT) phase with robust symmetry-protected edge modes. Using boundary conformal field theory arguments, we show that while the bulks of such gSPT phases are identical to conventional Luttinger liquids, their boundary critical behavior is controlled by a different, strongly coupled renormalization group fixed point. Our results are checked against extensive density matrix renormalization group calculations.

Modelling Dynamic Topologies via Extensions of VDM-RT

DEFF Research Database (Denmark)

Nielsen, Claus Ballegård

Only a few formal methods include descriptions of the network topology that the modelled system is deployed onto. In VDM Real-Time (VDM-RT) this has been enabled for distributed systems that have a static structure. However, when modelling dynamic systems this fixed topology becomes an issue....... Systems with highly distributed and alternating relationships cannot be expressed correctly in a static model. This document describes how VDM-RT can be extended with new language constructs to enable the description of dynamic reconfiguration of the network topology during the runtime execution...... of a model. The extension is developed on the basis of a case study involving a dynamic system that has a constant changing system topology. With a basis in the case study a model is developed that uses the static version of VDM-RT in order to reveal the limitations of the language. The case study...

Topological insulating phases of non-Abelian anyonic chains

Energy Technology Data Exchange (ETDEWEB)

DeGottardi, Wade

2014-08-01

Boundary conformal field theory is brought to bear on the study of topological insulating phases of non- Abelian anyonic chains. These phases display protected anyonic end modes. We consider spin-1/2 su(2)t chains at any level k, focusing on the most prominent examples: the case k = 2 describes Ising anyons (equivalent to Majorana fermions) and k = 3 corresponds to Fibonacci anyons. The method we develop is quite general and rests on a deep connection between boundary conformal field theory and topological symmetry. This method tightly constrains the nature of the topological insulating phases of these chains for general k. Emergent anyons which arise at domain walls are shown to have the same braiding properties as the physical quasiparticles. This suggests a "solid-stat.e" topological quantum computation scheme in which emergent anyons are braided by tuning the couplings of non-Abelian quasiparticles in a fixed network.

Calibrated birth-death phylogenetic time-tree priors for bayesian inference.

Science.gov (United States)

Heled, Joseph; Drummond, Alexei J

2015-05-01

Here we introduce a general class of multiple calibration birth-death tree priors for use in Bayesian phylogenetic inference. All tree priors in this class separate ancestral node heights into a set of "calibrated nodes" and "uncalibrated nodes" such that the marginal distribution of the calibrated nodes is user-specified whereas the density ratio of the birth-death prior is retained for trees with equal values for the calibrated nodes. We describe two formulations, one in which the calibration information informs the prior on ranked tree topologies, through the (conditional) prior, and the other which factorizes the prior on divergence times and ranked topologies, thus allowing uniform, or any arbitrary prior distribution on ranked topologies. Although the first of these formulations has some attractive properties, the algorithm we present for computing its prior density is computationally intensive. However, the second formulation is always faster and computationally efficient for up to six calibrations. We demonstrate the utility of the new class of multiple-calibration tree priors using both small simulations and a real-world analysis and compare the results to existing schemes. The two new calibrated tree priors described in this article offer greater flexibility and control of prior specification in calibrated time-tree inference and divergence time dating, and will remove the need for indirect approaches to the assessment of the combined effect of calibration densities and tree priors in Bayesian phylogenetic inference. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Random fields, topology, and the Imry-Ma argument.

Science.gov (United States)

Proctor, Thomas C; Garanin, Dmitry A; Chudnovsky, Eugene M

2014-03-07

We consider an n-component fixed-length order parameter interacting with a weak random field in d=1, 2, 3 dimensions. Relaxation from the initially ordered state and spin-spin correlation functions are studied on lattices containing hundreds of millions of sites. At n ≤ d the presence of topological defects leads to strong metastability and glassy behavior, with the final state depending on the initial condition. At n=d+1, when topological structures are nonsingular, the system possesses a weak metastability. At n>d+1, when topological objects are absent, the final, lowest-energy state is independent of the initial condition. It is characterized by the exponential decay of correlations that agrees quantitatively with the theory based upon the Imry-Ma argument.

Topological phase transitions from Harper to Fibonacci crystals

Science.gov (United States)

Amit, Guy; Dana, Itzhack

2018-02-01

Topological properties of Harper and generalized Fibonacci chains are studied in crystalline cases, i.e., for rational values of the modulation frequency. The Harper and Fibonacci crystals at fixed frequency are connected by an interpolating one-parameter Hamiltonian. As the parameter is varied, one observes topological phase transitions, i.e., changes in the Chern integers of two bands due to the degeneracy of these bands at some parameter value. For small frequency, corresponding to a semiclassical regime, the degeneracies are shown to occur when the average energy of the two bands is approximately equal to the energy of the classical separatrix. Spectral and topological features of the Fibonacci crystal for small frequency leave a clear imprint on the corresponding Hofstadter butterfly for arbitrary frequency.

Robustness of ancestral sequence reconstruction to phylogenetic uncertainty.

Science.gov (United States)

Hanson-Smith, Victor; Kolaczkowski, Bryan; Thornton, Joseph W

2010-09-01

Ancestral sequence reconstruction (ASR) is widely used to formulate and test hypotheses about the sequences, functions, and structures of ancient genes. Ancestral sequences are usually inferred from an alignment of extant sequences using a maximum likelihood (ML) phylogenetic algorithm, which calculates the most likely ancestral sequence assuming a probabilistic model of sequence evolution and a specific phylogeny--typically the tree with the ML. The true phylogeny is seldom known with certainty, however. ML methods ignore this uncertainty, whereas Bayesian methods incorporate it by integrating the likelihood of each ancestral state over a distribution of possible trees. It is not known whether Bayesian approaches to phylogenetic uncertainty improve the accuracy of inferred ancestral sequences. Here, we use simulation-based experiments under both simplified and empirically derived conditions to compare the accuracy of ASR carried out using ML and Bayesian approaches. We show that incorporating phylogenetic uncertainty by integrating over topologies very rarely changes the inferred ancestral state and does not improve the accuracy of the reconstructed ancestral sequence. Ancestral state reconstructions are robust to uncertainty about the underlying tree because the conditions that produce phylogenetic uncertainty also make the ancestral state identical across plausible trees; conversely, the conditions under which different phylogenies yield different inferred ancestral states produce little or no ambiguity about the true phylogeny. Our results suggest that ML can produce accurate ASRs, even in the face of phylogenetic uncertainty. Using Bayesian integration to incorporate this uncertainty is neither necessary nor beneficial.

Topology optimization of reinforced concrete beams by a spread-over reinforcement model with fixed grid mesh

Directory of Open Access Journals (Sweden)

Benjapon Wethyavivorn

2011-02-01

Full Text Available For this investigation, topology optimization was used as a tool to determine the optimal reinforcement for reinforcedconcrete beam. The topology optimization process was based on a unit finite element cell with layers of concrete and steel.The thickness of the reinforced steel layer of this unit cell was then adjusted when the concrete layer could not carry thetensile or compressive stress. At the same time, unit cells which carried very low stress were eliminated. The process wasperformed iteratively to create a topology of reinforced concrete beam which satisfied design conditions.

Phylogenetic congruence between subtropical trees and their associated fungi.

Science.gov (United States)

Liu, Xubing; Liang, Minxia; Etienne, Rampal S; Gilbert, Gregory S; Yu, Shixiao

2016-12-01

Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next-generation high-throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK , rbcL , atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host-fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant-fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant-fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.

Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

Directory of Open Access Journals (Sweden)

Vidal-Russell Romina

2004-10-01

Full Text Available Abstract Background The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str. in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae. Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales. Results Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene, Cucurbitales (matR or Fabales (atp1. The latter incongruencies suggest that horizontal gene transfer (HGT may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further. Conclusions Rafflesiales are not monophyletic but composed of three or four independent lineages (families: Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to

Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences.

Science.gov (United States)

Rosli, M K A; Zakaria, S S; Syed-Shabthar, S M F; Zainal, Z Z; Shukor, M N; Mahani, M C; Abas-Mazni, O; Md-Zain, B M

2011-03-22

The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.

The Real Topological String on a local Calabi-Yau

CERN Document Server

Krefl, Daniel

2009-01-01

We study the topological string on local P2 with O-plane and D-brane at its real locus, using three complementary techniques. In the A-model, we refine localization on the moduli space of maps with respect to the torus action preserved by the anti-holomorphic involution. This leads to a computation of open and unoriented Gromov-Witten invariants that can be applied to any toric Calabi-Yau with involution. We then show that the full topological string amplitudes can be reproduced within the topological vertex formalism. We obtain the real topological vertex with trivial fixed leg. Finally, we verify that the same results derive in the B-model from the extended holomorphic anomaly equation, together with appropriate boundary conditions. The expansion at the conifold exhibits a gap structure that belongs to a so far unidentified universality class.

Topological Analysis of Wireless Networks (TAWN)

Science.gov (United States)

2016-05-31

19b. TELEPHONE NUMBER (Include area code) 31-05-2016 FINAL REPORT 12-02-2015 -- 31-05-2016 Topological Analysis of Wireless Networks (TAWN) Robinson...Release, Distribution Unlimited) N/A The goal of this project was to develop topological methods to detect and localize vulnerabilities of wireless... topology U U U UU 32 Michael Robinson 202-885-3681 Final Report: May 2016 Topological Analysis of Wireless Networks Principal Investigator: Prof. Michael

On the number of vertices of each rank in phylogenetic trees and their generalizations

OpenAIRE

Bóna, Miklós

2015-01-01

We find surprisingly simple formulas for the limiting probability that the rank of a randomly selected vertex in a randomly selected phylogenetic tree or generalized phylogenetic tree is a given integer.

Topological strength of magnetic skyrmions

Energy Technology Data Exchange (ETDEWEB)

Bazeia, D.; Ramos, J.G.G.S.; Rodrigues, E.I.B.

2017-02-01

This work deals with magnetic structures that attain integer and half-integer skyrmion numbers. We model and solve the problem analytically, and show how the solutions appear in materials that engender distinct, very specific physical properties, and use them to describe their topological features. In particular, we found a way to model skyrmion with a large transition region correlated with the presence of a two-peak skyrmion number density. Moreover, we run into the issue concerning the topological strength of a vortex-like structure and suggest an experimental realization, important to decide how to modify and measure the topological strength of the magnetic structure.

A topological introduction to nonlinear analysis

CERN Document Server

Brown, Robert F

2014-01-01

This third edition of A Topological Introduction to Nonlinear Analysis is addressed to the mathematician or graduate student of mathematics - or even the well-prepared undergraduate - who would like, with a minimum of background and preparation, to understand some of the beautiful results at the heart of nonlinear analysis. Based on carefully-expounded ideas from several branches of topology, and illustrated by a wealth of figures that attest to the geometric nature of the exposition, the book will be of immense help in providing its readers with an understanding of the mathematics of the nonlinear phenomena that characterize our real world. For this third edition, several new chapters present the fixed point index and its applications. The exposition and mathematical content is improved throughout. This book is ideal for self-study for mathematicians and students interested in such areas of geometric and algebraic topology, functional analysis, differential equations, and applied mathematics. It is a sharply...

Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2.

Directory of Open Access Journals (Sweden)

David Talens-Perales

Full Text Available In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2. We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module with two β-sandwich domains (non-catalytic at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins. Our results led us to propose a model in which evolutionary diversity of GH2 enzymes is driven by the addition of different non-catalytic domains at the C-terminal region. This model accounts for the divergence of β-galactosidases from β-glucuronidases, the diversification of β-galactosidases with different transglycosylation specificities, and the emergence of bicistronic β-galactosidases. This study also allows the identification of groups of functionally uncharacterized protein sequences with potential biotechnological interest.

Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate.

Science.gov (United States)

Lin, Jiannan; Chen, Guangfeng; Gu, Liang; Shen, Yuefeng; Zheng, Meizhu; Zheng, Weisheng; Hu, Xinjie; Zhang, Xiaobai; Qiu, Yu; Liu, Xiaoqing; Jiang, Cizhong

2014-02-01

Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals. Tree shrews and Primates were monophyletic in the phylogenetic trees derived from the first or/and second codon positions whereas tree shrews and Glires formed a monophyly in the trees derived from the third or all codon positions. The same topology was obtained in the phylogeny inference using the slowly and fast evolving genes, respectively. This incongruence was likely attributed to the fast substitution rate in tree shrews and Glires. Notably, sequence GC content only was not informative to resolve the controversial phylogenetic relationships between tree shrews, Glires, and Primates. Finally, estimation in the confidence of the tree selection strongly supported the phylogenetic affiliation of tree shrews to Primates as a monophyly. Copyright © 2013 Elsevier Inc. All rights reserved.

Fixed point theory in metric type spaces

CERN Document Server

Agarwal, Ravi P; O’Regan, Donal; Roldán-López-de-Hierro, Antonio Francisco

2015-01-01

Written by a team of leading experts in the field, this volume presents a self-contained account of the theory, techniques and results in metric type spaces (in particular in G-metric spaces); that is, the text approaches this important area of fixed point analysis beginning from the basic ideas of metric space topology. The text is structured so that it leads the reader from preliminaries and historical notes on metric spaces (in particular G-metric spaces) and on mappings, to Banach type contraction theorems in metric type spaces, fixed point theory in partially ordered G-metric spaces, fixed point theory for expansive mappings in metric type spaces, generalizations, present results and techniques in a very general abstract setting and framework. Fixed point theory is one of the major research areas in nonlinear analysis. This is partly due to the fact that in many real world problems fixed point theory is the basic mathematical tool used to establish the existence of solutions to problems which arise natur...

A comparative test of phylogenetic diversity indices.

Science.gov (United States)

Schweiger, Oliver; Klotz, Stefan; Durka, Walter; Kühn, Ingolf

2008-09-01

Traditional measures of biodiversity, such as species richness, usually treat species as being equal. As this is obviously not the case, measuring diversity in terms of features accumulated over evolutionary history provides additional value to theoretical and applied ecology. Several phylogenetic diversity indices exist, but their behaviour has not yet been tested in a comparative framework. We provide a test of ten commonly used phylogenetic diversity indices based on 40 simulated phylogenies of varying topology. We restrict our analysis to a topological fully resolved tree without information on branch lengths and species lists with presence-absence data. A total of 38,000 artificial communities varying in species richness covering 5-95% of the phylogenies were created by random resampling. The indices were evaluated based on their ability to meet a priori defined requirements. No index meets all requirements, but three indices turned out to be more suitable than others under particular conditions. Average taxonomic distinctness (AvTD) and intensive quadratic entropy (J) are calculated by averaging and are, therefore, unbiased by species richness while reflecting phylogeny per se well. However, averaging leads to the violation of set monotonicity, which requires that species extinction cannot increase the index. Total taxonomic distinctness (TTD) sums up distinctiveness values for particular species across the community. It is therefore strongly linked to species richness and reflects phylogeny per se weakly but satisfies set monotonicity. We suggest that AvTD and J are best applied to studies that compare spatially or temporally rather independent communities that potentially vary strongly in their phylogenetic composition-i.e. where set monotonicity is a more negligible issue, but independence of species richness is desired. In contrast, we suggest that TTD be used in studies that compare rather interdependent communities where changes occur more gradually by

A heuristic approach to optimization of structural topology including self-weight

Science.gov (United States)

Tajs-Zielińska, Katarzyna; Bochenek, Bogdan

2018-01-01

Topology optimization of structures under a design-dependent self-weight load is investigated in this paper. The problem deserves attention because of its significant importance in the engineering practice, especially nowadays as topology optimization is more often applied when designing large engineering structures, for example, bridges or carrying systems of tall buildings. It is worth noting that well-known approaches of topology optimization which have been successfully applied to structures under fixed loads cannot be directly adapted to the case of design-dependent loads, so that topology generation can be a challenge also for numerical algorithms. The paper presents the application of a simple but efficient non-gradient method to topology optimization of elastic structures under self-weight loading. The algorithm is based on the Cellular Automata concept, the application of which can produce effective solutions with low computational cost.

Detection of Horizontal Gene Transfers from Phylogenetic Comparisons

Science.gov (United States)

Pylro, Victor Satler; Vespoli, Luciano de Souza; Duarte, Gabriela Frois; Yotoko, Karla Suemy Clemente

2012-01-01

Bacterial phylogenies have become one of the most important challenges for microbial ecology. This field started in the mid-1970s with the aim of using the sequence of the small subunit ribosomal RNA (16S) tool to infer bacterial phylogenies. Phylogenetic hypotheses based on other sequences usually give conflicting topologies that reveal different evolutionary histories, which in some cases may be the result of horizontal gene transfer events. Currently, one of the major goals of molecular biology is to understand the role that horizontal gene transfer plays in species adaptation and evolution. In this work, we compared the phylogenetic tree based on 16S with the tree based on dszC, a gene involved in the cleavage of carbon-sulfur bonds. Bacteria of several genera perform this survival task when living in environments lacking free mineral sulfur. The biochemical pathway of the desulphurization process was extensively studied due to its economic importance, since this step is expensive and indispensable in fuel production. Our results clearly show that horizontal gene transfer events could be detected using common phylogenetic methods with gene sequences obtained from public sequence databases. PMID:22675653

Phylogenetic signal dissection identifies the root of starfishes.

Directory of Open Access Journals (Sweden)

Roberto Feuda

Full Text Available Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.

Machine Learning Topological Invariants with Neural Networks

Science.gov (United States)

Zhang, Pengfei; Shen, Huitao; Zhai, Hui

2018-02-01

In this Letter we supervisedly train neural networks to distinguish different topological phases in the context of topological band insulators. After training with Hamiltonians of one-dimensional insulators with chiral symmetry, the neural network can predict their topological winding numbers with nearly 100% accuracy, even for Hamiltonians with larger winding numbers that are not included in the training data. These results show a remarkable success that the neural network can capture the global and nonlinear topological features of quantum phases from local inputs. By opening up the neural network, we confirm that the network does learn the discrete version of the winding number formula. We also make a couple of remarks regarding the role of the symmetry and the opposite effect of regularization techniques when applying machine learning to physical systems.

From geometry to topology

CERN Document Server

Flegg, H Graham

2001-01-01

This excellent introduction to topology eases first-year math students and general readers into the subject by surveying its concepts in a descriptive and intuitive way, attempting to build a bridge from the familiar concepts of geometry to the formalized study of topology. The first three chapters focus on congruence classes defined by transformations in real Euclidean space. As the number of permitted transformations increases, these classes become larger, and their common topological properties become intuitively clear. Chapters 4-12 give a largely intuitive presentation of selected topics.

Topological phases of topological-insulator thin films

Science.gov (United States)

Asmar, Mahmoud M.; Sheehy, Daniel E.; Vekhter, Ilya

2018-02-01

We study the properties of a thin film of topological insulator material. We treat the coupling between helical states at opposite surfaces of the film in the properly-adapted tunneling approximation, and show that the tunneling matrix element oscillates as a function of both the film thickness and the momentum in the plane of the film for Bi2Se3 and Bi2Te3 . As a result, while the magnitude of the matrix element at the center of the surface Brillouin zone gives the gap in the energy spectrum, the sign of the matrix element uniquely determines the topological properties of the film, as demonstrated by explicitly computing the pseudospin textures and the Chern number. We find a sequence of transitions between topological and nontopological phases, separated by semimetallic states, as the film thickness varies. In the topological phase, the edge states of the film always exist but only carry a spin current if the edge potentials break particle-hole symmetry. The edge states decay very slowly away from the boundary in Bi2Se3 , making Bi2Te3 , where this scale is shorter, a more promising candidate for the observation of these states. Our results hold for free-standing films as well as heterostructures with large-gap insulators.

Fluctuations in non-ideal pion gas with dynamically fixed particle number

Science.gov (United States)

Kolomeitsev, E. E.; Voskresensky, D. N.

2018-05-01

We consider a non-ideal hot pion gas with the dynamically fixed number of particles in the model with the λϕ4 interaction. The effective Lagrangian for the description of such a system is obtained after dropping the terms responsible for the change of the total particle number. Reactions π+π- ↔π0π0, which determine the isospin balance of the medium, are permitted. Within the self-consistent Hartree approximation we compute the effective pion mass, thermodynamic characteristics of the system and the variance of the particle number at temperatures above the critical point of the induced Bose-Einstein condensation when the pion chemical potential reaches the value of the effective pion mass. We analyze conditions for the condensate formation in the process of thermalization of an initially non-equilibrium pion gas. The normalized variance of the particle number increases with a temperature decrease but remains finite in the critical point of the Bose-Einstein condensation. This is due to the non-perturbative account of the interaction and is in contrast to the ideal-gas case. In the kinetic regime of the condensate formation the variance is shown to stay finite also.

Topological Aspects of Solitons in Ferromagnets

International Nuclear Information System (INIS)

Ren Jirong; Wang Jibiao; Li Ran; Xu Donghui; Duan Yishi

2008-01-01

Two kinds of topological soliton (skyrmion and magnetic vortex ring) in ferromagnets are studied. They have the common topological origin, a tensor H αβ = n-vector · (∂ α n-vector x ∂ β n-vector ), which describes the non-trivial distribution of local orientation of magnetization n-vector at large distances in space. The topological stability of skyrmion is protected by the winding number. Knot-like topological defect as magnetic vortex rings is also studied. On the assumption that magnetic vortex rings are geometric lines, we present their δ-function distribution in ferromagnetic materials. Furthermore, it is briefly shown that Hopf invariant is a proper topological invariant to describe the topology of magnetic vortex rings

Topological phases of interacting fermions in one-dimensional superconductor - normal metal geometry

Energy Technology Data Exchange (ETDEWEB)

Meidan, Dganit [Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105 (Israel); Dahlem Center for Complex Quantum Systems and Fachbereich Physik, Freie Universitaet Berlin, 14195 Berlin (Germany); Romito, Alessandro; Brouwer, Piet W. [Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105 (Israel)

2015-07-01

One-dimensional superconductors can be in non-trivial topological phases harboring Majorana end-states, which possess non-abelian statistics. It has been recently established that in the presence of interactions the classification of topological superconducting phases can be significantly altered. Specifically, for one-dimensional superconductors possessing a time reversal symmetry (BDI class), interactions reduce the infinitely many non-interacting phases (Z topological index) to eight distinct ones (Z{sub 8} topological index). In this talk I will consider multi-mode superconducting wires in such BDI class when probed by an external contact, and discuss their low temperature and voltage bias transport properties. I will first show that the Andreev reflection component of the scattering matrix of the probing lead provides a topological index, r=-4,.., 4, which distinguish the eight topological phases. The two topologically equivalent phases with r= 4,-4 support emergent many-body end states, which are identified to be a topologically protected Kondo-like resonance. The path in phase space that connects these equivalent phases crosses a non-fermi liquid fixed point where a multiple channel Kondo effect develops.

Extended holomorphic anomaly and loop amplitudes in open topological string

International Nuclear Information System (INIS)

Walcher, Johannes

2009-01-01

Open topological string amplitudes on compact Calabi-Yau threefolds are shown to satisfy an extension of the holomorphic anomaly equation of Bershadsky, Cecotti, Ooguri and Vafa. The total topological charge of the D-brane configuration must vanish in order to satisfy tadpole cancellation. The boundary state of such D-branes is holomorphically captured by a Hodge theoretic normal function. Its Griffiths' infinitesimal invariant is the analogue of the closed string Yukawa coupling and plays the role of the terminator in a Feynman diagram expansion for the topological string with D-branes. The holomorphic anomaly equation is solved and the holomorphic ambiguity is fixed for some representative worldsheets of low genus and with few boundaries on the real quintic.

On Krasnoselskii's Cone Fixed Point Theorem

Directory of Open Access Journals (Sweden)

Man Kam Kwong

2008-04-01

Full Text Available In recent years, the Krasnoselskii fixed point theorem for cone maps and its many generalizations have been successfully applied to establish the existence of multiple solutions in the study of boundary value problems of various types. In the first part of this paper, we revisit the Krasnoselskii theorem, in a more topological perspective, and show that it can be deduced in an elementary way from the classical Brouwer-Schauder theorem. This viewpoint also leads to a topology-theoretic generalization of the theorem. In the second part of the paper, we extend the cone theorem in a different direction using the notion of retraction and show that a stronger form of the often cited Leggett-Williams theorem is a special case of this extension.

A format for phylogenetic placements.

Directory of Open Access Journals (Sweden)

Frederick A Matsen

Full Text Available We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.

Chiral topological insulator of magnons

Science.gov (United States)

Li, Bo; Kovalev, Alexey A.

2018-05-01

We propose a magnon realization of 3D topological insulator in the AIII (chiral symmetry) topological class. The topological magnon gap opens due to the presence of Dzyaloshinskii-Moriya interactions. The existence of the topological invariant is established by calculating the bulk winding number of the system. Within our model, the surface magnon Dirac cone is protected by the sublattice chiral symmetry. By analyzing the magnon surface modes, we confirm that the backscattering is prohibited. By weakly breaking the chiral symmetry, we observe the magnon Hall response on the surface due to opening of the gap. Finally, we show that by changing certain parameters, the system can be tuned between the chiral topological insulator, three-dimensional magnon anomalous Hall, and Weyl magnon phases.

On Tree-Based Phylogenetic Networks.

Science.gov (United States)

Zhang, Louxin

2016-07-01

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

Tunable Topological Phononic Crystals

KAUST Repository

Chen, Zeguo

2016-05-27

Topological insulators first observed in electronic systems have inspired many analogues in photonic and phononic crystals in which remarkable one-way propagation edge states are supported by topologically nontrivial band gaps. Such band gaps can be achieved by breaking the time-reversal symmetry to lift the degeneracy associated with Dirac cones at the corners of the Brillouin zone. Here, we report on our construction of a phononic crystal exhibiting a Dirac-like cone in the Brillouin zone center. We demonstrate that simultaneously breaking the time-reversal symmetry and altering the geometric size of the unit cell result in a topological transition that we verify by the Chern number calculation and edge-mode analysis. We develop a complete model based on the tight binding to uncover the physical mechanisms of the topological transition. Both the model and numerical simulations show that the topology of the band gap is tunable by varying both the velocity field and the geometric size; such tunability may dramatically enrich the design and use of acoustic topological insulators.

Tunable Topological Phononic Crystals

KAUST Repository

Chen, Zeguo; Wu, Ying

2016-01-01

Topological insulators first observed in electronic systems have inspired many analogues in photonic and phononic crystals in which remarkable one-way propagation edge states are supported by topologically nontrivial band gaps. Such band gaps can be achieved by breaking the time-reversal symmetry to lift the degeneracy associated with Dirac cones at the corners of the Brillouin zone. Here, we report on our construction of a phononic crystal exhibiting a Dirac-like cone in the Brillouin zone center. We demonstrate that simultaneously breaking the time-reversal symmetry and altering the geometric size of the unit cell result in a topological transition that we verify by the Chern number calculation and edge-mode analysis. We develop a complete model based on the tight binding to uncover the physical mechanisms of the topological transition. Both the model and numerical simulations show that the topology of the band gap is tunable by varying both the velocity field and the geometric size; such tunability may dramatically enrich the design and use of acoustic topological insulators.

Topological magnetoelectric pump in three dimensions

Science.gov (United States)

Fukui, Takahiro; Fujiwara, Takanori

2017-11-01

We study the topological pump for a lattice fermion model mainly in three spatial dimensions. We first calculate the U(1) current density for the Dirac model defined in continuous space-time to review the known results as well as to introduce some technical details convenient for the calculations of the lattice model. We next investigate the U(1) current density for a lattice fermion model, a variant of the Wilson-Dirac model. The model we introduce is defined on a lattice in space but in continuous time, which is suited for the study of the topological pump. For such a model, we derive the conserved U(1) current density and calculate it directly for the (1 +1 )-dimensional system as well as (3 +1 )-dimensional system in the limit of the small lattice constant. We find that the current includes a nontrivial lattice effect characterized by the Chern number, and therefore the pumped particle number is quantized by the topological reason. Finally, we study the topological temporal pump in 3 +1 dimensions by numerical calculations. We discuss the relationship between the second Chern number and the first Chern number, the bulk-edge correspondence, and the generalized Streda formula which enables us to compute the second Chern number using the spectral asymmetry.

An improved hybrid topology optimization approach coupling simulated annealing and SIMP (SA-SIMP)

International Nuclear Information System (INIS)

Garcia-Lopez, N P; Sanchez-Silva, M; Medaglia, A L; Chateauneuf, A

2010-01-01

The Solid Isotropic Material with Penalization (SIMP) methodology has been used extensively due to its versatility and ease of implementation. However, one of its main drawbacks is that resulting topologies exhibit areas of intermediate densities which lack any physical meaning. This paper presents a hybrid methodology which couples simulated annealing and SIMP (SA-SIMP) in order to achieve solutions which are stiffer and predominantly black and white. Under a look-ahead strategy, the algorithm gradually fixes or removes those elements whose density resulting from SIMP is intermediate. Different strategies for selecting and fixing the fractional elements are examined using benchmark examples, which show that topologies resulting from SA-SIMP are more rigid than SIMP and predominantly black and white.

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

OpenAIRE

McCann, Jamie; Schneeweiss, Gerald M.; Stuessy, Tod F.; Villase?or, Jose L.; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (ma...

Topological vortices in gauge models of graphene

Science.gov (United States)

Zhang, Xin-Hui; Li, Xueqin; Hao, Jin-Bo

2018-06-01

Graphene-like structure possessing the topological vortices and knots, and the magnetic flux of the vortices configuration quantized, are proposed in this paper. The topological charges of the vortices are characterized by Hopf indices and Brower degrees. The Abelian background field action (BF action) is a topological invariant for the knot family, which is just the total sum of all the self-linking numbers and all the linking numbers. Flux quantization opens the possibility of having Aharonov-Bohm-type effects in graphene without external electromagnetic field.

Patterns and effects of GC3 heterogeneity and parsimony informative sites on the phylogenetic tree of genes.

Science.gov (United States)

Ma, Shuai; Wu, Qi; Hu, Yibo; Wei, Fuwen

2018-05-20

The explosive growth in genomic data has provided novel insights into the conflicting signals hidden in phylogenetic trees. Although some studies have explored the effects of the GC content and parsimony informative sites (PIS) on the phylogenetic tree, the effect of the heterogeneity of the GC content at the first/second/third codon position on parsimony informative sites (GC1/2/3 PIS ) among different species and the effect of PIS on phylogenetic tree construction remain largely unexplored. Here, we used two different mammal genomic datasets to explore the patterns of GC1/2/3 PIS heterogeneity and the effect of PIS on the phylogenetic tree of genes: (i) all GC1/2/3 PIS have obvious heterogeneity between different mammals, and the levels of heterogeneity are GC3 PIS  > GC2 PIS  > GC1 PIS ; (ii) the number of PIS is positively correlated with the metrics of "good" gene tree topologies, and excluding the third codon position (C3) decreases the quality of gene trees by removing too many PIS. These results provide novel insights into the heterogeneity pattern of GC1/2/3 PIS in mammals and the relationship between GC3/PIS and gene trees. Additionally, it is necessary to carefully consider whether to exclude C3 to improve the quality of gene trees, especially in the super-tree method. Copyright © 2018 Elsevier B.V. All rights reserved.

Fixed Point in Topological Vector Space-Valued Cone Metric Spaces

Directory of Open Access Journals (Sweden)

Muhammad Arshad

2010-01-01

Full Text Available We obtain common fixed points of a pair of mappings satisfying a generalized contractive type condition in TVS-valued cone metric spaces. Our results generalize some well-known recent results in the literature.

Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis.

Science.gov (United States)

Mubemba, B; Thompson, P N; Odendaal, L; Coetzee, P; Venter, E H

2017-05-01

Rift Valley fever (RVF), caused by an arthropod borne Phlebovirus in the family Bunyaviridae, is a haemorrhagic disease that affects ruminants and humans. Due to the zoonotic nature of the virus, a biosafety level 3 laboratory is required for isolation of the virus. Fresh and frozen samples are the preferred sample type for isolation and acquisition of sequence data. However, these samples are scarce in addition to posing a health risk to laboratory personnel. Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are safe and readily available, however FFPE derived RNA is in most cases degraded and cross-linked in peptide bonds and it is unknown whether the sample type would be suitable as reference material for retrospective phylogenetic studies. A RT-PCR assay targeting a 490 nt portion of the structural G N glycoprotein encoding gene of the RVFV M-segment was applied to total RNA extracted from archived RVFV positive FFPE samples. Several attempts to obtain target amplicons were unsuccessful. FFPE samples were then analysed using next generation sequencing (NGS), i.e. Truseq ® (Illumina) and sequenced on the Miseq ® genome analyser (Illumina). Using reference mapping, gapped virus sequence data of varying degrees of shallow depth was aligned to a reference sequence. However, the NGS did not yield long enough contigs that consistently covered the same genome regions in all samples to allow phylogenetic analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Stiffness design of geometrically nonlinear structures using topology optimization

DEFF Research Database (Denmark)

Buhl, Thomas; Pedersen, Claus B. Wittendorf; Sigmund, Ole

2000-01-01

of the objective functions are found with the adjoint method and the optimization problem is solved using the Method of Moving Asymptotes. A filtering scheme is used to obtain checkerboard-free and mesh-independent designs and a continuation approach improves convergence to efficient designs. Different objective......The paper deals with topology optimization of structures undergoing large deformations. The geometrically nonlinear behaviour of the structures are modelled using a total Lagrangian finite element formulation and the equilibrium is found using a Newton-Raphson iterative scheme. The sensitivities...... functions are tested. Minimizing compliance for a fixed load results in degenerated topologies which are very inefficient for smaller or larger loads. The problem of obtaining degenerated "optimal" topologies which only can support the design load is even more pronounced than for structures with linear...

Topology, the Wilson flow and the HMC algorithm

CERN Document Server

Luscher, Martin

2010-01-01

An old and apparently persistent problem in numerical lattice QCD is that the simulations tend to get trapped in a sector of fixed topological charge when the lattice spacing is taken to zero. The effect sets in very rapidly and may invalidate the simulation results in certain cases. In this talk, the issue is discussed using the Wilson flow as a tool. The flow has a simple scaling behaviour and allows one to understand how exactly the topological sectors emerge in the continuum limit. Further studies however suggest that the observed slowdown of the simulations at small lattice spacings is only partly caused by the emergence of the sectors.

Sustainable Load-Balancing Scheme for Inter-Sensor Convergence Processing of Routing Cooperation Topology

Directory of Open Access Journals (Sweden)

Hyun-Woo Kim

2016-05-01

Full Text Available Recent advancements in Information Technology (IT have sparked the creation of numerous and diverse types of devices and services. Manual data collection measurement methods have been automated through the use of various wireless or wired sensors. Single sensor devices are included in smart devices such as smartphones. Data transmission is critical for big data collected from sensor nodes, such as Mobile Sensor Nodes (MSNs, where sensors move dynamically according to sensor mobility, or Fixed Sensor Nodes (FSNs, where sensor locations are decided by the users. False data transfer processing of big data results in topology lifespan reduction and data transfer delays. Hence, a variety of simulators and diverse load-balancing algorithms have been developed as protocol verification tools for topology lifespan maximization and effective data transfer processing. However, those previously developed simulators have limited functions, such as an event function for a specific sensor or a battery consumption rate test for sensor deployment. Moreover, since the previous load-balancing algorithms consider only the general traffic distribution and the number of connected nodes without considering the current topology condition, the sustainable load-balancing technique that takes into account the battery consumption rate of the dispersed sensor nodes is required. Therefore, this paper proposes the Sustainable Load-balancing Scheme (SLS, which maximizes the overall topology lifespan through effective and sustainable load-balancing of data transfer among the sensors. SLS is capable of maintaining an effective topology as it considers both the battery consumption rate of the sensors and the data transfer delay.

Topology for analysis

CERN Document Server

Wilansky, Albert

2008-01-01

Three levels of examples and problems make this volume appropriate for students and professionals. Abundant exercises, ordered and numbered by degree of difficulty, illustrate important topological concepts. 1970 edition.

Using heteroclinic orbits to quantify topological entropy in fluid flows

International Nuclear Information System (INIS)

Sattari, Sulimon; Chen, Qianting; Mitchell, Kevin A.

2016-01-01

Topological approaches to mixing are important tools to understand chaotic fluid flows, ranging from oceanic transport to the design of micro-mixers. Typically, topological entropy, the exponential growth rate of material lines, is used to quantify topological mixing. Computing topological entropy from the direct stretching rate is computationally expensive and sheds little light on the source of the mixing. Earlier approaches emphasized that topological entropy could be viewed as generated by the braiding of virtual, or “ghost,” rods stirring the fluid in a periodic manner. Here, we demonstrate that topological entropy can also be viewed as generated by the braiding of ghost rods following heteroclinic orbits instead. We use the machinery of homotopic lobe dynamics, which extracts symbolic dynamics from finite-length pieces of stable and unstable manifolds attached to fixed points of the fluid flow. As an example, we focus on the topological entropy of a bounded, chaotic, two-dimensional, double-vortex cavity flow. Over a certain parameter range, the topological entropy is primarily due to the braiding of a period-three orbit. However, this orbit does not explain the topological entropy for parameter values where it does not exist, nor does it explain the excess of topological entropy for the entire range of its existence. We show that braiding by heteroclinic orbits provides an accurate computation of topological entropy when the period-three orbit does not exist, and that it provides an explanation for some of the excess topological entropy when the period-three orbit does exist. Furthermore, the computation of symbolic dynamics using heteroclinic orbits has been automated and can be used to compute topological entropy for a general 2D fluid flow.

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

Directory of Open Access Journals (Sweden)

Sarah M Hykin

Full Text Available For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles, attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp. We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

Science.gov (United States)

Hykin, Sarah M; Bi, Ke; McGuire, Jimmy A

2015-01-01

For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for

Phylogenetic and Phylogenomic Definition of Rhizopus Species

Directory of Open Access Journals (Sweden)

Andrii P. Gryganskyi

2018-06-01

Full Text Available Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. arrhizus and R. delemar. A comparative analysis of the mating type locus across Rhizopus reveals that its structure is flexible even between different species in the same genus, but shows similarities between Rhizopus and other mucoralean fungi. The topology of single-gene phylogenies built for two genes involved in mating is similar to the phylogenomic tree. Comparison of the total length of the genome assemblies showed that genome size varies by as much as threefold within a species and is driven by changes in transposable element copy numbers and genome duplications.

Singular trajectories: space-time domain topology of developing speckle fields

Science.gov (United States)

Vasil'ev, Vasiliy; Soskin, Marat S.

2010-02-01

It is shown the space-time dynamics of optical singularities is fully described by singularities trajectories in space-time domain, or evolution of transverse coordinates(x, y) in some fixed plane z0. The dynamics of generic developing speckle fields was realized experimentally by laser induced scattering in LiNbO3:Fe photorefractive crystal. The space-time trajectories of singularities can be divided topologically on two classes with essentially different scenario and duration. Some of them (direct topological reactions) consist from nucleation of singularities pair at some (x, y, z0, t) point, their movement and annihilation. They possess form of closed loops with relatively short time of existence. Another much more probable class of trajectories are chain topological reactions. Each of them consists from sequence of links, i.e. of singularities nucleation in various points (xi yi, ti) and following annihilation of both singularities in other space-time points with alien singularities of opposite topological indices. Their topology and properties are established. Chain topological reactions can stop on the borders of a developing speckle field or go to infinity. Examples of measured both types of topological reactions for optical vortices (polarization C points) in scalar (elliptically polarized) natural developing speckle fields are presented.

Toward a Novel Multilocus Phylogenetic Taxonomy for the Dermatophytes.

Science.gov (United States)

de Hoog, G Sybren; Dukik, Karolina; Monod, Michel; Packeu, Ann; Stubbe, Dirk; Hendrickx, Marijke; Kupsch, Christiane; Stielow, J Benjamin; Freeke, Joanna; Göker, Markus; Rezaei-Matehkolaei, Ali; Mirhendi, Hossein; Gräser, Yvonne

2017-02-01

Type and reference strains of members of the onygenalean family Arthrodermataceae have been sequenced for rDNA ITS and partial LSU, the ribosomal 60S protein, and fragments of β-tubulin and translation elongation factor 3. The resulting phylogenetic trees showed a large degree of correspondence, and topologies matched those of earlier published phylogenies demonstrating that the phylogenetic representation of dermatophytes and dermatophyte-like fungi has reached an acceptable level of stability. All trees showed Trichophyton to be polyphyletic. In the present paper, Trichophyton is restricted to mainly the derived clade, resulting in classification of nearly all anthropophilic dermatophytes in Trichophyton and Epidermophyton, along with some zoophilic species that regularly infect humans. Microsporum is restricted to some species around M. canis, while the geophilic species and zoophilic species that are more remote from the human sphere are divided over Arthroderma, Lophophyton and Nannizzia. A new genus Guarromyces is proposed for Keratinomyces ceretanicus. Thirteen new combinations are proposed; in an overview of all described species it is noted that the largest number of novelties was introduced during the decades 1920-1940, when morphological characters were used in addition to clinical features. Species are neo- or epi-typified where necessary, which was the case in Arthroderma curreyi, Epidermophyton floccosum, Lophophyton gallinae, Trichophyton equinum, T. mentagrophytes, T. quinckeanum, T. schoenleinii, T. soudanense, and T. verrucosum. In the newly proposed taxonomy, Trichophyton contains 16 species, Epidermophyton one species, Nannizzia 9 species, Microsporum 3 species, Lophophyton 1 species, Arthroderma 21 species and Ctenomyces 1 species, but more detailed studies remain needed to establish species borderlines. Each species now has a single valid name. Two new genera are introduced: Guarromyces and Paraphyton. The number of genera has increased, but

Illustrated introduction to topology and homotopy

CERN Document Server

Kalajdzievski, Sasho

2015-01-01

TOPOLOGYSets, Numbers, Cardinals, and Ordinals Sets and Numbers Sets and Cardinal Numbers Axiom of Choice and Equivalent Statements Metric Spaces: Definition, Examples, and BasicsMetric Spaces: Definition and Examples Metric Spaces: Basics Topological Spaces: Definition and ExamplesThe Definition and Some Simple Examples Some Basic Notions Bases Dense and Nowhere Dense Sets Continuous Mappings Subspaces, Quotient Spaces, Manifolds, and CW-Complexes Subspaces Quotient Spaces The Gluing Lemma, Topological Sums, and Some Special Quotient Spaces Manifolds and CW-ComplexesProducts of SpacesFinite Products of Spaces Infinite Products of Spaces Box Topology Connected Spaces and Path Connected Spaces Connected Spaces: Definition and Basic Facts Properties of Connected Spaces Path Connected Spaces Path Connected Spaces: More Properties and Related Matters Locally Connected and Locally Path Connected Spaces Compactness and Related Matters Compact Spaces: Definition Properties of Compact Spaces Compact, Lindelöf, and C...

The chromatic number of a graph of girth 5 on a fixed surface

DEFF Research Database (Denmark)

Thomassen, Carsten

2003-01-01

We prove a color extension result implying that, for every fixed surface S, there are only finitely many 4-color-critical graphs of girth 5 on S. The result is best possible in the sense that there are infinitely many 4-color-critical graphs of girth 4 on S, except when S is the sphere, As a cons......, As a consequence, the chromatic number of graphs of girth 5 on S can be found in polynomial time....

Exact phase boundaries and topological phase transitions of the X Y Z spin chain

Science.gov (United States)

Jafari, S. A.

2017-07-01

Within the block spin renormalization group, we give a very simple derivation of the exact phase boundaries of the X Y Z spin chain. First, we identify the Ising order along x ̂ or y ̂ as attractive renormalization group fixed points of the Kitaev chain. Then, in a global phase space composed of the anisotropy λ of the X Y interaction and the coupling Δ of the Δ σzσz interaction, we find that the above fixed points remain attractive in the two-dimesional parameter space. We therefore classify the gapped phases of the X Y Z spin chain as: (1) either attracted to the Ising limit of the Kitaev-chain, which in turn is characterized by winding number ±1 , depending on whether the Ising order parameter is along x ̂ or y ̂ directions; or (2) attracted to the charge density wave (CDW) phases of the underlying Jordan-Wigner fermions, which is characterized by zero winding number. We therefore establish that the exact phase boundaries of the X Y Z model in Baxter's solution indeed correspond to topological phase transitions. The topological nature of the phase transitions of the X Y Z model justifies why our analytical solution of the three-site problem that is at the core of the present renormalization group treatment is able to produce the exact phase boundaries of Baxter's solution. We argue that the distribution of the winding numbers between the three Ising phases is a matter of choice of the coordinate system, and therefore the CDW-Ising phase is entitled to host appropriate form of zero modes. We further observe that in the Kitaev-chain the renormalization group flow can be cast into a geometric progression of a properly identified parameter. We show that this new parameter is actually the size of the (Majorana) zero modes.

Topological Field Theory of Time-Reversal Invariant Insulators

Energy Technology Data Exchange (ETDEWEB)

Qi, Xiao-Liang; Hughes, Taylor; Zhang, Shou-Cheng; /Stanford U., Phys. Dept.

2010-03-19

We show that the fundamental time reversal invariant (TRI) insulator exists in 4 + 1 dimensions, where the effective field theory is described by the 4 + 1 dimensional Chern-Simons theory and the topological properties of the electronic structure is classified by the second Chern number. These topological properties are the natural generalizations of the time reversal breaking (TRB) quantum Hall insulator in 2 + 1 dimensions. The TRI quantum spin Hall insulator in 2 + 1 dimensions and the topological insulator in 3 + 1 dimension can be obtained as descendants from the fundamental TRI insulator in 4 + 1 dimensions through a dimensional reduction procedure. The effective topological field theory, and the Z{sub 2} topological classification for the TRI insulators in 2+1 and 3+1 dimensions are naturally obtained from this procedure. All physically measurable topological response functions of the TRI insulators are completely described by the effective topological field theory. Our effective topological field theory predicts a number of novel and measurable phenomena, the most striking of which is the topological magneto-electric effect, where an electric field generates a magnetic field in the same direction, with an universal constant of proportionality quantized in odd multiples of the fine structure constant {alpha} = e{sup 2}/hc. Finally, we present a general classification of all topological insulators in various dimensions, and describe them in terms of a unified topological Chern-Simons field theory in phase space.

Common fixed point theorems for finite number of mappings without continuity and compatibility on intuitionistic fuzzy metric spaces

International Nuclear Information System (INIS)

Sharma, Sushil; Deshpande, Bhavana

2009-01-01

The purpose of this paper is to prove some common fixed point theorems for finite number of discontinuous, noncompatible mappings on noncomplete intuitionistic fuzzy metric spaces. Our results extend, generalize and intuitionistic fuzzify several known results in fuzzy metric spaces. We give an example and also give formulas for total number of commutativity conditions for finite number of mappings.

Analyzing Dynamic Probabilistic Risk Assessment Data through Topology-Based Clustering

Energy Technology Data Exchange (ETDEWEB)

Diego Mandelli; Dan Maljovec; BeiWang; Valerio Pascucci; Peer-Timo Bremer

2013-09-01

We investigate the use of a topology-based clustering technique on the data generated by dynamic event tree methodologies. The clustering technique we utilizes focuses on a domain-partitioning algorithm based on topological structures known as the Morse-Smale complex, which partitions the data points into clusters based on their uniform gradient flow behavior. We perform both end state analysis and transient analysis to classify the set of nuclear scenarios. We demonstrate our methodology on a dataset generated for a sodium-cooled fast reactor during an aircraft crash scenario. The simulation tracks the temperature of the reactor as well as the time for a recovery team to fix the passive cooling system. Combined with clustering results obtained previously through mean shift methodology, we present the user with complementary views of the data that help illuminate key features that may be otherwise hidden using a single methodology. By clustering the data, the number of relevant test cases to be selected for further analysis can be drastically reduced by selecting a representative from each cluster. Identifying the similarities of simulations within a cluster can also aid in the drawing of important conclusions with respect to safety analysis.

A topology optimization method for design of negative permeability metamaterials

DEFF Research Database (Denmark)

Diaz, A. R.; Sigmund, Ole

2010-01-01

A methodology based on topology optimization for the design of metamaterials with negative permeability is presented. The formulation is based on the design of a thin layer of copper printed on a dielectric, rectangular plate of fixed dimensions. An effective media theory is used to estimate the ...

Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees.

Science.gov (United States)

Mirzaei, Sajad; Wu, Yufeng

2016-01-01

Hybridization networks represent plausible evolutionary histories of species that are affected by reticulate evolutionary processes. An established computational problem on hybridization networks is constructing the most parsimonious hybridization network such that each of the given phylogenetic trees (called gene trees) is "displayed" in the network. There have been several previous approaches, including an exact method and several heuristics, for this NP-hard problem. However, the exact method is only applicable to a limited range of data, and heuristic methods can be less accurate and also slow sometimes. In this paper, we develop a new algorithm for constructing near parsimonious networks for multiple binary gene trees. This method is more efficient for large numbers of gene trees than previous heuristics. This new method also produces more parsimonious results on many simulated datasets as well as a real biological dataset than a previous method. We also show that our method produces topologically more accurate networks for many datasets.

Ranking beta sheet topologies with applications to protein structure prediction

DEFF Research Database (Denmark)

Fonseca, Rasmus; Helles, Glennie; Winter, Pawel

2011-01-01

One reason why ab initio protein structure predictors do not perform very well is their inability to reliably identify long-range interactions between amino acids. To achieve reliable long-range interactions, all potential pairings of ß-strands (ß-topologies) of a given protein are enumerated......, including the native ß-topology. Two very different ß-topology scoring methods from the literature are then used to rank all potential ß-topologies. This has not previously been attempted for any scoring method. The main result of this paper is a justification that one of the scoring methods, in particular......, consistently top-ranks native ß-topologies. Since the number of potential ß-topologies grows exponentially with the number of ß-strands, it is unrealistic to expect that all potential ß-topologies can be enumerated for large proteins. The second result of this paper is an enumeration scheme of a subset of ß-topologies...

Topological photonic orbital-angular-momentum switch

Science.gov (United States)

Luo, Xi-Wang; Zhang, Chuanwei; Guo, Guang-Can; Zhou, Zheng-Wei

2018-04-01

The large number of available orbital-angular-momentum (OAM) states of photons provides a unique resource for many important applications in quantum information and optical communications. However, conventional OAM switching devices usually rely on precise parameter control and are limited by slow switching rate and low efficiency. Here we propose a robust, fast, and efficient photonic OAM switch device based on a topological process, where photons are adiabatically pumped to a target OAM state on demand. Such topological OAM pumping can be realized through manipulating photons in a few degenerate main cavities and involves only a limited number of optical elements. A large change of OAM at ˜10q can be realized with only q degenerate main cavities and at most 5 q pumping cycles. The topological photonic OAM switch may become a powerful device for broad applications in many different fields and motivate a topological design of conventional optical devices.

Topological insulators and topological superconductors

CERN Document Server

Bernevig, Andrei B

2013-01-01

This graduate-level textbook is the first pedagogical synthesis of the field of topological insulators and superconductors, one of the most exciting areas of research in condensed matter physics. Presenting the latest developments, while providing all the calculations necessary for a self-contained and complete description of the discipline, it is ideal for graduate students and researchers preparing to work in this area, and it will be an essential reference both within and outside the classroom. The book begins with simple concepts such as Berry phases, Dirac fermions, Hall conductance and its link to topology, and the Hofstadter problem of lattice electrons in a magnetic field. It moves on to explain topological phases of matter such as Chern insulators, two- and three-dimensional topological insulators, and Majorana p-wave wires. Additionally, the book covers zero modes on vortices in topological superconductors, time-reversal topological superconductors, and topological responses/field theory and topolo...

[Phylogenetic analysis of closely related Leuconostoc citreum species based on partial housekeeping genes].

Science.gov (United States)

Lv, Qiang; Chen, Ming; Xu, Haiyan; Song, Yuqin; Sun, Zhihong; Dan, Tong; Sun, Tiansong

2013-07-04

Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as phylogenetic markers. Then, we estimated the genetic distance and constructed the phylogenetic trees including 16S rRNA and above mentioned three housekeeping genes combining with published corresponding sequences. By comparing the phylogenetic trees, the topology of three housekeeping genes trees were consistent with that of 16S rRNA gene. The homology of closely related Leu. citreum species among dnaA, murC, pyrG and 16S rRNA gene sequences were different, ranged from75.5% to 97.2%, 50.2% to 99.7%, 65.0% to 99.8% and 98.5% 100%, respectively. The phylogenetic relationship of three housekeeping genes sequences were highly consistent with the results of 16S rRNA gene sequence, while the genetic distance of these housekeeping genes were extremely high than 16S rRNA gene. Consequently, the dnaA, murC and pyrG gene are suitable for classification and identification closely related Leu. citreum species.

Topological photonic crystals with zero Berry curvature

Science.gov (United States)

Liu, Feng; Deng, Hai-Yao; Wakabayashi, Katsunori

2018-02-01

Topological photonic crystals are designed based on the concept of Zak's phase rather than the topological invariants such as the Chern number and spin Chern number, which rely on the existence of a nonvanishing Berry curvature. Our photonic crystals (PCs) are made of pure dielectrics and sit on a square lattice obeying the C4 v point-group symmetry. Two varieties of PCs are considered: one closely resembles the electronic two-dimensional Su-Schrieffer-Heeger model, and the other continues as an extension of this analogy. In both cases, the topological transitions are induced by adjusting the lattice constants. Topological edge modes (TEMs) are shown to exist within the nontrivial photonic band gaps on the termination of those PCs. The high efficiency of these TEMs transferring electromagnetic energy against several types of disorders has been demonstrated using the finite-element method.

Phylogenetic diversity and biodiversity indices on phylogenetic networks.

Science.gov (United States)

Wicke, Kristina; Fischer, Mareike

2018-04-01

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been developed as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as hybridization. Here, we extend the concepts of phylogenetic diversity and phylogenetic diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider the treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed by a network and the so-called lowest stable ancestor tree associated with it. On the other hand, we derive the phylogenetic diversity of subsets of taxa and biodiversity indices directly from the internal structure of the network. We consider both approaches that are independent of so-called inheritance probabilities as well as approaches that explicitly incorporate these probabilities. Furthermore, we introduce our software package NetDiversity, which is implemented in Perl and allows for the calculation of all generalized measures of phylogenetic diversity and generalized phylogenetic diversity indices established in this note that are independent of inheritance probabilities. We apply our methods to a phylogenetic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization. Copyright © 2018 Elsevier Inc. All rights reserved.

Experimental verification of acoustic pseudospin multipoles in a symmetry-broken snowflakelike topological insulator

Science.gov (United States)

Zhang, Zhiwang; Tian, Ye; Cheng, Ying; Liu, Xiaojun; Christensen, Johan

2017-12-01

Topologically protected wave engineering in artificially structured media resides at the frontier of ongoing metamaterials research, which is inspired by quantum mechanics. Acoustic analogs of electronic topological insulators have recently led to a wealth of new opportunities in manipulating sound propagation by means of robust edge mode excitations through analogies drawn to exotic quantum states. A variety of artificial acoustic systems hosting topological edge states have been proposed analogous to the quantum Hall effect, topological insulators, and Floquet topological insulators in electronic systems. However, those systems were characterized by a fixed geometry and a very narrow frequency response, which severely hinders the exploration and design of useful applications. Here we establish acoustic multipolar pseudospin states as an engineering degree of freedom in time-reversal invariant flow-free phononic crystals and develop reconfigurable topological insulators through rotation of their meta-atoms and reshaping of the metamolecules. Specifically, we show how rotation forms man-made snowflakelike molecules, whose topological phase mimics pseudospin-down (pseudospin-up) dipolar and quadrupolar states, which are responsible for a plethora of robust edge confined properties and topological controlled refraction disobeying Snell's law.

Topology in SU(2) lattice gauge theory and parallelization of functional magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Solbrig, Stefan

2008-07-01

In this thesis, I discuss topological properties of quenched SU(2) lattice gauge fields. In particular, clusters of topological charge density exhibit a power-law. The exponent of that power-law can be used to validate models for lattice gauge fields. Instead of working with fixed cutoffs of the topological charge density, using the notion of a ''watermark'' is more convenient. Furthermore, I discuss how a parallel computer, originally designed for lattice gauge field simulations, can be used for functional magnetic resonance imaging. Multi parameter fits can be parallelized to achieve almost real-time evaluation of fMRI data. (orig.)

Topology in SU(2) lattice gauge theory and parallelization of functional magnetic resonance imaging

International Nuclear Information System (INIS)

Solbrig, Stefan

2008-01-01

In this thesis, I discuss topological properties of quenched SU(2) lattice gauge fields. In particular, clusters of topological charge density exhibit a power-law. The exponent of that power-law can be used to validate models for lattice gauge fields. Instead of working with fixed cutoffs of the topological charge density, using the notion of a ''watermark'' is more convenient. Furthermore, I discuss how a parallel computer, originally designed for lattice gauge field simulations, can be used for functional magnetic resonance imaging. Multi parameter fits can be parallelized to achieve almost real-time evaluation of fMRI data. (orig.)

Topological Rankings in Communication Networks

DEFF Research Database (Denmark)

Aabrandt, Andreas; Hansen, Vagn Lundsgaard; Træholt, Chresten

2015-01-01

In the theory of communication the central problem is to study how agents exchange information. This problem may be studied using the theory of connected spaces in topology, since a communication network can be modelled as a topological space such that agents can communicate if and only...... if they belong to the same path connected component of that space. In order to study combinatorial properties of such a communication network, notions from algebraic topology are applied. This makes it possible to determine the shape of a network by concrete invariants, e.g. the number of connected components...

Tensor Network Wavefunctions for Topological Phases

Science.gov (United States)

Ware, Brayden Alexander

The combination of quantum effects and interactions in quantum many-body systems can result in exotic phases with fundamentally entangled ground state wavefunctions--topological phases. Topological phases come in two types, both of which will be studied in this thesis. In topologically ordered phases, the pattern of entanglement in the ground state wavefunction encodes the statistics of exotic emergent excitations, a universal indicator of a phase that is robust to all types of perturbations. In symmetry protected topological phases, the entanglement instead encodes a universal response of the system to symmetry defects, an indicator that is robust only to perturbations respecting the protecting symmetry. Finding and creating these phases in physical systems is a motivating challenge that tests all aspects--analytical, numerical, and experimental--of our understanding of the quantum many-body problem. Nearly three decades ago, the creation of simple ansatz wavefunctions--such as the Laughlin fractional quantum hall state, the AKLT state, and the resonating valence bond state--spurred analytical understanding of both the role of entanglement in topological physics and physical mechanisms by which it can arise. However, quantitative understanding of the relevant phase diagrams is still challenging. For this purpose, tensor networks provide a toolbox for systematically improving wavefunction ansatz while still capturing the relevant entanglement properties. In this thesis, we use the tools of entanglement and tensor networks to analyze ansatz states for several proposed new phases. In the first part, we study a featureless phase of bosons on the honeycomb lattice and argue that this phase can be topologically protected under any one of several distinct subsets of the crystalline lattice symmetries. We discuss methods of detecting such phases with entanglement and without. In the second part, we consider the problem of constructing fixed-point wavefunctions for

Context-Based Topology Control for Wireless Mesh Networks

Directory of Open Access Journals (Sweden)

Pragasen Mudali

2016-01-01

Full Text Available Topology Control has been shown to provide several benefits to wireless ad hoc and mesh networks. However these benefits have largely been demonstrated using simulation-based evaluations. In this paper, we demonstrate the negative impact that the PlainTC Topology Control prototype has on topology stability. This instability is found to be caused by the large number of transceiver power adjustments undertaken by the prototype. A context-based solution is offered to reduce the number of transceiver power adjustments undertaken without sacrificing the cumulative transceiver power savings and spatial reuse advantages gained from employing Topology Control in an infrastructure wireless mesh network. We propose the context-based PlainTC+ prototype and show that incorporating context information in the transceiver power adjustment process significantly reduces topology instability. In addition, improvements to network performance arising from the improved topology stability are also observed. Future plans to add real-time context-awareness to PlainTC+ will have the scheme being prototyped in a software-defined wireless mesh network test-bed being planned.

Long-branch attraction bias and inconsistency in Bayesian phylogenetics.

Science.gov (United States)

Kolaczkowski, Bryan; Thornton, Joseph W

2009-12-09

Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias--which is apparent under both controlled simulation conditions and in analyses of empirical sequence data--also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages--that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis.

Nodal distances for rooted phylogenetic trees.

Science.gov (United States)

Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

2010-08-01

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).

Rendering the Topological Spines

Energy Technology Data Exchange (ETDEWEB)

Nieves-Rivera, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-05-05

Many tools to analyze and represent high dimensional data already exits yet most of them are not flexible, informative and intuitive enough to help the scientists make the corresponding analysis and predictions, understand the structure and complexity of scientific data, get a complete picture of it and explore a greater number of hypotheses. With this in mind, N-Dimensional Data Analysis and Visualization (ND²AV) is being developed to serve as an interactive visual analysis platform with the purpose of coupling together a number of these existing tools that range from statistics, machine learning, and data mining, with new techniques, in particular with new visualization approaches. My task is to create the rendering and implementation of a new concept called topological spines in order to extend ND²AV's scope. Other existing visualization tools create a representation preserving either the topological properties or the structural (geometric) ones because it is challenging to preserve them both simultaneously. Overcoming such challenge by creating a balance in between them, the topological spines are introduced as a new approach that aims to preserve them both. Its render using OpenGL and C++ and is currently being tested to further on be implemented on ND²AV. In this paper I will present what are the Topological Spines and how they are rendered.

A new bidirectional heteroassociative memory encompassing correlational, competitive and topological properties.

Science.gov (United States)

Chartier, Sylvain; Giguère, Gyslain; Langlois, Dominic

2009-01-01

In this paper, we present a new recurrent bidirectional model that encompasses correlational, competitive and topological model properties. The simultaneous use of many classes of network behaviors allows for the unsupervised learning/categorization of perceptual patterns (through input compression) and the concurrent encoding of proximities in a multidimensional space. All of these operations are achieved within a common learning operation, and using a single set of defining properties. It is shown that the model can learn categories by developing prototype representations strictly from exposition to specific exemplars. Moreover, because the model is recurrent, it can reconstruct perfect outputs from incomplete and noisy patterns. Empirical exploration of the model's properties and performance shows that its ability for adequate clustering stems from: (1) properly distributing connection weights, and (2) producing a weight space with a low dispersion level (or higher density). In addition, since the model uses a sparse representation (k-winners), the size of topological neighborhood can be fixed, and no longer requires a decrease through time as was the case with classic self-organizing feature maps. Since the model's learning and transmission parameters are independent from learning trials, the model can develop stable fixed points in a constrained topological architecture, while being flexible enough to learn novel patterns.

Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods.

Science.gov (United States)

Duchêne, Sebastian; Lanfear, Robert

2015-09-01

Ancestral state reconstruction (ASR) is a popular method for exploring the evolutionary history of traits that leave little or no trace in the fossil record. For example, it has been used to test hypotheses about the number of evolutionary origins of key life-history traits such as oviparity, or key morphological structures such as wings. Many studies that use ASR have suggested that the number of evolutionary origins of such traits is higher than was previously thought. The scope of such inferences is increasing rapidly, facilitated by the construction of very large phylogenies and life-history databases. In this paper, we use simulations to show that the number of evolutionary origins of a trait tends to be overestimated when the phylogeny is not perfect. In some cases, the estimated number of transitions can be several fold higher than the true value. Furthermore, we show that the bias is not always corrected by standard approaches to account for phylogenetic uncertainty, such as repeating the analysis on a large collection of possible trees. These findings have important implications for studies that seek to estimate the number of origins of a trait, particularly those that use large phylogenies that are associated with considerable uncertainty. We discuss the implications of this bias, and methods to ameliorate it. © 2015 Wiley Periodicals, Inc.

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

Science.gov (United States)

Kasey K. Pham; Andrew L. Hipp; Paul S. Manos; Richard C. Cronn

2017-01-01

Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect...

Phylogenetic relationships within and among Brassica species from ...

African Journals Online (AJOL)

Consequently, two potentially susceptible B. napus accessions were identified. The high polymorphic information content (PIC) and number of phylogenetically informative bands established RAPD as a useful tool for phylogenetic reconstruction, quantification of genetic diversity for conservation, cultivar classification and ...

Topological classification of trigonometric polynomials related to affine Coxeter group A-tilde2

International Nuclear Information System (INIS)

Arnold, V.I.

2006-06-01

The family of trigonometric polynomials, is defined by the six?Cparametrical expression f(x, y) = a cos x + b sin x + c cos y + d sin y + p cos(x + y) + q sin(x + y). The trigonometric polynomials of this family, having the most complicated topological structure, have 6 critical points. These functions are classified up to the actions of the following groups: two functions are called to be topologically equivalent, if one is transformed to the other by two smooth diffeomorphisms of the manifolds T 2 and R (of the preimages and of the images of mapping f : T 2 → R). We suppose, that the images diffeomorphisms (dependent variable changes) preserve the orientation of the real line, and that the preimages spaces diffeomorphism is homotopic to the identity mapping of the torus. We shall see, that the trigonometric polynomials which have 6 nondegenerated critical points and six different critical values (that might be fixed at points {1, 2, 3, 4, 5, 6 }) form 6 equivalence classes of topologically different functions, while the general Morse functions on the torus, having six critical points and six fixed critical values, form an infinite set of the equivalence classes of functions. With respect to the Diff-equivalence all these functions form only 16 classes. All these unexpected results suggest, that in the 16 Cth Hilbert's problem (on the topological classification of real algebraic manifolds) one would ask to classify topologically rather the defining polynomials, than the real hypersurfaces of their zeros

Quantum Hall Conductivity and Topological Invariants

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Reyes, Andres

2001-04-01

A short survey of the theory of the Quantum Hall effect is given emphasizing topological aspects of the quantization of the conductivity and showing how topological invariants can be derived from the hamiltonian. We express these invariants in terms of Chern numbers and show in precise mathematical terms how this relates to the Kubo formula.

Topological insulators and superconductors: tenfold way and dimensional hierarchy

International Nuclear Information System (INIS)

Ryu, Shinsei; Schnyder, Andreas P; Furusaki, Akira; Ludwig, Andreas W W

2010-01-01

It has recently been shown that in every spatial dimension there exist precisely five distinct classes of topological insulators or superconductors. Within a given class, the different topological sectors can be distinguished, depending on the case, by a Z or a Z 2 topological invariant. This is an exhaustive classification. Here we construct representatives of topological insulators and superconductors for all five classes and in arbitrary spatial dimension d, in terms of Dirac Hamiltonians. Using these representatives we demonstrate how topological insulators (superconductors) in different dimensions and different classes can be related via 'dimensional reduction' by compactifying one or more spatial dimensions (in 'Kaluza-Klein'-like fashion). For Z-topological insulators (superconductors) this proceeds by descending by one dimension at a time into a different class. The Z 2 -topological insulators (superconductors), on the other hand, are shown to be lower-dimensional descendants of parent Z-topological insulators in the same class, from which they inherit their topological properties. The eightfold periodicity in dimension d that exists for topological insulators (superconductors) with Hamiltonians satisfying at least one reality condition (arising from time-reversal or charge-conjugation/particle-hole symmetries) is a reflection of the eightfold periodicity of the spinor representations of the orthogonal groups SO(N) (a form of Bott periodicity). Furthermore, we derive for general spatial dimensions a relation between the topological invariant that characterizes topological insulators and superconductors with chiral symmetry (i.e., the winding number) and the Chern-Simons invariant. For lower-dimensional cases, this formula relates the winding number to the electric polarization (d=1 spatial dimensions) or to the magnetoelectric polarizability (d=3 spatial dimensions). Finally, we also discuss topological field theories describing the spacetime theory of

Standardization of the CFU-GM assay: Advantages of plating a fixed number of CD34+ cells in collagen gels.

Science.gov (United States)

Dobo, Irène; Pineau, Danielle; Robillard, Nelly; Geneviève, Frank; Piard, Nicole; Zandecki, Marc; Hermouet, Sylvie

2003-10-01

We investigated whether plating a stable amount of CD34(+) cells improves the CFU-GM assay. Data of CFU-GM assays performed with leukaphereses products in two transplant centers using a commercial collagen-based medium and unified CFU-GM scoring criteria were pooled and analyzed according to the numbers of CD34(+) cells plated. A first series of 113 CFU-GM assays was performed with a fixed number of mononuclear cells (i.e., a variable number of CD34(+) cells). In these cultures the CFU-GM/CD34 ratio varied according to the number of CD34(+) cells plated: median CFUGM/CD34 ratios were 1/6.2 to 1/6.6 for grafts containing or =2% CD34(+) cells. The median CFU-GM/CD34 ratio also varied depending on pathology: 1/9.3 for multiple myeloma (MM), 1/6.8 for Hodgkin's disease (HD), 1/6.5 for non-Hodgkin lymphoma (NHL), and 1/4.5 for solid tumors (ST). A second series of 95 CFU-GM assays was performed with a fixed number of CD34(+) cells (220/ml). The range of median CFU-GM/CD34 ratios was narrowed to 1/7.0 to 1/5.2, and coefficients of variation for CFU-GM counts decreased by half to 38.1% (NHL), 36.1% (MM), 49.9% (HD), and 22.4% (ST). In addition, CFU-GM scoring was facilitated as the percentages of cultures with >50 CFU/GM/ml decreased from 6.7% to 43.8% when a variable number of CD34(+) cells was plated, to 4.5% to 16.7% when 220 CD34(+) cells/ml were plated. Hence, plating a fixed number of CD34(+) cells in collagen gels improves the CFU-GM assay by eliminating cell number-related variability and reducing pathology-related variability in colony growth.

On topological RNA interaction structures.

Science.gov (United States)

Qin, Jing; Reidys, Christian M

2013-07-01

Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures. These are RNA-RNA interaction structures that are constructed by a finite number of building blocks over two backbones having genus at most γ. Combinatorial properties of γ-interaction structures are of practical interest since they have direct implications for the folding of topological interaction structures. We compute the generating function of γ-interaction structures and show that it is algebraic, which implies that the numbers of interaction structures can be computed recursively. We obtain simple asymptotic formulas for 0- and 1-interaction structures. The simplest class of interaction structures are the 0-interaction structures, which represent the two backbone analogues of secondary structures.

On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems

NARCIS (Netherlands)

van Iersel, L.J.J.; Kelk, Steven; Stougie, Leen; Boes, Olivier

2017-01-01

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic

Geometric entanglement in topologically ordered states

International Nuclear Information System (INIS)

Orús, Román; Wei, Tzu-Chieh; Buerschaper, Oliver; Nest, Maarten Van den

2014-01-01

Here we investigate the connection between topological order and the geometric entanglement, as measured by the logarithm of the overlap between a given state and its closest product state of blocks. We do this for a variety of topologically ordered systems such as the toric code, double semion, colour code and quantum double models. As happens for the entanglement entropy, we find that for sufficiently large block sizes the geometric entanglement is, up to possible sub-leading corrections, the sum of two contributions: a bulk contribution obeying a boundary law times the number of blocks and a contribution quantifying the underlying pattern of long-range entanglement of the topologically ordered state. This topological contribution is also present in the case of single-spin blocks in most cases, and constitutes an alternative characterization of topological order for these quantum states based on a multipartite entanglement measure. In particular, we see that the topological term for the two-dimensional colour code is twice as much as the one for the toric code, in accordance with recent renormalization group arguments (Bombin et al 2012 New J. Phys. 14 073048). Motivated by these results, we also derive a general formalism to obtain upper- and lower-bounds to the geometric entanglement of states with a non-Abelian group symmetry, and which we explicitly use to analyse quantum double models. Furthermore, we also provide an analysis of the robustness of the topological contribution in terms of renormalization and perturbation theory arguments, as well as a numerical estimation for small systems. Some of the results in this paper rely on the ability to disentangle single sites from the quantum state, which is always possible for the systems that we consider. Additionally we relate our results to the behaviour of the relative entropy of entanglement in topologically ordered systems, and discuss a number of numerical approaches based on tensor networks that could be

An extended topological Yang-Mills theory

International Nuclear Information System (INIS)

Deguchi, Shinichi

1992-01-01

Introducing infinite number of fields, we construct an extended version of the topological Yang-Mills theory. The properties of the extended topological Yang-Mills theory (ETYMT) are discussed from standpoint of the covariant canonical quantization. It is shown that the ETYMT becomes a cohomological topological field theory or a theory equivalent to a quantum Yang-Mills theory with anti-self-dual constraint according to subsidiary conditions imposed on state-vector space. On the basis of the ETYMT, we may understand a transition from an unbroken phase to a physical phase (broken phase). (author)

Molecular phylogenetics, historical biogeography, and chromosome number evolution of Portulaca (Portulacaceae).

Science.gov (United States)

Ocampo, Gilberto; Columbus, J Travis

2012-04-01

Portulaca is the only genus in Portulacaceae and has ca. 100 species distributed worldwide, mainly in the tropics and subtropics. Molecular data place the genus as one of the closest relatives of Cactaceae, but phylogenetic relationships within Portulaca are barely known. This study samples 59 species of Portulaca, 10 infraspecific taxa, and three cultivars, including multiple samples of widespread species. The sampled taxa represent all subgenera in the classifications of von Poellnitz (1934), Legrand (1958), and Geesink (1969) and come from around the world. Nuclear ITS and chloroplast ndhF, trnT-psbD intergenic spacer, and ndhA intron DNA sequences were analyzed using maximum likelihood and Bayesian methods to produce a hypothesis of relationships within Portulaca. Divergence times were estimated using Hawaiian endemics for calibration, and biogeographical patterns were examined using a Bayes-DIVA approach. In addition, the evolution of chromosome numbers in the genus was investigated using probabilistic models. The analyses strongly support the monophyly of Portulaca, with an age of the most recent common ancestor (MRCA) of 23 Myr. Within Portulaca are two major lineages: the OL clade (comprising opposite-leaved species) distributed in Africa, Asia, and Australia, and the AL clade (comprising alternate to subopposite-leaved species), which is more widespread and originated in the New World. Sedopsis, a genus sometimes recognized as distinct from Portulaca based on a long corolla tube, is nested within the OL clade and does not merit taxonomic recognition. Samples of Portulaca grandiflora, Portulaca halimoides, and Portulaca oleracea were found to be non-monophyletic. It is hypothesized that the ancestral distribution area of Portulaca included southern hemisphere continents and Asia. The OL clade remained restricted to the Old World (except Portulaca quadrifida, a pantropical weed), while the AL clade, with a South American origin, was able to disperse multiple

The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions.

Science.gov (United States)

Brown, Jeremy M; Thomson, Robert C

2018-02-15

Bayesian phylogenetic inference involves sampling from posterior distributions of trees, which sometimes exhibit local optima, or peaks, separated by regions of low posterior density. Markov chain Monte Carlo (MCMC) algorithms are the most widely used numerical method for generating samples from these posterior distributions, but they are susceptible to entrapment on individual optima in rugged distributions when they are unable to easily cross through or jump across regions of low posterior density. Ruggedness of posterior distributions can result from a variety of factors, including unmodeled variation in evolutionary processes and unrecognized variation in the true topology across sites or genes. Ruggedness can also become exaggerated when constraints are placed on topologies that require the presence or absence of particular bipartitions (often referred to as positive or negative constraints, respectively). These types of constraints are frequently employed when conducting tests of topological hypotheses (Bergsten et al. 2013; Brown and Thomson 2017). Negative constraints can lead to particularly rugged distributions when the data strongly support a forbidden clade, because monophyly of the clade can be disrupted by inserting outgroup taxa in many different ways. However, topological moves between the alternative disruptions are very difficult, because they require swaps between the inserted outgroup taxa while the data constrain taxa from the forbidden clade to remain close together on the tree. While this precise form of ruggedness is particular to negative constraints, trees with high posterior density can be separated by similarly complicated topological rearrangements, even in the absence of constraints.

Phylogenetic reconstruction methods: an overview.

Science.gov (United States)

De Bruyn, Alexandre; Martin, Darren P; Lefeuvre, Pierre

2014-01-01

Initially designed to infer evolutionary relationships based on morphological and physiological characters, phylogenetic reconstruction methods have greatly benefited from recent developments in molecular biology and sequencing technologies with a number of powerful methods having been developed specifically to infer phylogenies from macromolecular data. This chapter, while presenting an overview of basic concepts and methods used in phylogenetic reconstruction, is primarily intended as a simplified step-by-step guide to the construction of phylogenetic trees from nucleotide sequences using fairly up-to-date maximum likelihood methods implemented in freely available computer programs. While the analysis of chloroplast sequences from various Vanilla species is used as an illustrative example, the techniques covered here are relevant to the comparative analysis of homologous sequences datasets sampled from any group of organisms.

Topological phases in a three-dimensional topological insulator with a time-reversal invariant external field

International Nuclear Information System (INIS)

Guo, Xiaoyong; Ren, Xiaobin; Wang, Gangzhi; Peng, Jie

2014-01-01

We investigate the impact of a time-reversal invariant external field on the topological phases of a three-dimensional (3D) topological insulator. By taking the momentum k z as a parameter, we calculate the spin-Chern number analytically. It is shown that both the quantum spin Hall phase and the integer quantum Hall phase can be realized in our system. When the strength of the external field is varied, a series of topological phase transitions occurs with the closing of the energy gap or the spin-spectrum gap. In a tight-binding form, the surface modes are discussed numerically to confirm the analytically results. (paper)

Topology in SU(2) lattice gauge theory and parallelization of functional magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Solbrig, Stefan

2008-07-01

In this thesis, I discuss topological properties of quenched SU(2) lattice gauge fields. In particular, clusters of topological charge density exhibit a power-law. The exponent of that power-law can be used to validate models for lattice gauge fields. Instead of working with fixed cutoffs of the topological charge density, using the notion of a ''watermark'' is more convenient. Furthermore, I discuss how a parallel computer, originally designed for lattice gauge field simulations, can be used for functional magnetic resonance imaging. Multi parameter fits can be parallelized to achieve almost real-time evaluation of fMRI data. (orig.)

Phylogenetic characterization of the ubiquitous electron transfer flavoprotein families ETF-alpha and ETF-beta.

Science.gov (United States)

Tsai, M H; Saier, M H

1995-06-01

Electron transfer flavoproteins (ETF) are alpha beta-heterodimers found in eukaryotic mitochondria and bacteria. We have identified currently sequenced protein members of the ETF-alpha and ETF-beta families. Members of these two families include (a) the ETF subunits of mammals and bacteria, (b) homologous pairs of proteins (FixB/FixA) that are essential for nitrogen fixation in some bacteria, and (c) a pair of carnitine-inducible proteins encoded by two open reading frames in Escherichia coli (YaaQ and YaaR). These three groups of proteins comprise three clusters on both the ETF-alpha and ETF-beta phylogenetic trees, separated from each other by comparable phylogenetic distances. This fact suggests that these two protein families evolved with similar overall rates of evolutionary divergence. Relative regions of sequence conservation are evaluated, and signature sequences for both families are derived.

Phylogenetic relationships of Hemiptera inferred from mitochondrial and nuclear genes.

Science.gov (United States)

Song, Nan; Li, Hu; Cai, Wanzhi; Yan, Fengming; Wang, Jianyun; Song, Fan

2016-11-01

Here, we reconstructed the Hemiptera phylogeny based on the expanded mitochondrial protein-coding genes and the nuclear 18S rRNA gene, separately. The differential rates of change across lineages may associate with long-branch attraction (LBA) effect and result in conflicting estimates of phylogeny from different types of data. To reduce the potential effects of systematic biases on inferences of topology, various data coding schemes, site removal method, and different algorithms were utilized in phylogenetic reconstruction. We show that the outgroups Phthiraptera, Thysanoptera, and the ingroup Sternorrhyncha share similar base composition, and exhibit "long branches" relative to other hemipterans. Thus, the long-branch attraction between these groups is suspected to cause the failure of recovering Hemiptera under the homogeneous model. In contrast, a monophyletic Hemiptera is supported when heterogeneous model is utilized in the analysis. Although higher level phylogenetic relationships within Hemiptera remain to be answered, consensus between analyses is beginning to converge on a stable phylogeny.

Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

Directory of Open Access Journals (Sweden)

de Stephanis Renaud

2011-03-01

Full Text Available Abstract Background Previous DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships (polytomies for some of the species within this group. Using an increased amount of sequence data we test between alternative hypotheses of soft polytomies caused by rapid speciation, slow evolutionary rate and/or insufficient sequence data, and hard polytomies caused by simultaneous speciation within this family. Combining the mitogenome sequences of five new and 12 previously published species within the Delphinidae, we used Bayesian and maximum-likelihood methods to estimate the phylogeny from partitioned and unpartitioned mitogenome sequences. Further ad hoc tests were then conducted to estimate the support for alternative topologies. Results We found high support for all the relationships within our reconstructed phylogenies, and topologies were consistent between the Bayesian and maximum-likelihood trees inferred from partitioned and unpartitioned data. Resolved relationships included the placement of the killer whale (Orcinus orca as sister taxon to the rest of the Globicephalinae subfamily, placement of the Risso's dolphin (Grampus griseus within the Globicephalinae subfamily, removal of the white-beaked dolphin (Lagenorhynchus albirostris from the Delphininae subfamily and the placement of the rough-toothed dolphin (Steno bredanensis as sister taxon to the rest of the Delphininae subfamily rather than within the Globicephalinae subfamily. The additional testing of alternative topologies allowed us to reject all other putative relationships, with the exception that we were unable to reject the hypothesis that the relationship between L. albirostris and the Globicephalinae and Delphininae subfamilies was polytomic. Conclusion Despite their rapid diversification, the increased sequence data yielded by mitogenomes enables the

Persistent topological features of dynamical systems

Energy Technology Data Exchange (ETDEWEB)

Maletić, Slobodan, E-mail: slobodan@hitsz.edu.cn [Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen (China); Institute of Nuclear Sciences Vinča, University of Belgrade, Belgrade (Serbia); Zhao, Yi, E-mail: zhao.yi@hitsz.edu.cn [Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen (China); Rajković, Milan, E-mail: milanr@vinca.rs [Institute of Nuclear Sciences Vinča, University of Belgrade, Belgrade (Serbia)

2016-05-15

Inspired by an early work of Muldoon et al., Physica D 65, 1–16 (1993), we present a general method for constructing simplicial complex from observed time series of dynamical systems based on the delay coordinate reconstruction procedure. The obtained simplicial complex preserves all pertinent topological features of the reconstructed phase space, and it may be analyzed from topological, combinatorial, and algebraic aspects. In focus of this study is the computation of homology of the invariant set of some well known dynamical systems that display chaotic behavior. Persistent homology of simplicial complex and its relationship with the embedding dimensions are examined by studying the lifetime of topological features and topological noise. The consistency of topological properties for different dynamic regimes and embedding dimensions is examined. The obtained results shed new light on the topological properties of the reconstructed phase space and open up new possibilities for application of advanced topological methods. The method presented here may be used as a generic method for constructing simplicial complex from a scalar time series that has a number of advantages compared to the mapping of the same time series to a complex network.

On topological properties of sierpinski networks

International Nuclear Information System (INIS)

Imran, Muhammad; Sabeel-e-Hafi; Gao, Wei; Reza Farahani, Mohammad

2017-01-01

Sierpinski graphs constitute an extensively studied class of graphs of fractal nature applicable in topology, mathematics of Tower of Hanoi, computer science, and elsewhere. A large number of properties like physico-chemical properties, thermodynamic properties, chemical activity, biological activity, etc. are determined by the chemical applications of graph theory. These properties can be characterized by certain graph invariants referred to as topological indices. In QRAR/QSPR study these graph invariants has played a vital role. In this paper, we study the molecular topological properties of Sierpinski networks and derive the analytical closed formulas for the atom-bond connectivity (ABC) index, geometric-arithmetic (GA) index, and fourth and fifth version of these topological indices for Sierpinski networks denoted by S(n, k).

Topological interpretation of Luttinger theorem

OpenAIRE

Seki, Kazuhiro; Yunoki, Seiji

2017-01-01

Based solely on the analytical properties of the single-particle Green's function of fermions at finite temperatures, we show that the generalized Luttinger theorem inherently possesses topological aspects. The topological interpretation of the generalized Luttinger theorem can be introduced because i) the Luttinger volume is represented as the winding number of the single-particle Green's function and thus ii) the deviation of the theorem, expressed with a ratio between the interacting and n...

Photoinduced Topological Phase Transitions in Topological Magnon Insulators.

Science.gov (United States)

Owerre, S A

2018-03-13

Topological magnon insulators are the bosonic analogs of electronic topological insulators. They are manifested in magnetic materials with topologically nontrivial magnon bands as realized experimentally in a quasi-two-dimensional (quasi-2D) kagomé ferromagnet Cu(1-3, bdc), and they also possess protected magnon edge modes. These topological magnetic materials can transport heat as well as spin currents, hence they can be useful for spintronic applications. Moreover, as magnons are charge-neutral spin-1 bosonic quasiparticles with a magnetic dipole moment, topological magnon materials can also interact with electromagnetic fields through the Aharonov-Casher effect. In this report, we study photoinduced topological phase transitions in intrinsic topological magnon insulators in the kagomé ferromagnets. Using magnonic Floquet-Bloch theory, we show that by varying the light intensity, periodically driven intrinsic topological magnetic materials can be manipulated into different topological phases with different sign of the Berry curvatures and the thermal Hall conductivity. We further show that, under certain conditions, periodically driven gapped topological magnon insulators can also be tuned to synthetic gapless topological magnon semimetals with Dirac-Weyl magnon cones. We envision that this work will pave the way for interesting new potential practical applications in topological magnetic materials.

Phylogenetic search through partial tree mixing

Science.gov (United States)

2012-01-01

Background Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. Results When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda Conclusions The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution. PMID:23320449

On the topology of flux transfer events

Science.gov (United States)

Hesse, Michael; Birn, Joachim; Schindler, Karl

1990-01-01

A topological analysis is made of a simple model magnetic field of a perturbation at the magnetopause that shares magnetic properties with flux transfer events. The aim is to clarify a number of topological aspects that arise in the case of fully three-dimensional magnetic fields. It is shown that a localized perturbation at the magnetopause can in principle open a closed magnetosphere by establishing magnetic connections across the magnetopause by the formation of a ropelike magnetic field structure. For this purpose a global topological model of a closed magnetosphere is considered as the unperturbed state. The topological substructure of the model flux rope is discussed in detail.

Wall shear stress fixed points in cardiovascular fluid mechanics.

Science.gov (United States)

Arzani, Amirhossein; Shadden, Shawn C

2018-05-17

Complex blood flow in large arteries creates rich wall shear stress (WSS) vectorial features. WSS acts as a link between blood flow dynamics and the biology of various cardiovascular diseases. WSS has been of great interest in a wide range of studies and has been the most popular measure to correlate blood flow to cardiovascular disease. Recent studies have emphasized different vectorial features of WSS. However, fixed points in the WSS vector field have not received much attention. A WSS fixed point is a point on the vessel wall where the WSS vector vanishes. In this article, WSS fixed points are classified and the aspects by which they could influence cardiovascular disease are reviewed. First, the connection between WSS fixed points and the flow topology away from the vessel wall is discussed. Second, the potential role of time-averaged WSS fixed points in biochemical mass transport is demonstrated using the recent concept of Lagrangian WSS structures. Finally, simple measures are proposed to quantify the exposure of the endothelial cells to WSS fixed points. Examples from various arterial flow applications are demonstrated. Copyright © 2018 Elsevier Ltd. All rights reserved.

Long-branch attraction bias and inconsistency in Bayesian phylogenetics.

Directory of Open Access Journals (Sweden)

Bryan Kolaczkowski

Full Text Available Bayesian inference (BI of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML, so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model. This bias--which is apparent under both controlled simulation conditions and in analyses of empirical sequence data--also makes BI less efficient and less robust to the use of an incorrect evolutionary model than ML. Surprisingly, BI's bias is caused by one of the method's stated advantages--that it incorporates uncertainty about branch lengths by integrating over a distribution of possible values instead of estimating them from the data, as ML does. Our findings suggest that trees inferred using BI should be interpreted with caution and that ML may be a more reliable framework for modern phylogenetic analysis.

Topological Photonics for Continuous Media

Science.gov (United States)

Silveirinha, Mario

Photonic crystals have revolutionized light-based technologies during the last three decades. Notably, it was recently discovered that the light propagation in photonic crystals may depend on some topological characteristics determined by the manner how the light states are mutually entangled. The usual topological classification of photonic crystals explores the fact that these structures are periodic. The periodicity is essential to ensure that the underlying wave vector space is a closed surface with no boundary. In this talk, we prove that it is possible calculate Chern invariants for a wide class of continuous bianisotropic electromagnetic media with no intrinsic periodicity. The nontrivial topology of the relevant continuous materials is linked with the emergence of edge states. Moreover, we will demonstrate that continuous photonic media with the time-reversal symmetry can be topologically characterized by a Z2 integer. This novel classification extends for the first time the theory of electronic topological insulators to a wide range of photonic platforms, and is expected to have an impact in the design of novel photonic systems that enable a topologically protected transport of optical energy. This work is supported in part by Fundacao para a Ciencia e a Tecnologia Grant Number PTDC/EEI-TEL/4543/2014.

Topological orders in rigid states

International Nuclear Information System (INIS)

Wen, X.G.

1990-01-01

The authors study a new kind of ordering topological order in rigid states (the states with no local gapless excitations). This paper concentrates on characterization of the different topological orders. As an example the authors discuss in detail chiral spin states of 2+1 dimensional spin systems. Chiral spin states are described by the topological Chern-Simons theories in the continuum limit. The authors show that the topological orders can be characterized by a non-Abelian gauge structure over the moduli space which parametrizes a family of the model Hamiltonians supporting topologically ordered ground states. In 2 + 1 dimensions, the non-Abelian gauge structure determines possible fractional statistics of the quasi-particle excitations over the topologically ordered ground states. The dynamics of the low lying global excitations is shown to be independent of random spatial dependent perturbations. The ground state degeneracy and the non-Abelian gauge structures discussed in this paper are very robust, even against those perturbations that break translation symmetry. The authors also discuss the symmetry properties of the degenerate ground states of chiral spin states. The authors find that some degenerate ground states of chiral spin states on torus carry non-trivial quantum numbers of the 90 degrees rotation

Phylogenetic relationships of typical antbirds (Thamnophilidae and test of incongruence based on Bayes factors

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Nylander Johan AA

2004-07-01

Full Text Available Abstract Background The typical antbirds (Thamnophilidae form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set. Results The phylogenetic analysis supports both novel relationships, as well as traditional groupings. Among the more interesting novel relationship suggested is that the Terenura antwrens, the wing-banded antbird (Myrmornis torquata, the spot-winged antshrike (Pygiptila stellaris and the russet antshrike (Thamnistes anabatinus are sisters to all other typical antbirds. The remaining genera fall into two major clades. The first includes antshrikes, antvireos and the Herpsilochmus antwrens, while the second clade consists of most antwren genera, the Myrmeciza antbirds, the "professional" ant-following antbirds, and allied species. Our results also support previously suggested polyphyly of Myrmotherula antwrens and Myrmeciza antbirds. The tests of phylogenetic incongruence, using Bayes factors, clearly suggests that allowing the gene partitions to have separate topology parameters clearly increased the model likelihood. However, changing a component of the nucleotide substitution model had much higher impact on the model likelihood. Conclusions The phylogenetic results are in broad agreement with traditional classification of the typical antbirds, but some relationships are unexpected based on external morphology. In these cases their true affinities may have been obscured by convergent evolution and

Metadynamics surfing on topology barriers: the CP{sup N−1} case

Energy Technology Data Exchange (ETDEWEB)

Laio, A. [SISSA,Via Bonomea 265, I-34136, Trieste (Italy); Martinelli, G. [SISSA,Via Bonomea 265, I-34136, Trieste (Italy); INFN - Sezione di Roma La Sapienza,Piazzale Aldo Moro 5, 00185 Roma (Italy); Sanfilippo, F. [School of Physics and Astronomy, University of Southampton,Southampton SO17 1BJ (United Kingdom)

2016-07-18

As one approaches the continuum limit, QCD systems, investigated via numerical simulations, remain trapped in sectors of field space with fixed topological charge. As a consequence the numerical studies of physical quantities may give biased results. The same is true in the case of two dimensional CP{sup N−1} models. In this paper we show that metadynamics, when used to simulate CP{sup N−1}, allows to address efficiently this problem. By studying CP{sup 20} we show that we are able to reconstruct the free energy of the topological charge F(Q) and compute the topological susceptibility as a function of the coupling and of the volume. This is a very important physical quantity in studies of the dynamics of the θ vacuum and of the axion. This method can in principle be extended to QCD applications.

Topologies of multiterminal HVDC-VSC transmission for large offshore wind farms

Energy Technology Data Exchange (ETDEWEB)

Gomis-Bellmunt, Oriol [Centre d' Innovacio Tecnologica en Convertidors Estatics i Accionaments (CITCEA-UPC), Universitat Politecnica de Catalunya UPC, Av. Diagonal, 647, Pl. 2. 08028 Barcelona (Spain); IREC Catalonia Institute for Energy Research, Barcelona (Spain); Liang, Jun; Ekanayake, Janaka; King, Rosemary; Jenkins, Nicholas [School of Engineering, Cardiff University, Queen' s Buildings, The Parade, Cardiff CF24 3AA, Wales (United Kingdom)

2011-02-15

Topologies of multiterminal HVDC-VSC transmission systems for large offshore wind farms are investigated. System requirements for multiterminal HVDC are described, particularly the maximum power loss allowed in the event of a fault. Alternative control schemes and HVDC circuit topologies are reviewed, including the need for HVDC circuit breakers. Various topologies are analyzed and compared according to a number of criteria: number and capacity of HVDC circuits, number of HVDC circuit breakers, maximum power loss, flexibility, redundancy, lines utilization, need for offshore switching platforms and fast communications. (author)

constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints.

Science.gov (United States)

Matsen, Frederick A

2010-06-01

This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints.

Empirical correlations for axial dispersion coefficient and Peclet number in fixed-bed columns.

Science.gov (United States)

Rastegar, Seyed Omid; Gu, Tingyue

2017-03-24

In this work, a new correlation for the axial dispersion coefficient was obtained using experimental data in the literature for axial dispersion in fixed-bed columns packed with particles. The Chung and Wen correlation, the De Ligny correlation are two popular empirical correlations. However, the former lacks the molecular diffusion term and the latter does not consider bed voidage. The new axial dispersion coefficient correlation in this work was based on additional experimental data in the literature by considering both molecular diffusion and bed voidage. It is more comprehensive and accurate. The Peclet number correlation from the new axial dispersion coefficient correlation on the average leads to 12% lower Peclet number values compared to the values from the Chung and Wen correlation, and in many cases much smaller than those from the De Ligny correlation. Copyright © 2017 Elsevier B.V. All rights reserved.

Lateral topological crystalline insulator heterostructure

Science.gov (United States)

Sun, Qilong; Dai, Ying; Niu, Chengwang; Ma, Yandong; Wei, Wei; Yu, Lin; Huang, Baibiao

2017-06-01

The emergence of lateral heterostructures fabricated by two-dimensional building blocks brings many exciting realms in material science and device physics. Enriching available nanomaterials for creating such heterostructures and enabling the underlying new physics is highly coveted for the integration of next-generation devices. Here, we report a breakthrough in lateral heterostructure based on the monolayer square transition-metal dichalcogenides MX2 (M  =  W, X  =  S/Se) modules. Our results reveal that the MX2 lateral heterostructure (1S-MX2 LHS) can possess excellent thermal and dynamical stability. Remarkably, the highly desired two-dimensional topological crystalline insulator phase is confirmed by the calculated mirror Chern number {{n}\\text{M}}=-1 . A nontrivial band gap of 65 meV is obtained with SOC, indicating the potential for room-temperature observation and applications. The topologically protected edge states emerge at the edges of two different nanoribbons between the bulk band gap, which is consistent with the mirror Chern number. In addition, a strain-induced topological phase transition in 1S-MX2 LHS is also revealed, endowing the potential utilities in electronics and spintronics. Our predictions not only introduce new member and vitality into the studies of lateral heterostructures, but also highlight the promise of lateral heterostructure as appealing topological crystalline insulator platforms with excellent stability for future devices.

Phylogenetic trees

OpenAIRE

Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert

2016-01-01

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences.

Science.gov (United States)

Chang, B S; Campbell, D L

2000-08-01

Two spurious nodes were found in phylogenetic analyses of vertebrate rhodopsin sequences in comparison with well-established vertebrate relationships. These spurious reconstructions were well supported in bootstrap analyses and occurred independently of the method of phylogenetic analysis used (parsimony, distance, or likelihood). Use of this data set of vertebrate rhodopsin sequences allowed us to exploit established vertebrate relationships, as well as the considerable amount known about the molecular evolution of this gene, in order to identify important factors contributing to the spurious reconstructions. Simulation studies using parametric bootstrapping indicate that it is unlikely that the spurious nodes in the parsimony analyses are due to long branches or other topological effects. Rather, they appear to be due to base compositional bias at third positions, codon bias, and convergent evolution at nucleotide positions encoding the hydrophobic residues isoleucine, leucine, and valine. LogDet distance methods, as well as maximum-likelihood methods which allow for nonstationary changes in base composition, reduce but do not entirely eliminate support for the spurious resolutions. Inclusion of five additional rhodopsin sequences in the phylogenetic analyses largely corrected one of the spurious reconstructions while leaving the other unaffected. The additional sequences not only were more proximal to the corrected node, but were also found to have intermediate levels of base composition and codon bias as compared with neighboring sequences on the tree. This study shows that the spurious reconstructions can be corrected either by excluding third positions, as well as those encoding the amino acids Ile, Val, and Leu (which may not be ideal, as these sites can contain useful phylogenetic signal for other parts of the tree), or by the addition of sequences that reduce problems associated with convergent evolution.

Elements of mathematics general topology

CERN Document Server

Bourbaki, Nicolas

1995-01-01

This is the softcover reprint of the English translation of 1971 (available from Springer since 1989) of the first 4 chapters of Bourbaki's Topologie générale. It gives all the basics of the subject, starting from definitions. Important classes of topological spaces are studied, uniform structures are introduced and applied to topological groups. Real numbers are constructed and their properties established. Part II, comprising the later chapters, Ch. 5-10, is also available in English in softcover.

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.

Science.gov (United States)

Keller, Alexander; Förster, Frank; Müller, Tobias; Dandekar, Thomas; Schultz, Jörg; Wolf, Matthias

2010-01-15

In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

Electronic structure and transport on the surface of topological insulator attached to an electromagnetic superlattice

International Nuclear Information System (INIS)

Wang Haiyan; Chen Xiongwen; Zhou Xiaoying; Zhang Lebo; Zhou Guanghui

2012-01-01

We study the electronic structure and transport for Dirac electron on the surface of a three-dimensional (3D) topological insulator attached to an electromagnetic superlattice. It is found that, by means of the transfer-matrix method, the number of electronic tunneling channels for magnetic barriers in antiparallel alignment is larger than that in parallel alignment, which stems to the energy band structures. Interestingly, a remarkable semiconducting transport behavior appears in this system with a strong magnetic barrier due to low energy band nearly paralleling to the Fermi level. Consequently, there is only small incident angle transport in the higher energy region when the system is modulated mainly by the higher electric barriers. We further find that the spatial distribution of the spin polarization oscillates periodically in the incoming region, but it is almost in-plane with a fixed direction in the transmitting region. The results may provide a further understanding of the nature of 3D TI surface states, and may be useful in the design of topological insulator-based electronic devices such as collimating electron beam.

A New Topology of Solutions of Chemical Equations

International Nuclear Information System (INIS)

Risteski, Ice B.

2013-01-01

In this work is induced a new topology of solutions of chemical equations by virtue of point-set topology in an abstract stoichiometrical space. Subgenerators of this topology are the coefficients of chemical reaction. Complex chemical reactions, as those of direct reduction of hematite with a carbon, often exhibit distinct properties which can be interpreted as higher level mathematical structures. Here we used a mathematical model that exploits the stoichiometric structure, which can be seen as a topology too, to derive an algebraic picture of chemical equations. This abstract expression suggests exploring the chemical meaning of topological concept. Topological models at different levels of realism can be used to generate a large number of reaction modifications, with a particular aim to determine their general properties. The more abstract the theory is, the stronger the cognitive power is

Quartet-based methods to reconstruct phylogenetic networks.

Science.gov (United States)

Yang, Jialiang; Grünewald, Stefan; Xu, Yifei; Wan, Xiu-Feng

2014-02-20

Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and horizontal gene transfer are believed to be involved. In comparison to traditional distance-based methods, quartet-based methods consider more information in the reconstruction process and thus have the potential to be more accurate. We introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS, QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We tested their performances and compared them with other popular methods on two simulated nucleotide sequence data sets: one generated from a tree topology and the other from a complicated evolutionary history containing three reticulate events. We further validated these methods to two real data sets: a bacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza data set related to recently emerging H7N9 low pathogenic avian influenza viruses in China. QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenarios from simple branching trees to complicated networks containing many reticulate events. These methods could provide insights into the understanding of complicated biological evolutionary processes such as bacterial taxonomy and reassortant of influenza viruses.

Topological phase transition in anisotropic square-octagon lattice with spin-orbit coupling and exchange field

Science.gov (United States)

Yang, Yuan; Yang, Jian; Li, Xiaobing; Zhao, Yue

2018-03-01

We investigate the topological phase transitions in an anisotropic square-octagon lattice in the presence of spin-orbit coupling and exchange field. On the basis of the Chern number and spin Chern number, we find a number of topologically distinct phases with tuning the exchange field, including time-reversal-symmetry-broken quantum spin Hall phases, quantum anomalous Hall phases and a topologically trivial phase. Particularly, we observe a coexistent state of both the quantum spin Hall effect and quantum anomalous Hall effect. Besides, by adjusting the exchange filed, we find the phase transition from time-reversal-symmetry-broken quantum spin Hall phase to spin-imbalanced and spin-polarized quantum anomalous Hall phases, providing an opportunity for quantum spin manipulation. The bulk band gap closes when topological phase transitions occur between different topological phases. Furthermore, the energy and spin spectra of the edge states corresponding to different topological phases are consistent with the topological characterization based on the Chern and spin Chern numbers.

High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

Directory of Open Access Journals (Sweden)

X. S. Tai

2013-08-01

Full Text Available Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China, located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon–Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g−1 soil and 0.97 × 106 to 12.78 × 106 g−1 soil, respectively. Redundancy analysis (RDA revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial

High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

Science.gov (United States)

Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.; Zhang, Y.

2013-08-01

Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China), located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon-Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs) of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g-1 soil and 0.97 × 106 to 12.78 × 106 g-1 soil, respectively. Redundancy analysis (RDA) revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial communities beneath Potentilla

The topological entropy of iterated piecewise affine maps is uncomputable

Directory of Open Access Journals (Sweden)

Pascal Koiran

2001-12-01

Full Text Available We show that it is impossible to compute (or even to approximate the topological entropy of a continuous piecewise affine function in dimension four. The same result holds for saturated linear functions in unbounded dimension. We ask whether the topological entropy of a piecewise affine function is always a computable real number, and conversely whether every non-negative computable real number can be obtained as the topological entropy of a piecewise affine function. It seems that these two questions are also open for cellular automata.

Optimization of communication network topology for navigation sharing among distributed satellites

Science.gov (United States)

Dang, Zhaohui; Zhang, Yulin

2013-01-01

Navigation sharing among distributed satellites is quite important for coordinated motion and collision avoidance. This paper proposes optimization methods of the communication network topology to achieve navigation sharing. The whole communication network constructing by inter-satellite links are considered as a topology graph. The aim of this paper is to find the communication network topology with minimum communication connections' number (MCCN) in different conditions. It has found that the communication capacity and the number of channels are two key parameters affecting the results. The model of MCCN topology for navigation sharing is established and corresponding method is designed. Two main scenarios, viz., homogeneous case and heterogeneous case, are considered. For the homogeneous case where each member has the same communication capacity, it designs a construction method (Algorithm 1) to find the MCCN topology. For the heterogeneous case, it introduces a modified genetic algorithm (Algorithm 2) to find the MCCN topology. When considering the fact that the number of channels is limited, the Algorithm 2 is further modified by adding a penalized term in the fitness function. The effectiveness of these algorithms is all proved in theoretical. Three examples are further tested to illustrate the methods developed in this paper.

The separating topology for the space-times of general relativity

International Nuclear Information System (INIS)

Lindstroem, U.

1977-08-01

The separating topology, first suggested by Zeeman, is defined for the space-times of general relativity. It is defined by a basis. A number of properties are derived. The topology induces the ordinary Euclidean topology on space-like hypersurfaces as well as on timelike curves and the discrete topology on null-cones. The group of auto-homeomorphisms is found to be the group of smooth conformal diffeomorphisms if the space-time is strongly causal. (author)

High-throughput sequencing and copy number variation detection using formalin fixed embedded tissue in metastatic gastric cancer.

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Seokhwi Kim

Full Text Available In the era of targeted therapy, mutation profiling of cancer is a crucial aspect of making therapeutic decisions. To characterize cancer at a molecular level, the use of formalin-fixed paraffin-embedded tissue is important. We tested the Ion AmpliSeq Cancer Hotspot Panel v2 and nCounter Copy Number Variation Assay in 89 formalin-fixed paraffin-embedded gastric cancer samples to determine whether they are applicable in archival clinical samples for personalized targeted therapies. We validated the results with Sanger sequencing, real-time quantitative PCR, fluorescence in situ hybridization and immunohistochemistry. Frequently detected somatic mutations included TP53 (28.17%, APC (10.1%, PIK3CA (5.6%, KRAS (4.5%, SMO (3.4%, STK11 (3.4%, CDKN2A (3.4% and SMAD4 (3.4%. Amplifications of HER2, CCNE1, MYC, KRAS and EGFR genes were observed in 8 (8.9%, 4 (4.5%, 2 (2.2%, 1 (1.1% and 1 (1.1% cases, respectively. In the cases with amplification, fluorescence in situ hybridization for HER2 verified gene amplification and immunohistochemistry for HER2, EGFR and CCNE1 verified the overexpression of proteins in tumor cells. In conclusion, we successfully performed semiconductor-based sequencing and nCounter copy number variation analyses in formalin-fixed paraffin-embedded gastric cancer samples. High-throughput screening in archival clinical samples enables faster, more accurate and cost-effective detection of hotspot mutations or amplification in genes.

Dynamical mechanism of atrial fibrillation: A topological approach

Science.gov (United States)

Marcotte, Christopher D.; Grigoriev, Roman O.

2017-09-01

While spiral wave breakup has been implicated in the emergence of atrial fibrillation, its role in maintaining this complex type of cardiac arrhythmia is less clear. We used the Karma model of cardiac excitation to investigate the dynamical mechanisms that sustain atrial fibrillation once it has been established. The results of our numerical study show that spatiotemporally chaotic dynamics in this regime can be described as a dynamical equilibrium between topologically distinct types of transitions that increase or decrease the number of wavelets, in general agreement with the multiple wavelets' hypothesis. Surprisingly, we found that the process of continuous excitation waves breaking up into discontinuous pieces plays no role whatsoever in maintaining spatiotemporal complexity. Instead, this complexity is maintained as a dynamical balance between wave coalescence—a unique, previously unidentified, topological process that increases the number of wavelets—and wave collapse—a different topological process that decreases their number.

Characterizing granular networks using topological metrics

Science.gov (United States)

Dijksman, Joshua A.; Kovalcinova, Lenka; Ren, Jie; Behringer, Robert P.; Kramar, Miroslav; Mischaikow, Konstantin; Kondic, Lou

2018-04-01

We carry out a direct comparison of experimental and numerical realizations of the exact same granular system as it undergoes shear jamming. We adjust the numerical methods used to optimally represent the experimental settings and outcomes up to microscopic contact force dynamics. Measures presented here range from microscopic through mesoscopic to systemwide characteristics of the system. Topological properties of the mesoscopic force networks provide a key link between microscales and macroscales. We report two main findings: (1) The number of particles in the packing that have at least two contacts is a good predictor for the mechanical state of the system, regardless of strain history and packing density. All measures explored in both experiments and numerics, including stress-tensor-derived measures and contact numbers depend in a universal manner on the fraction of nonrattler particles, fNR. (2) The force network topology also tends to show this universality, yet the shape of the master curve depends much more on the details of the numerical simulations. In particular we show that adding force noise to the numerical data set can significantly alter the topological features in the data. We conclude that both fNR and topological metrics are useful measures to consider when quantifying the state of a granular system.

Multiple homoplasious insertions and deletions of a Triticeae (Poaceae DNA transposon: a phylogenetic perspective

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Mason-Gamer Roberta J

2007-06-01

Full Text Available Abstract Background Stowaway elements are short, non-autonomous DNA transposons categorized as miniature inverted-repeat transposable elements (MITEs. The high MITE copy number in grass genomes suggests an active history of amplification and insertion, but ongoing MITE activity has only rarely been seen, and ongoing Stowaway activity has never been observed. Thus, a phylogenetic perspective on presence vs. absence of elements in an aligned data set can provide valuable historical insights into the dynamics of MITE acquisition and loss. Results A Stowaway-like element resides within the fourth intron of a β-amylase gene in representatives of five genera in the wheat tribe, Triticeae. Its presence vs. absence was examined with reference to the β-amylase gene tree topology, and in light of sequence comparisons of the β-amylase elements to Triticeae Stowaway elements in the Entrez nucleotide database. Among the sequences lacking the element, there are five distinct putative excision footprints (one widespread and four restricted to unrelated lineages and two flanking deletions. The sequences that do contain elements are polyphyletic on the β-amylase tree, and their elements are divergent at the sequence level. The β-amylase elements do not form a monophyletic group relative to other Stowaway elements in Entrez; most are more similar to elements from other loci in other Triticeae genomes than they are to one another. Conclusion Combined, the phylogenetic distribution, sequence variation, and Entrez database comparisons indicate that a Stowaway-like element has undergone multiple deletions from and insertions into the same site in β-amylase intron 4 during the history of the tribe. The elements currently at the site represent multiple, distinct lineages that transcend generic boundaries. While patterns of Stowaway polymorphism across a phylogenetic data set do not allow evolutionary mechanisms to be inferred with certainty, they do provide

Induced topological pressure for topological dynamical systems

International Nuclear Information System (INIS)

Xing, Zhitao; Chen, Ercai

2015-01-01

In this paper, inspired by the article [J. Jaerisch et al., Stochastics Dyn. 14, 1350016, pp. 1-30 (2014)], we introduce the induced topological pressure for a topological dynamical system. In particular, we prove a variational principle for the induced topological pressure

Topological strings on singular elliptic Calabi-Yau 3-folds and minimal 6d SCFTs

Science.gov (United States)

Del Zotto, Michele; Gu, Jie; Huang, Min-xin; Kashani-Poor, Amir-Kian; Klemm, Albrecht; Lockhart, Guglielmo

2018-03-01

We apply the modular approach to computing the topological string partition function on non-compact elliptically fibered Calabi-Yau 3-folds with higher Kodaira singularities in the fiber. The approach consists in making an ansatz for the partition function at given base degree, exact in all fiber classes to arbitrary order and to all genus, in terms of a rational function of weak Jacobi forms. Our results yield, at given base degree, the elliptic genus of the corresponding non-critical 6d string, and thus the associated BPS invariants of the 6d theory. The required elliptic indices are determined from the chiral anomaly 4-form of the 2d worldsheet theories, or the 8-form of the corresponding 6d theories, and completely fix the holomorphic anomaly equation constraining the partition function. We introduce subrings of the known rings of Weyl invariant Jacobi forms which are adapted to the additional symmetries of the partition function, making its computation feasible to low base wrapping number. In contradistinction to the case of simpler singularities, generic vanishing conditions on BPS numbers are no longer sufficient to fix the modular ansatz at arbitrary base wrapping degree. We show that to low degree, imposing exact vanishing conditions does suffice, and conjecture this to be the case generally.

Topological superconductivity, topological confinement, and the vortex quantum Hall effect

International Nuclear Information System (INIS)

Diamantini, M. Cristina; Trugenberger, Carlo A.

2011-01-01

Topological matter is characterized by the presence of a topological BF term in its long-distance effective action. Topological defects due to the compactness of the U(1) gauge fields induce quantum phase transitions between topological insulators, topological superconductors, and topological confinement. In conventional superconductivity, because of spontaneous symmetry breaking, the photon acquires a mass due to the Anderson-Higgs mechanism. In this paper we derive the corresponding effective actions for the electromagnetic field in topological superconductors and topological confinement phases. In topological superconductors magnetic flux is confined and the photon acquires a topological mass through the BF mechanism: no symmetry breaking is involved, the ground state has topological order, and the transition is induced by quantum fluctuations. In topological confinement, instead, electric charge is linearly confined and the photon becomes a massive antisymmetric tensor via the Stueckelberg mechanism. Oblique confinement phases arise when the string condensate carries both magnetic and electric flux (dyonic strings). Such phases are characterized by a vortex quantum Hall effect potentially relevant for the dissipationless transport of information stored on vortices.

On topological string theory with Calabi-Yau backgrounds

International Nuclear Information System (INIS)

Haghighat, Babak

2009-01-01

String theory represents a unifying framework for quantum field theory as well as for general relativity combining them into a theory of quantum gravity. The topological string is a subsector of the full string theory capturing physical amplitudes which only depend on the topology of the compactification manifold. Starting with a review of the physical applications of topological string theory we go on to give a detailed description of its theoretical framework and mathematical principles. Having this way provided the grounding for concrete calculations we proceed to solve the theory on three major types of Calabi-Yau manifolds, namely Grassmannian Calabi-Yau manifolds, local Calabi-Yau manifolds, and K3 fibrations. Our method of solution is the integration of the holomorphic anomaly equations and fixing the holomorphic ambiguity by physical boundary conditions. We determine the correct parameterization of the ambiguity and new boundary conditions at various singularity loci in moduli space. Among the main results of this thesis are the tables of degeneracies of BPS states in the appendices and the verification of the correct microscopic entropy interpretation for five dimensional extremal black holes arising from compactifications on Grassmannian Calabi-Yau manifolds. (orig.)

On topological string theory with Calabi-Yau backgrounds

International Nuclear Information System (INIS)

Haghighat, Babak

2010-06-01

String theory represents a unifying framework for quantum field theory as well as for general relativity combining them into a theory of quantum gravity. The topological string is a subsector of the full string theory capturing physical amplitudes which only depend on the topology of the compactification manifold. Starting with a review of the physical applications of topological string theory we go on to give a detailed description of its theoretical framework and mathematical principles. Having this way provided the grounding for concrete calculations we proceed to solve the theory on three major types of Calabi-Yau manifolds, namely Grassmannian Calabi-Yau manifolds, local Calabi-Yau manifolds, and K3 fibrations. Our method of solution is the integration of the holomorphic anomaly equations and fixing the holomorphic ambiguity by physical boundary conditions. We determine the correct parameterization of the ambiguity and new boundary conditions at various singularity loci in moduli space. Among the main results of this thesis are the tables of degeneracies of BPS states in the appendices and the veri cation of the correct microscopic entropy interpretation for five dimensional extremal black holes arising from compactifications on Grassmannian Calabi-Yau manifolds. (orig.)

On topological string theory with Calabi-Yau backgrounds

Energy Technology Data Exchange (ETDEWEB)

Haghighat, Babak

2010-06-15

String theory represents a unifying framework for quantum field theory as well as for general relativity combining them into a theory of quantum gravity. The topological string is a subsector of the full string theory capturing physical amplitudes which only depend on the topology of the compactification manifold. Starting with a review of the physical applications of topological string theory we go on to give a detailed description of its theoretical framework and mathematical principles. Having this way provided the grounding for concrete calculations we proceed to solve the theory on three major types of Calabi-Yau manifolds, namely Grassmannian Calabi-Yau manifolds, local Calabi-Yau manifolds, and K3 fibrations. Our method of solution is the integration of the holomorphic anomaly equations and fixing the holomorphic ambiguity by physical boundary conditions. We determine the correct parameterization of the ambiguity and new boundary conditions at various singularity loci in moduli space. Among the main results of this thesis are the tables of degeneracies of BPS states in the appendices and the veri cation of the correct microscopic entropy interpretation for five dimensional extremal black holes arising from compactifications on Grassmannian Calabi-Yau manifolds. (orig.)

On topological string theory with Calabi-Yau backgrounds

Energy Technology Data Exchange (ETDEWEB)

Haghighat, Babak

2009-10-29

String theory represents a unifying framework for quantum field theory as well as for general relativity combining them into a theory of quantum gravity. The topological string is a subsector of the full string theory capturing physical amplitudes which only depend on the topology of the compactification manifold. Starting with a review of the physical applications of topological string theory we go on to give a detailed description of its theoretical framework and mathematical principles. Having this way provided the grounding for concrete calculations we proceed to solve the theory on three major types of Calabi-Yau manifolds, namely Grassmannian Calabi-Yau manifolds, local Calabi-Yau manifolds, and K3 fibrations. Our method of solution is the integration of the holomorphic anomaly equations and fixing the holomorphic ambiguity by physical boundary conditions. We determine the correct parameterization of the ambiguity and new boundary conditions at various singularity loci in moduli space. Among the main results of this thesis are the tables of degeneracies of BPS states in the appendices and the verification of the correct microscopic entropy interpretation for five dimensional extremal black holes arising from compactifications on Grassmannian Calabi-Yau manifolds. (orig.)

Tracing the evolutionary path to nitrogen-fixing crops.

Science.gov (United States)

Delaux, Pierre-Marc; Radhakrishnan, Guru; Oldroyd, Giles

2015-08-01

Nitrogen-fixing symbioses between plants and bacteria are restricted to a few plant lineages. The plant partner benefits from these associations by gaining access to the pool of atmospheric nitrogen. By contrast, other plant species, including all cereals, rely only on the scarce nitrogen present in the soil and what they can glean from associative bacteria. Global cereal yields from conventional agriculture are dependent on the application of massive levels of chemical fertilisers. Engineering nitrogen-fixing symbioses into cereal crops could in part mitigate the economic and ecological impacts caused by the overuse of fertilisers and provide better global parity in crop yields. Comparative phylogenetics and phylogenomics are powerful tools to identify genetic and genomic innovations behind key plant traits. In this review we highlight recent discoveries made using such approaches and we discuss how these approaches could be used to help direct the engineering of nitrogen-fixing symbioses into cereals. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Topology optimization for nano-photonics

DEFF Research Database (Denmark)

Jensen, Jakob Søndergaard; Sigmund, Ole

2011-01-01

Topology optimization is a computational tool that can be used for the systematic design of photonic crystals, waveguides, resonators, filters and plasmonics. The method was originally developed for mechanical design problems but has within the last six years been applied to a range of photonics...... applications. Topology optimization may be based on finite element and finite difference type modeling methods in both frequency and time domain. The basic idea is that the material density of each element or grid point is a design variable, hence the geometry is parameterized in a pixel-like fashion....... The optimization problem is efficiently solved using mathematical programming-based optimization methods and analytical gradient calculations. The paper reviews the basic procedures behind topology optimization, a large number of applications ranging from photonic crystal design to surface plasmonic devices...

CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome.

Directory of Open Access Journals (Sweden)

Ann L Griffen

2011-04-01

Full Text Available Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximum-likelihood-based topology and bootstrap support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.

Gauge-invariant factorization and canonical quantization of topologically massive gauge theories in any dimension

International Nuclear Information System (INIS)

Bertrand, Bruno; Govaerts, Jan

2007-01-01

Abelian topologically massive gauge theories (TMGT) provide a topological mechanism to generate mass for a bosonic p-tensor field in any spacetime dimension. These theories include the (2+1)-dimensional Maxwell-Chern-Simons and (3+1)-dimensional Cremmer-Scherk actions as particular cases. Within the Hamiltonian formulation, the embedded topological field theory (TFT) sector related to the topological mass term is not manifest in the original phase space. However, through an appropriate canonical transformation, a gauge-invariant factorization of phase space into two orthogonal sectors is feasible. The first of these sectors includes canonically conjugate gauge-invariant variables with free massive excitations. The second sector, which decouples from the total Hamiltonian, is equivalent to the phase-space description of the associated non-dynamical pure TFT. Within canonical quantization, a likewise factorization of quantum states thus arises for the full spectrum of TMGT in any dimension. This new factorization scheme also enables a definition of the usual projection from TMGT onto topological quantum field theories in a most natural and transparent way. None of these results rely on any gauge-fixing procedure whatsoever

Genetic Characterization of Echinococcus granulosus from a Large Number of Formalin-Fixed, Paraffin-Embedded Tissue Samples of Human Isolates in Iran

Science.gov (United States)

Rostami, Sima; Torbaghan, Shams Shariat; Dabiri, Shahriar; Babaei, Zahra; Mohammadi, Mohammad Ali; Sharbatkhori, Mitra; Harandi, Majid Fasihi

2015-01-01

Cystic echinococcosis (CE), caused by the larval stage of Echinococcus granulosus, presents an important medical and veterinary problem globally, including that in Iran. Different genotypes of E. granulosus have been reported from human isolates worldwide. This study identifies the genotype of the parasite responsible for human hydatidosis in three provinces of Iran using formalin-fixed paraffin-embedded tissue samples. In this study, 200 formalin-fixed paraffin-embedded tissue samples from human CE cases were collected from Alborz, Tehran, and Kerman provinces. Polymerase chain reaction amplification and sequencing of the partial mitochondrial cytochrome c oxidase subunit 1 gene were performed for genetic characterization of the samples. Phylogenetic analysis of the isolates from this study and reference sequences of different genotypes was done using a maximum likelihood method. In total, 54.4%, 0.8%, 1%, and 40.8% of the samples were identified as the G1, G2, G3, and G6 genotypes, respectively. The findings of the current study confirm the G1 genotype (sheep strain) to be the most prevalent genotype involved in human CE cases in Iran and indicates the high prevalence of the G6 genotype with a high infectivity for humans. Furthermore, this study illustrates the first documented human CE case in Iran infected with the G2 genotype. PMID:25535316

Realization of a topological phase transition in a gyroscopic lattice

Science.gov (United States)

Mitchell, Noah P.; Nash, Lisa M.; Irvine, William T. M.

2018-03-01

Topological metamaterials exhibit unusual behaviors at their boundaries, such as unidirectional chiral waves, that are protected by a topological feature of their band structures. The ability to tune such a material through a topological phase transition in real time could enable the use of protected waves for information storage and readout. Here we dynamically tune through a topological phase transition by breaking inversion symmetry in a metamaterial composed of interacting gyroscopes. Through the transition, we track the divergence of the edge modes' localization length and the change in Chern number characterizing the topology of the material's band structure. This Rapid Communication provides a new axis with which to tune the response of mechanical topological metamaterials.

Spin-torque generation in topological insulator based heterostructures

KAUST Repository

Fischer, Mark H.

2016-03-11

Heterostructures utilizing topological insulators exhibit a remarkable spin-torque efficiency. However, the exact origin of the strong torque, in particular whether it stems from the spin-momentum locking of the topological surface states or rather from spin-Hall physics of the topological-insulator bulk, remains unclear. Here, we explore a mechanism of spin-torque generation purely based on the topological surface states. We consider topological-insulator-based bilayers involving ferromagnetic metal (TI/FM) and magnetically doped topological insulators (TI/mdTI), respectively. By ascribing the key theoretical differences between the two setups to location and number of active surface states, we describe both setups within the same framework of spin diffusion of the nonequilibrium spin density of the topological surface states. For the TI/FM bilayer, we find large spin-torque efficiencies of roughly equal magnitude for both in-plane and out-of-plane spin torques. For the TI/mdTI bilayer, we elucidate the dominance of the spin-transfer-like torque. However, we cannot explain the orders of magnitude enhancement reported. Nevertheless, our model gives an intuitive picture of spin-torque generation in topological-insulator-based bilayers and provides theoretical constraints on spin-torque generation due to topological surface states.

Topological structure of dictionary graphs

International Nuclear Information System (INIS)

Fuks, Henryk; Krzeminski, Mark

2009-01-01

We investigate the topological structure of the subgraphs of dictionary graphs constructed from WordNet and Moby thesaurus data. In the process of learning a foreign language, the learner knows only a subset of all words of the language, corresponding to a subgraph of a dictionary graph. When this subgraph grows with time, its topological properties change. We introduce the notion of the pseudocore and argue that the growth of the vocabulary roughly follows decreasing pseudocore numbers-that is, one first learns words with a high pseudocore number followed by smaller pseudocores. We also propose an alternative strategy for vocabulary growth, involving decreasing core numbers as opposed to pseudocore numbers. We find that as the core or pseudocore grows in size, the clustering coefficient first decreases, then reaches a minimum and starts increasing again. The minimum occurs when the vocabulary reaches a size between 10 3 and 10 4 . A simple model exhibiting similar behavior is proposed. The model is based on a generalized geometric random graph. Possible implications for language learning are discussed.

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

Science.gov (United States)

Davies, T Jonathan; Kraft, Nathan J B; Salamin, Nicolas; Wolkovich, Elizabeth M

2012-02-01

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

Signatures of topological phase transitions in mesoscopic superconducting rings

International Nuclear Information System (INIS)

Pientka, Falko; Romito, Alessandro; Duckheim, Mathias; Oppen, Felix von; Oreg, Yuval

2013-01-01

We investigate Josephson currents in mesoscopic rings with a weak link which are in or near a topological superconducting phase. As a paradigmatic example, we consider the Kitaev model of a spinless p-wave superconductor in one dimension, emphasizing how this model emerges from more realistic settings based on semiconductor nanowires. We show that the flux periodicity of the Josephson current provides signatures of the topological phase transition and the emergence of Majorana fermions (MF) situated on both sides of the weak link even when fermion parity is not a good quantum number. In large rings, the MF hybridize only across the weak link. In this case, the Josephson current is h/e periodic in the flux threading the loop when fermion parity is a good quantum number but reverts to the more conventional h/2e periodicity in the presence of fermion-parity changing relaxation processes. In mesoscopic rings, the MF also hybridize through their overlap in the interior of the superconducting ring. We find that in the topological superconducting phase, this gives rise to an h/e-periodic contribution even when fermion parity is not conserved and that this contribution exhibits a peak near the topological phase transition. This signature of the topological phase transition is robust to the effects of disorder. As a byproduct, we find that close to the topological phase transition, disorder drives the system deeper into the topological phase. This is in stark contrast to the known behavior far from the phase transition, where disorder tends to suppress the topological phase. (paper)

General topology

CERN Document Server

Willard, Stephen

2004-01-01

Among the best available reference introductions to general topology, this volume is appropriate for advanced undergraduate and beginning graduate students. Its treatment encompasses two broad areas of topology: ""continuous topology,"" represented by sections on convergence, compactness, metrization and complete metric spaces, uniform spaces, and function spaces; and ""geometric topology,"" covered by nine sections on connectivity properties, topological characterization theorems, and homotopy theory. Many standard spaces are introduced in the related problems that accompany each section (340

Chiodo formulas for the r-th roots and topological recursion

OpenAIRE

Lewanski, Danilo; Popolitov, Alexandr; Shadrin, Sergey; Zvonkine, Dimitri

2015-01-01

We analyze Chiodo's formulas for the Chern classes related to the r-th roots of the suitably twisted integer powers of the canonical class on the moduli space of curves. The intersection numbers of these classes with psi-classes are reproduced via the Chekhov-Eynard-Orantin topological recursion. As an application, we prove that the Johnson-Pandharipande-Tseng formula for the orbifold Hurwitz numbers is equivalent to the topological recursion for the orbifold Hurwitz numbers. In particular, t...

Topological insulators and superconductors from string theory

International Nuclear Information System (INIS)

Ryu, Shinsei; Takayanagi, Tadashi

2010-01-01

Topological insulators and superconductors in different spatial dimensions and with different discrete symmetries have been fully classified recently, revealing a periodic structure for the pattern of possible types of topological insulators and superconductors, both in terms of spatial dimensions and in terms of symmetry classes. It was proposed that K theory is behind the periodicity. On the other hand, D-branes, a solitonic object in string theory, are also known to be classified by K theory. In this paper, by inspecting low-energy effective field theories realized by two parallel D-branes, we establish a one-to-one correspondence between the K-theory classification of topological insulators/superconductors and D-brane charges. In addition, the string theory realization of topological insulators and superconductors comes naturally with gauge interactions, and the Wess-Zumino term of the D-branes gives rise to a gauge field theory of topological nature, such as ones with the Chern-Simons term or the θ term in various dimensions. This sheds light on topological insulators and superconductors beyond noninteracting systems, and the underlying topological field theory description thereof. In particular, our string theory realization includes the honeycomb lattice Kitaev model in two spatial dimensions, and its higher-dimensional extensions. Increasing the number of D-branes naturally leads to a realization of topological insulators and superconductors in terms of holography (AdS/CFT).

Mechanized extraction of topology anti-patterns in wireless networks

NARCIS (Netherlands)

Woehrle, M.; Bakhshi, R.; Mousavi, M.R.; Derrick, J.; Gnesi, S.; Latella, D.; Treharne, H.

2012-01-01

Exhaustive and mechanized formal verification of wireless networks is hampered by the huge number of possible topologies and the large size of the actual networks. However, the generic communication structure in such networks allows for reducing the root causes of faults to faulty (sub-)topologies,

Strain-induced topological magnon phase transitions: applications to kagome-lattice ferromagnets

Science.gov (United States)

Owerre, S. A.

2018-06-01

A common feature of topological insulators is that they are characterized by topologically invariant quantity such as the Chern number and the index. This quantity distinguishes a nontrivial topological system from a trivial one. A topological phase transition may occur when there are two topologically distinct phases, and it is usually defined by a gap closing point where the topologically invariant quantity is ill-defined. In this paper, we show that the magnon bands in the strained (distorted) kagome-lattice ferromagnets realize an example of a topological magnon phase transition in the realistic parameter regime of the system. When spin–orbit coupling (SOC) is neglected (i.e. no Dzyaloshinskii–Moriya interaction), we show that all three magnon branches are dispersive with no flat band, and there exists a critical point where tilted Dirac and semi-Dirac point coexist in the magnon spectra. The critical point separates two gapless magnon phases as opposed to the usual phase transition. Upon the inclusion of SOC, we realize a topological magnon phase transition point at the critical strain , where D and J denote the perturbative SOC and the Heisenberg spin exchange interaction respectively. It separates two distinct topological magnon phases with different Chern numbers for and for . The associated anomalous thermal Hall conductivity develops an abrupt change at , due to the divergence of the Berry curvature in momentum space. The proposed topological magnon phase transition is experimentally feasible by applying external perturbations such as uniaxial strain or pressure.

A topological classification of the Chaplygin systems in the dynamics of a rigid body in a fluid

International Nuclear Information System (INIS)

Nikolaenko, S S

2014-01-01

The paper is concerned with the topological analysis of the Chaplygin integrable case in the dynamics of a rigid body in a fluid. A full list of the topological types of Chaplygin systems in their dependence on the energy level is compiled on the basis of the Fomenko-Zieschang theory. An effective description of the topology of the Liouville foliation in terms of natural coordinate variables is also presented, which opens a direct way to calculating topological invariants. It turns out that on all nonsingular energy levels Chaplygin systems are Liouville equivalent to the well-known Euler case in the dynamics of a rigid body with fixed point. Bibliography: 23 titles

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

Directory of Open Access Journals (Sweden)

Dandekar Thomas

2010-01-01

Full Text Available Abstract Background In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. Open peer review Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

Evaluation of properties over phylogenetic trees using stochastic logics.

Science.gov (United States)

Requeno, José Ignacio; Colom, José Manuel

2016-06-14

Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny. In this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn't be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods. We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our

Biochemical and Molecular Phylogenetic Study of Agriculturally Useful Association of a Nitrogen-Fixing Cyanobacterium and Nodule Sinorhizobium with Medicago sativa L.

Directory of Open Access Journals (Sweden)

E. V. Karaushu

2015-01-01

Full Text Available Seed inoculation with bacterial consortium was found to increase legume yield, providing a higher growth than the standard nitrogen treatment methods. Alfalfa plants were inoculated by mono- and binary compositions of nitrogen-fixing microorganisms. Their physiological and biochemical properties were estimated. Inoculation by microbial consortium of Sinorhizobium meliloti T17 together with a new cyanobacterial isolate Nostoc PTV was more efficient than the single-rhizobium strain inoculation. This treatment provides an intensification of the processes of biological nitrogen fixation by rhizobia bacteria in the root nodules and an intensification of plant photosynthesis. Inoculation by bacterial consortium stimulates growth of plant mass and rhizogenesis and leads to increased productivity of alfalfa and to improving the amino acid composition of plant leaves. The full nucleotide sequence of the rRNA gene cluster and partial sequence of the dinitrogenase reductase (nifH gene of Nostoc PTV were deposited to GenBank (JQ259185.1, JQ259186.1. Comparison of these gene sequences of Nostoc PTV with all sequences present at the GenBank shows that this cyanobacterial strain does not have 100% identity with any organisms investigated previously. Phylogenetic analysis showed that this cyanobacterium clustered with high credibility values with Nostoc muscorum.

Number to finger mapping is topological.

NARCIS (Netherlands)

Plaisier, M.A.; Smeets, J.B.J.

2011-01-01

It has been shown that humans associate fingers with numbers because finger counting strategies interact with numerical judgements. At the same time, there is evidence that there is a relation between number magnitude and space as small to large numbers seem to be represented from left to right. In

Dimensional Reduction for the General Markov Model on Phylogenetic Trees.

Science.gov (United States)

Sumner, Jeremy G

2017-03-01

We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the dimensionality of the model from exponential in the number of extant taxa, to quadratic in the number of taxa, while retaining the ability to statistically identify phylogenetic divergence events. A key feature is the identification of an invariant subspace which depends only bilinearly on the model parameters, in contrast to the usual multi-linear dependence in the full space. We discuss potential applications including the computation of split (edge) weights on phylogenetic trees from observed sequence data.

Tendril perversion-a physical implication of the topological conservation law

International Nuclear Information System (INIS)

Pieranski, Piotr; Baranska, Justyna; Skjeltorp, Arne

2004-01-01

Tendril perversion-a phenomenon ruled by the topological conservation law-is presented. A contemporary, quantitative analysis of the phenomenon is confronted with its qualitative, intuitive analysis carried out by Charles Darwin. The linking number, twist and writhe are defined. The topological conservation law is introduced. The Gauss formula for calculating the linking number and the Calugareanu formula for calculating writhe are derived and discussed using physical arguments

Tendril perversion-a physical implication of the topological conservation law

Energy Technology Data Exchange (ETDEWEB)

Pieranski, Piotr [Laboratory of Computational Physics and Semiconductors, Poznan University of Technology, Nieszawska 13A, 60 965 Poznan (Poland); Baranska, Justyna [Laboratory of Computational Physics and Semiconductors, Poznan University of Technology, Nieszawska 13A, 60 965 Poznan (Poland); Skjeltorp, Arne [Institute for Energy Technology, Kjeller (Norway)

2004-09-10

Tendril perversion-a phenomenon ruled by the topological conservation law-is presented. A contemporary, quantitative analysis of the phenomenon is confronted with its qualitative, intuitive analysis carried out by Charles Darwin. The linking number, twist and writhe are defined. The topological conservation law is introduced. The Gauss formula for calculating the linking number and the Calugareanu formula for calculating writhe are derived and discussed using physical arguments.

Efficient parsimony-based methods for phylogenetic network reconstruction.

Science.gov (United States)

Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir

2007-01-15

Phylogenies--the evolutionary histories of groups of organisms-play a major role in representing relationships among biological entities. Although many biological processes can be effectively modeled as tree-like relationships, others, such as hybrid speciation and horizontal gene transfer (HGT), result in networks, rather than trees, of relationships. Hybrid speciation is a significant evolutionary mechanism in plants, fish and other groups of species. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Maximum parsimony is one of the most commonly used criteria for phylogenetic tree inference. Roughly speaking, inference based on this criterion seeks the tree that minimizes the amount of evolution. In 1990, Jotun Hein proposed using this criterion for inferring the evolution of sequences subject to recombination. Preliminary results on small synthetic datasets. Nakhleh et al. (2005) demonstrated the criterion's application to phylogenetic network reconstruction in general and HGT detection in particular. However, the naive algorithms used by the authors are inapplicable to large datasets due to their demanding computational requirements. Further, no rigorous theoretical analysis of computing the criterion was given, nor was it tested on biological data. In the present work we prove that the problem of scoring the parsimony of a phylogenetic network is NP-hard and provide an improved fixed parameter tractable algorithm for it. Further, we devise efficient heuristics for parsimony-based reconstruction of phylogenetic networks. We test our methods on both synthetic and biological data (rbcL gene in bacteria) and obtain very promising results.

Combining Topological Hardware and Topological Software: Color-Code Quantum Computing with Topological Superconductor Networks

Science.gov (United States)

Litinski, Daniel; Kesselring, Markus S.; Eisert, Jens; von Oppen, Felix

2017-07-01

We present a scalable architecture for fault-tolerant topological quantum computation using networks of voltage-controlled Majorana Cooper pair boxes and topological color codes for error correction. Color codes have a set of transversal gates which coincides with the set of topologically protected gates in Majorana-based systems, namely, the Clifford gates. In this way, we establish color codes as providing a natural setting in which advantages offered by topological hardware can be combined with those arising from topological error-correcting software for full-fledged fault-tolerant quantum computing. We provide a complete description of our architecture, including the underlying physical ingredients. We start by showing that in topological superconductor networks, hexagonal cells can be employed to serve as physical qubits for universal quantum computation, and we present protocols for realizing topologically protected Clifford gates. These hexagonal-cell qubits allow for a direct implementation of open-boundary color codes with ancilla-free syndrome read-out and logical T gates via magic-state distillation. For concreteness, we describe how the necessary operations can be implemented using networks of Majorana Cooper pair boxes, and we give a feasibility estimate for error correction in this architecture. Our approach is motivated by nanowire-based networks of topological superconductors, but it could also be realized in alternative settings such as quantum-Hall-superconductor hybrids.

Combining Topological Hardware and Topological Software: Color-Code Quantum Computing with Topological Superconductor Networks

Directory of Open Access Journals (Sweden)

Daniel Litinski

2017-09-01

Full Text Available We present a scalable architecture for fault-tolerant topological quantum computation using networks of voltage-controlled Majorana Cooper pair boxes and topological color codes for error correction. Color codes have a set of transversal gates which coincides with the set of topologically protected gates in Majorana-based systems, namely, the Clifford gates. In this way, we establish color codes as providing a natural setting in which advantages offered by topological hardware can be combined with those arising from topological error-correcting software for full-fledged fault-tolerant quantum computing. We provide a complete description of our architecture, including the underlying physical ingredients. We start by showing that in topological superconductor networks, hexagonal cells can be employed to serve as physical qubits for universal quantum computation, and we present protocols for realizing topologically protected Clifford gates. These hexagonal-cell qubits allow for a direct implementation of open-boundary color codes with ancilla-free syndrome read-out and logical T gates via magic-state distillation. For concreteness, we describe how the necessary operations can be implemented using networks of Majorana Cooper pair boxes, and we give a feasibility estimate for error correction in this architecture. Our approach is motivated by nanowire-based networks of topological superconductors, but it could also be realized in alternative settings such as quantum-Hall–superconductor hybrids.

Topological quantum error correction in the Kitaev honeycomb model

Science.gov (United States)

Lee, Yi-Chan; Brell, Courtney G.; Flammia, Steven T.

2017-08-01

The Kitaev honeycomb model is an approximate topological quantum error correcting code in the same phase as the toric code, but requiring only a 2-body Hamiltonian. As a frustrated spin model, it is well outside the commuting models of topological quantum codes that are typically studied, but its exact solubility makes it more amenable to analysis of effects arising in this noncommutative setting than a generic topologically ordered Hamiltonian. Here we study quantum error correction in the honeycomb model using both analytic and numerical techniques. We first prove explicit exponential bounds on the approximate degeneracy, local indistinguishability, and correctability of the code space. These bounds are tighter than can be achieved using known general properties of topological phases. Our proofs are specialized to the honeycomb model, but some of the methods may nonetheless be of broader interest. Following this, we numerically study noise caused by thermalization processes in the perturbative regime close to the toric code renormalization group fixed point. The appearance of non-topological excitations in this setting has no significant effect on the error correction properties of the honeycomb model in the regimes we study. Although the behavior of this model is found to be qualitatively similar to that of the standard toric code in most regimes, we find numerical evidence of an interesting effect in the low-temperature, finite-size regime where a preferred lattice direction emerges and anyon diffusion is geometrically constrained. We expect this effect to yield an improvement in the scaling of the lifetime with system size as compared to the standard toric code.

Topological objects in hadron physics

International Nuclear Information System (INIS)

Rho, M.

1988-01-01

The notion of topological objects in hadronic physics is discussed, with emphasis on the role of the Wess-Zumino term and induced transmutation of quantum numbers in chiral bag models. Some applications to nuclear systems are given

Optimization of Network Topology in Computer-Aided Detection Schemes Using Phased Searching with NEAT in a Time-Scaled Framework.

Science.gov (United States)

Tan, Maxine; Pu, Jiantao; Zheng, Bin

2014-01-01

In the field of computer-aided mammographic mass detection, many different features and classifiers have been tested. Frequently, the relevant features and optimal topology for the artificial neural network (ANN)-based approaches at the classification stage are unknown, and thus determined by trial-and-error experiments. In this study, we analyzed a classifier that evolves ANNs using genetic algorithms (GAs), which combines feature selection with the learning task. The classifier named "Phased Searching with NEAT in a Time-Scaled Framework" was analyzed using a dataset with 800 malignant and 800 normal tissue regions in a 10-fold cross-validation framework. The classification performance measured by the area under a receiver operating characteristic (ROC) curve was 0.856 ± 0.029. The result was also compared with four other well-established classifiers that include fixed-topology ANNs, support vector machines (SVMs), linear discriminant analysis (LDA), and bagged decision trees. The results show that Phased Searching outperformed the LDA and bagged decision tree classifiers, and was only significantly outperformed by SVM. Furthermore, the Phased Searching method required fewer features and discarded superfluous structure or topology, thus incurring a lower feature computational and training and validation time requirement. Analyses performed on the network complexities evolved by Phased Searching indicate that it can evolve optimal network topologies based on its complexification and simplification parameter selection process. From the results, the study also concluded that the three classifiers - SVM, fixed-topology ANN, and Phased Searching with NeuroEvolution of Augmenting Topologies (NEAT) in a Time-Scaled Framework - are performing comparably well in our mammographic mass detection scheme.

Topological properties and functionalities in oxide thin films and interfaces

Science.gov (United States)

Uchida, Masaki; Kawasaki, Masashi

2018-04-01

As symbolized by the Nobel Prize in Physics 2016, ‘topology’ has been recognized as an essential standpoint to understand and control the physics of condensed matter. This concept may be spreading even into application areas such as novel electronics. In this trend, there has been reported a number of studies for oxide films and heterostructures with topologically non-trivial electronic or magnetic states. In this review, we overview the trends of new topological properties and functionalities in oxide materials by sorting out a number of examples. The technological advances in oxide film growth achieved over the last few decades are now opening the door for harnessing novel topological properties.

Abelian Chern-Simons theory and linking numbers via oscillatory integrals

International Nuclear Information System (INIS)

Albeverio, S.; Schaefer, J.

1994-06-01

We introduce a rigorous mathematical model of abelian Chern-Simons theory based on the theory of infinite dimensional oscillatory integrals developed by Albeverio and Hoeegh-Krohn. We construct a gauge-fixed Chern-Simons path integral as a Fresnel integral in a certain Hilbert space. Wilson loop variables are defined as Fresnel integrable functions and it is shown in this context that the expectation value of products of Wilson loops w.r.t. the Chern-Simons path integral is a topological invariant which can be computed in terms of pairwise linking numbers of the loops, as conjectured by Witten. We also propose a lattice Chern-Simons action which converges to the continuum limit. (orig.)

Adiabatic photo-steering theory in topological insulators

Science.gov (United States)

Inoue, Jun-ichi

2014-12-01

Feasible external control of material properties is a crucial issue in condensed matter physics. A new approach to achieving this aim, named adiabatic photo-steering, is reviewed. The core principle of this scheme is that several material constants are effectively turned into externally tunable variables by irradiation of monochromatic laser light. Two-dimensional topological insulators are selected as the optimal systems that exhibit a prominent change in their properties following the application of this method. Two specific examples of photo-steered quantum phenomena, which reflect topological aspects of the electronic systems at hand, are presented. One is the integer quantum Hall effect described by the Haldane model, and the other is the quantum spin Hall effect described by the Kane-Mele model. The topological quantities associated with these phenomena are the conventional Chern number and spin Chern number, respectively. A recent interesting idea, time-reversal symmetry breaking via a temporary periodic external stimulation, is also discussed.

Adiabatic photo-steering theory in topological insulators

International Nuclear Information System (INIS)

Inoue, Jun-ichi

2014-01-01

Feasible external control of material properties is a crucial issue in condensed matter physics. A new approach to achieving this aim, named adiabatic photo-steering, is reviewed. The core principle of this scheme is that several material constants are effectively turned into externally tunable variables by irradiation of monochromatic laser light. Two-dimensional topological insulators are selected as the optimal systems that exhibit a prominent change in their properties following the application of this method. Two specific examples of photo-steered quantum phenomena, which reflect topological aspects of the electronic systems at hand, are presented. One is the integer quantum Hall effect described by the Haldane model, and the other is the quantum spin Hall effect described by the Kane–Mele model. The topological quantities associated with these phenomena are the conventional Chern number and spin Chern number, respectively. A recent interesting idea, time-reversal symmetry breaking via a temporary periodic external stimulation, is also discussed. (focus issue review)

Topological M Theory from Pure Spinor Formalism

CERN Document Server

Grassi, P A; Grassi, Pietro Antonio; Vanhove, Pierre

2005-01-01

We construct multiloop superparticle amplitudes in 11d using the pure spinor formalism. We explain how this construction reduces to the superparticle limit of the multiloop pure spinor superstring amplitudes prescription. We then argue that this construction points to some evidence for the existence of a topological M theory based on a relation between the ghost number of the full-fledged supersymmetric critical models and the dimension of the spacetime for topological models. In particular, we show that the extensions at higher orders of the previous results for the tree and one-loop level expansion for the superparticle in 11 dimensions is related to a topological model in 7 dimensions.

Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory.

Science.gov (United States)

Reeb, Valérie; Lutzoni, François; Roux, Claude

2004-09-01

Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

Science.gov (United States)

Leonard, Guy; Stevens, Jamie R.; Richards, Thomas A.

2009-01-01

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends. PMID:19812722

Topology Explains Why Automobile Sunshades Fold Oddly

Science.gov (United States)

Feist, Curtis; Naimi, Ramin

2009-01-01

Automobile sunshades always fold into an "odd" number of loops. The explanation why involves elementary topology (braid theory and linking number, both explained in detail here with definitions and examples), and an elementary fact from algebra about symmetric group.

The topological Anderson insulator phase in the Kane-Mele model

Science.gov (United States)

Orth, Christoph P.; Sekera, Tibor; Bruder, Christoph; Schmidt, Thomas L.

2016-04-01

It has been proposed that adding disorder to a topologically trivial mercury telluride/cadmium telluride (HgTe/CdTe) quantum well can induce a transition to a topologically nontrivial state. The resulting state was termed topological Anderson insulator and was found in computer simulations of the Bernevig-Hughes-Zhang model. Here, we show that the topological Anderson insulator is a more universal phenomenon and also appears in the Kane-Mele model of topological insulators on a honeycomb lattice. We numerically investigate the interplay of the relevant parameters, and establish the parameter range in which the topological Anderson insulator exists. A staggered sublattice potential turns out to be a necessary condition for the transition to the topological Anderson insulator. For weak enough disorder, a calculation based on the lowest-order Born approximation reproduces quantitatively the numerical data. Our results thus considerably increase the number of candidate materials for the topological Anderson insulator phase.

Topology of Large-Scale Structure by Galaxy Type: Hydrodynamic Simulations

Science.gov (United States)

Gott, J. Richard, III; Cen, Renyue; Ostriker, Jeremiah P.

1996-07-01

The topology of large-scale structure is studied as a function of galaxy type using the genus statistic. In hydrodynamical cosmological cold dark matter simulations, galaxies form on caustic surfaces (Zeldovich pancakes) and then slowly drain onto filaments and clusters. The earliest forming galaxies in the simulations (defined as "ellipticals") are thus seen at the present epoch preferentially in clusters (tending toward a meatball topology), while the latest forming galaxies (defined as "spirals") are seen currently in a spongelike topology. The topology is measured by the genus (number of "doughnut" holes minus number of isolated regions) of the smoothed density-contour surfaces. The measured genus curve for all galaxies as a function of density obeys approximately the theoretical curve expected for random- phase initial conditions, but the early-forming elliptical galaxies show a shift toward a meatball topology relative to the late-forming spirals. Simulations using standard biasing schemes fail to show such an effect. Large observational samples separated by galaxy type could be used to test for this effect.

Matrix product density operators: Renormalization fixed points and boundary theories

Energy Technology Data Exchange (ETDEWEB)

Cirac, J.I. [Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Str. 1, D-85748 Garching (Germany); Pérez-García, D., E-mail: dperezga@ucm.es [Departamento de Análisis Matemático, Universidad Complutense de Madrid, Plaza de Ciencias 3, 28040 Madrid (Spain); ICMAT, Nicolas Cabrera, Campus de Cantoblanco, 28049 Madrid (Spain); Schuch, N. [Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Str. 1, D-85748 Garching (Germany); Verstraete, F. [Department of Physics and Astronomy, Ghent University (Belgium); Vienna Center for Quantum Technology, University of Vienna (Austria)

2017-03-15

We consider the tensors generating matrix product states and density operators in a spin chain. For pure states, we revise the renormalization procedure introduced in (Verstraete et al., 2005) and characterize the tensors corresponding to the fixed points. We relate them to the states possessing zero correlation length, saturation of the area law, as well as to those which generate ground states of local and commuting Hamiltonians. For mixed states, we introduce the concept of renormalization fixed points and characterize the corresponding tensors. We also relate them to concepts like finite correlation length, saturation of the area law, as well as to those which generate Gibbs states of local and commuting Hamiltonians. One of the main result of this work is that the resulting fixed points can be associated to the boundary theories of two-dimensional topological states, through the bulk-boundary correspondence introduced in (Cirac et al., 2011).

Topological Nematic States and Non-Abelian Lattice Dislocations

Directory of Open Access Journals (Sweden)

Maissam Barkeshli

2012-08-01

Full Text Available An exciting new prospect in condensed matter physics is the possibility of realizing fractional quantum Hall states in simple lattice models without a large external magnetic field. A fundamental question is whether qualitatively new states can be realized on the lattice as compared with ordinary fractional quantum Hall states. Here we propose new symmetry-enriched topological states, topological nematic states, which are a dramatic consequence of the interplay between the lattice translational symmetry and topological properties of these fractional Chern insulators. The topological nematic states are realized in a partially filled flat band with a Chern number N, which can be mapped to an N-layer quantum Hall system on a regular lattice. However, in the topological nematic states the lattice dislocations can act as wormholes connecting the different layers and effectively change the topology of the space. Consequently, lattice dislocations become defects with a nontrivial quantum dimension, even when the fractional quantum Hall state being realized is, by itself, Abelian. Our proposal leads to the possibility of realizing the physics of topologically ordered states on high-genus surfaces in the lab even though the sample has only the disk geometry.

Topological Nematic States and Non-Abelian Lattice Dislocations

Science.gov (United States)

Barkeshli, Maissam; Qi, Xiao-Liang

2012-07-01

An exciting new prospect in condensed matter physics is the possibility of realizing fractional quantum Hall states in simple lattice models without a large external magnetic field. A fundamental question is whether qualitatively new states can be realized on the lattice as compared with ordinary fractional quantum Hall states. Here we propose new symmetry-enriched topological states, topological nematic states, which are a dramatic consequence of the interplay between the lattice translational symmetry and topological properties of these fractional Chern insulators. The topological nematic states are realized in a partially filled flat band with a Chern number N, which can be mapped to an N-layer quantum Hall system on a regular lattice. However, in the topological nematic states the lattice dislocations can act as wormholes connecting the different layers and effectively change the topology of the space. Consequently, lattice dislocations become defects with a nontrivial quantum dimension, even when the fractional quantum Hall state being realized is, by itself, Abelian. Our proposal leads to the possibility of realizing the physics of topologically ordered states on high-genus surfaces in the lab even though the sample has only the disk geometry.

Countable Fuzzy Topological Space and Countable Fuzzy Topological Vector Space

Directory of Open Access Journals (Sweden)

Apu Kumar Saha

2015-06-01

Full Text Available This paper deals with countable fuzzy topological spaces, a generalization of the notion of fuzzy topological spaces. A collection of fuzzy sets F on a universe X forms a countable fuzzy topology if in the definition of a fuzzy topology, the condition of arbitrary supremum is relaxed to countable supremum. In this generalized fuzzy structure, the continuity of fuzzy functions and some other related properties are studied. Also the class of countable fuzzy topological vector spaces as a generalization of the class of fuzzy topological vector spaces has been introduced and investigated.

Grain topology in Ti-6Al-4V welds-Monte Carlo simulation and experiments

International Nuclear Information System (INIS)

Mishra, S; DebRoy, T

2004-01-01

The importance of topological features of grains in the evolution of grain structure is well recognized in isothermal systems. However, during fusion welding, strong spatial gradients of temperature exist in the heat-affected zone (HAZ), and this region undergoes rapid heating and cooling. The effects of spatial and temporal variations of temperature on the topological class distribution, relationship between size and topology of grains and the interdependence between grain topology and its neighbours are not known. Topological features of grains in the HAZ of Ti-6Al-4V alloy welds were measured for various heat inputs in the range 0.55-4.33 MJ m -1 . The topological class distributions were also calculated using a three-dimensional Monte Carlo model utilizing thermal cycles computed from a well tested numerical heat transfer and fluid flow model. The computed results showed that the topological class distributions were unaffected by the spatial and temporal variations of temperature. Experimental investigations of a few sections confirmed the simulation results. The average grain size for each edge class varied linearly with the edge class number. The local topological environment, i.e. the average number of sides of neighbours, n n , varied linearly with the inverse of the number of sides of grains, 1/n r , at a given location in the HAZ. Locations with the same topological environment showed the same grain size, indicating the significant influence of grain topology on grain growth in the HAZ

Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces

Directory of Open Access Journals (Sweden)

York Thomas

2009-01-01

Full Text Available Abstract Background In phylogenetic inference one is interested in obtaining samples from the posterior distribution over the tree space on the basis of some observed DNA sequence data. One of the simplest sampling methods is the rejection sampler due to von Neumann. Here we introduce an auto-validating version of the rejection sampler, via interval analysis, to rigorously draw samples from posterior distributions over small phylogenetic tree spaces. Results The posterior samples from the auto-validating sampler are used to rigorously (i estimate posterior probabilities for different rooted topologies based on mitochondrial DNA from human, chimpanzee and gorilla, (ii conduct a non-parametric test of rate variation between protein-coding and tRNA-coding sites from three primates and (iii obtain a posterior estimate of the human-neanderthal divergence time. Conclusion This solves the open problem of rigorously drawing independent and identically distributed samples from the posterior distribution over rooted and unrooted small tree spaces (3 or 4 taxa based on any multiply-aligned sequence data.

Topology Design for Directional Range Extension Networks with Antenna Blockage

Science.gov (United States)

2017-03-19

this is equivalent to the Hamiltonian Path Problem, which is NP- hard . More work on computationally efficient topology formation and maintenance... formation and maintenance of low-degree air topologies. 1 I. INTRODUCTION Tactical military networks both on land and at sea often have restricted...constraints on the number of antenna beams that a pod can support, a string topology formation and maintenance algorithm may be the best design choice

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides)

Science.gov (United States)

Moyle, R.G.; Chesser, R.T.; Brumfield, R.T.; Tello, J.G.; Marchese, D.J.; Cracraft, J.

2009-01-01

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods. ?? 2009 The Willi Hennig Society.

The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR

Science.gov (United States)

Zhang, Peng

2012-01-01

Background Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications in molecular phylogenetic studies. For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups. However, such markers with broad working range and high phylogenetic performance are still scarce. It is necessary to develop more universal NPCL markers comparable to RAG1 for osteichthyan phylogenetics. Methodology/Principal Findings We developed three long universal NPCL markers (>1.6 kb each) based on single-copy nuclear genes (KIAA1239, SACS and TTN) that possess large exons and exhibit the appropriate evolutionary rates. We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species. In comparison with RAG1, each of the three long universal markers yielded similar topologies and branch supports, all in congruence with the currently accepted osteichthyan phylogeny. To compare their phylogenetic performance visually, we also estimated the phylogenetic informativeness (PI) profile for each of the four long universal NPCL markers. The PI curves indicated that SACS performed best over the whole timescale, while RAG1, KIAA1239 and TTN exhibited similar phylogenetic performances. In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments. The amplification success rate and efficiency of the nested PCR were overwhelmingly higher than those of standard PCR. Conclusions/Significance Our work clearly demonstrates the superiority of nested PCR over the conventional PCR in phylogenetic studies and develops three long universal NPCL markers (KIAA1239, SACS and TTN) with the nested PCR strategy. The three markers exhibit high phylogenetic utilities in osteichthyan phylogenetics and can be widely used as pilot genes for

Universal transport characteristics of multiple topological superconducting wires with large charging energy

Energy Technology Data Exchange (ETDEWEB)

Kashuba, Oleksiy; Trauzettel, Bjoern [Institut fuer Theoretische Physik und Astrophysik, Universitaet Wuerzburg, 97074 Wuerzburg (Germany); Timm, Carsten [Institut fuer Theoretische Physik, TU Dresden, 01062 Dresden (Germany)

2016-07-01

The system with multiple Majorana states coupled to the normal lead can potentially support the interaction between Majorana fermions and electrons. Such system can be implemented by several floating topological superconducting wires with large charging energy asymmetrically coupled to two normal leads. The analysis of the renormalization flow shows that there is a single fixed point - the strong coupling limit of isotropic antiferromagnetic Kondo model. The topological Kondo-like interaction leads also to the selective renormalization of the tunneling coefficients, strongly enhancing one component and suppressing others. Thus, charging energy crucially changes the transport properties of the system leading to the universal single-channel conductance independently from the values of the initial leads-wires coupling.

Network topology exploration of mesh-based coarse-grain reconfigurable architectures

NARCIS (Netherlands)

Bansal, N.; Gupta, S.; Dutt, N.D.; Nicolau, A.; Gupta, R.

2004-01-01

Several coarse-grain reconfigurable architectures proposed recently consist of a large number of processing elements (PEs) connected in a mesh-like network topology. We study the effects of three aspects of network topology exploration on the performance of applications on these architectures: (a)

Engineering topological phases with a three-dimensional nodal-loop semimetal

Science.gov (United States)

Li, Linhu; Yap, Han Hoe; Araújo, Miguel A. N.; Gong, Jiangbin

2017-12-01

A three-dimensional (3D) nodal-loop semimetal phase is exploited to engineer a number of intriguing phases featuring different peculiar topological surface states. In particular, by introducing various two-dimensional gap terms to a 3D tight-binding model of a nodal-loop semimetal, we obtain a rich variety of topological phases of great interest to ongoing theoretical and experimental studies, including a chiral insulator, degenerate-surface-loop insulator, and second-order topological insulator, as well as a Weyl semimetal with tunable Fermi arc profiles. The unique concept underlying our approach is to engineer topological surface states that inherit their dispersion relations from a gap term. The results provide one rather unified principle for the creation of novel topological phases and can guide the search for new topological materials. Two-terminal transport studies are also carried out to distinguish the engineered topological phases.

Grassmannian topological Kazama-Suzuki models and cohomology

International Nuclear Information System (INIS)

Blau, M.; Hussain, F.; Thompson, G.

1995-10-01

We investigate in detail the topological gauged Wess-Zumino-Witten models describing topological Kazama-Suzuki models based on complex Grassmannians. We show that there is a topological sector in which the ring of observables (constructed from the Grassmann odd scalars of the theory) coincides with the classical cohomology ring of the Grassmanian for all values of the level k. We also analyze the general ring structure of bosonic correlation functions, uncovering a whole hierarchy of level-rank relations (including the standard level-rank duality) among models based on different Grassmannians. Using the previously established localization of the topological Kazama-Suzuki model to an Abelian topological field theory, we reduce the correlators to finite-dimensional purely algebraic expressions. As an application, these are evaluated explicitly for the CP(2) model at level k and shown for all k to coincide with the cohomological intersection numbers of the two-plane Grassmannian G(2,K + 2), thus realizing the level-rank duality between this model and the G(2, k + 2) model at level one. (author). 28 refs

A new 6d fixed point from holography

Energy Technology Data Exchange (ETDEWEB)

Apruzzi, Fabio [Department of Physics, University of North Carolina,Chapel Hill, NC 27599 (United States); CUNY Graduate Center, Initiative for the Theoretical Sciences,New York, NY 10016 (United States); Department of Physics, Columbia University,New York, NY 10027 (United States); Dibitetto, Giuseppe; Tizzano, Luigi [Department of Physics and Astronomy, Uppsala university,Box 516, SE-75120 Uppsala (Sweden)

2016-11-22

We propose a stringy construction giving rise to a class of interacting and non-supersymmetric CFT’s in six dimensions. Such theories may be obtained as an IR conformal fixed point of an RG flow ending up in a (1,0) theory in the UV. We provide the due holographic evidence in the context of massive type IIA on AdS{sub 7}×M{sub 3}, where M{sub 3} is topologically an S{sup 3}. In particular, in this paper we present a 10d flow solution which may be interpreted as a non-BPS bound state of NS5, D6 and (D6)-bar branes. Moreover, by adopting its 7d effective description, we are able to holographically compute the free energy and the operator spectrum in the novel IR conformal fixed point.

Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

Science.gov (United States)

Ypma, Rolf J F; van Ballegooijen, W Marijn; Wallinga, Jacco

2013-11-01

Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology.

Phylogenetic analysis using parsimony and likelihood methods.

Science.gov (United States)

Yang, Z

1996-02-01

The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981, J. Mol. Evol. 17: 368-376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were

Spin-transfer torque generated by a topological insulator

KAUST Repository

Mellnik, A. R.

2014-07-23

Magnetic devices are a leading contender for the implementation of memory and logic technologies that are non-volatile, that can scale to high density and high speed, and that do not wear out. However, widespread application of magnetic memory and logic devices will require the development of efficient mechanisms for reorienting their magnetization using the least possible current and power. There has been considerable recent progress in this effort; in particular, it has been discovered that spin-orbit interactions in heavy-metal/ferromagnet bilayers can produce strong current-driven torques on the magnetic layer, via the spin Hall effect in the heavy metal or the Rashba-Edelstein effect in the ferromagnet. In the search for materials to provide even more efficient spin-orbit-induced torques, some proposals have suggested topological insulators, which possess a surface state in which the effects of spin-orbit coupling are maximal in the sense that an electron\\' s spin orientation is fixed relative to its propagation direction. Here we report experiments showing that charge current flowing in-plane in a thin film of the topological insulator bismuth selenide (Bi2Se3) at room temperature can indeed exert a strong spin-transfer torque on an adjacent ferromagnetic permalloy (Ni81Fe19) thin film, with a direction consistent with that expected from the topological surface state. We find that the strength of the torque per unit charge current density in Bi 2Se3 is greater than for any source of spin-transfer torque measured so far, even for non-ideal topological insulator films in which the surface states coexist with bulk conduction. Our data suggest that topological insulators could enable very efficient electrical manipulation of magnetic materials at room temperature, for memory and logic applications. © 2014 Macmillan Publishers Limited. All rights reserved.

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Directory of Open Access Journals (Sweden)

David Lee Erickson

2014-11-01

Full Text Available Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1,347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK and psbA-trnH and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance metrics that are commonly used to infer assembly processes were estimated for each plot (Phylogenetic Distance [PD], Mean Phylogenetic Distance [MPD], and Mean Nearest Taxon Distance [MNTD]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

Directory of Open Access Journals (Sweden)

Guy Leonard

2009-01-01

Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

Length scale and manufacturability in density-based topology optimization

DEFF Research Database (Denmark)

Lazarov, Boyan Stefanov; Wang, Fengwen; Sigmund, Ole

2016-01-01

Since its original introduction in structural design, density-based topology optimization has been applied to a number of other fields such as microelectromechanical systems, photonics, acoustics and fluid mechanics. The methodology has been well accepted in industrial design processes where it can...... provide competitive designs in terms of cost, materials and functionality under a wide set of constraints. However, the optimized topologies are often considered as conceptual due to loosely defined topologies and the need of postprocessing. Subsequent amendments can affect the optimized design...

Evaluation of Topology-Aware Broadcast Algorithms for Dragonfly Networks

Energy Technology Data Exchange (ETDEWEB)

Dorier, Matthieu; Mubarak, Misbah; Ross, Rob; Li, Jianping Kelvin; Carothers, Christopher D.; Ma, Kwan-Liu

2016-09-12

Two-tiered direct network topologies such as Dragonflies have been proposed for future post-petascale and exascale machines, since they provide a high-radix, low-diameter, fast interconnection network. Such topologies call for redesigning MPI collective communication algorithms in order to attain the best performance. Yet as increasingly more applications share a machine, it is not clear how these topology-aware algorithms will react to interference with concurrent jobs accessing the same network. In this paper, we study three topology-aware broadcast algorithms, including one designed by ourselves. We evaluate their performance through event-driven simulation for small- and large-sized broadcasts (in terms of both data size and number of processes). We study the effect of different routing mechanisms on the topology-aware collective algorithms, as well as their sensitivity to network contention with other jobs. Our results show that while topology-aware algorithms dramatically reduce link utilization, their advantage in terms of latency is more limited.

On the Hardness of Topology Inference

Science.gov (United States)

Acharya, H. B.; Gouda, M. G.

Many systems require information about the topology of networks on the Internet, for purposes like management, efficiency, testing of new protocols and so on. However, ISPs usually do not share the actual topology maps with outsiders; thus, in order to obtain the topology of a network on the Internet, a system must reconstruct it from publicly observable data. The standard method employs traceroute to obtain paths between nodes; next, a topology is generated such that the observed paths occur in the graph. However, traceroute has the problem that some routers refuse to reveal their addresses, and appear as anonymous nodes in traces. Previous research on the problem of topology inference with anonymous nodes has demonstrated that it is at best NP-complete. In this paper, we improve upon this result. In our previous research, we showed that in the special case where nodes may be anonymous in some traces but not in all traces (so all node identifiers are known), there exist trace sets that are generable from multiple topologies. This paper extends our theory of network tracing to the general case (with strictly anonymous nodes), and shows that the problem of computing the network that generated a trace set, given the trace set, has no general solution. The weak version of the problem, which allows an algorithm to output a "small" set of networks- any one of which is the correct one- is also not solvable. Any algorithm guaranteed to output the correct topology outputs at least an exponential number of networks. Our results are surprisingly robust: they hold even when the network is known to have exactly two anonymous nodes, and every node as well as every edge in the network is guaranteed to occur in some trace. On the basis of this result, we suggest that exact reconstruction of network topology requires more powerful tools than traceroute.

Topology optimization of microfluidic mixers

DEFF Research Database (Denmark)

Andreasen, Casper Schousboe; Gersborg, Allan Roulund; Sigmund, Ole

2009-01-01

This paper demonstrates the application of the topology optimization method as a general and systematic approach for microfluidic mixer design. The mixing process is modeled as convection dominated transport in low Reynolds number incompressible flow. The mixer performance is maximized by altering...

Reconstructing phylogenetic networks using maximum parsimony.

Science.gov (United States)

Nakhleh, Luay; Jin, Guohua; Zhao, Fengmei; Mellor-Crummey, John

2005-01-01

Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.

Baryon number violation and string topologies

International Nuclear Information System (INIS)

Sjoestrand, T.; Skands, P.Z.

2003-01-01

In supersymmetric scenarios with broken R-parity, baryon number violating sparticle decays become possible. In order to search for such decays, a good understanding of expected event properties is essential. We here develop a complete framework that allows detailed studies. Special attention is given to the hadronization phase, wherein the baryon number violating vertex is associated with the appearance of a junction in the colour confinement field. This allows us to tell where to look for the extra (anti)baryon directly associated with the baryon number violating decay

Streamline topology of steady axisymmetric vortex breakdown in a cylinder with co- and counter-rotating end-covers

DEFF Research Database (Denmark)

Brøns, Morten; Voigt, Lars Peter Køllgaard; Sørensen, Jens Nørkær

1998-01-01

Using a combination of bifurcation theory for two-dimensional dynamical systems and numerical simulations, we systematically determine the possible flow topologies of the steady vortex breakdown in axisymmetric flow in a cylindrical container with rotating end-covers. For fixed values...

A Sample WebQuest Applicable in Teaching Topological Concepts

Science.gov (United States)

Yildiz, Sevda Goktepe; Korpeoglu, Seda Goktepe

2016-01-01

In recent years, WebQuests have received a great deal of attention and have been used effectively in teaching-learning process in various courses. In this study, a WebQuest that can be applicable in teaching topological concepts for undergraduate level students was prepared. A number of topological concepts, such as countability, infinity, and…

Phylogenetic comparative methods on phylogenetic networks with reticulations.

Science.gov (United States)

Bastide, Paul; Solís-Lemus, Claudia; Kriebel, Ricardo; Sparks, K William; Ané, Cécile

2018-04-25

The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

Topological analysis of long-chain branching patterns in polyolefins.

Science.gov (United States)

Bonchev, D; Markel, E; Dekmezian, A

2001-01-01

Patterns in molecular topology and complexity for long-chain branching are quantitatively described. The Wiener number, the topological complexity index, and a new index of 3-starness are used to quantify polymer structure. General formulas for these indices were derived for the cases of 3-arm star, H-shaped, and B-arm comb polymers. The factors affecting complexity in monodisperse polymer systems are ranked as follows: number of arms > arm length > arm central position approximately equal to arm clustering > total molecular weight approximately equal to backbone molecular weight. Topological indices change rapidly and then plateau as the molecular weight of branches on a polyolefin backbone increases from 0 to 5 kD. Complexity calculations relate 2-arm or 3-arm comb structures to the corresponding 3-arm stars of equivalent complexity but much higher molecular weight. In a subsequent paper, we report the application of topological analysis for developing structure/property relationships for monodisperse polymers. While the focus of the present work is on the description of monodisperse, well-defined architectures, the methods may be extended to the description of polydisperse systems.

Effects of topologies on signal propagation in feedforward networks

Science.gov (United States)

Zhao, Jia; Qin, Ying-Mei; Che, Yan-Qiu

2018-01-01

We systematically investigate the effects of topologies on signal propagation in feedforward networks (FFNs) based on the FitzHugh-Nagumo neuron model. FFNs with different topological structures are constructed with same number of both in-degrees and out-degrees in each layer and given the same input signal. The propagation of firing patterns and firing rates are found to be affected by the distribution of neuron connections in the FFNs. Synchronous firing patterns emerge in the later layers of FFNs with identical, uniform, and exponential degree distributions, but the number of synchronous spike trains in the output layers of the three topologies obviously differs from one another. The firing rates in the output layers of the three FFNs can be ordered from high to low according to their topological structures as exponential, uniform, and identical distributions, respectively. Interestingly, the sequence of spiking regularity in the output layers of the three FFNs is consistent with the firing rates, but their firing synchronization is in the opposite order. In summary, the node degree is an important factor that can dramatically influence the neuronal network activity.

Introduction to topology

CERN Document Server

Gamelin, Theodore W

1999-01-01

A fresh approach to introductory topology, this volume explains nontrivial applications of metric space topology to analysis, clearly establishing their relationship. Also, topics from elementary algebraic topology focus on concrete results with minimal algebraic formalism. The first two chapters consider metric space and point-set topology; the second two, algebraic topological material. 1983 edition. Solutions to Selected Exercises. List of Notations. Index. 51 illustrations.

A topological extension of GR: Black holes induce dark energy

International Nuclear Information System (INIS)

Spaans, M

2013-01-01

A topological extension of general relativity is presented. The superposition principle of quantum mechanics, as formulated by the Feynman path integral, is taken as a starting point. It is argued that the trajectories that enter this path integral are distinct and thus that space-time topology is multiply connected. Specifically, space-time at the Planck scale consists of a lattice of three-tori that facilitates many distinct paths for particles to travel along. To add gravity, mini black holes are attached to this lattice. These mini black holes represent Wheeler's quantum foam and result from the fact that GR is not conformally invariant. The number of such mini black holes in any time-slice through four-space is found to be equal to the number of macroscopic (so long-lived) black holes in the entire universe. This connection, by which macroscopic black holes induce mini black holes, is a topological expression of Mach's principle. The proposed topological extension of GR can be tested because, if correct, the dark energy density of the universe should be proportional the total number of macroscopic black holes in the universe at any time. This prediction, although strange, agrees with current astrophysical observations.

Magnetic susceptibility in the edged topological disordered nanoscopic cylinder

International Nuclear Information System (INIS)

Faizabadi, Edris; Omidi, Mahboubeh

2011-01-01

The effects of edged topological disorder on magnetic susceptibility are investigated in a nanoscopic cylinder threaded by a magnetic flux. Persistent current versus even or odd number of electrons shows different signs in ordered and disordered cylinders and also in short or long ones. In addition, temperature-averaged susceptibility has only diamagnetic signs in strong regimes and it is associated with paramagnetic signs in ordered and weak disordered ones. Besides, in an edged topological disordered cylinder, the temperature-averaged susceptibility decreases by raising the temperature somewhat and then increasing initiates and finally at high temperature tends to zero as the ordered one. - Research highlights: → Magnetic susceptibility in one-dimensional topological disordered quantum ring. → Edged topological disorder effect on magnetic susceptibility in nanoscopic cylinder. → Edged topological disorder effect on temperature-averaged susceptibility in cylinder.

Magnetic Monopoles and Topology of Yang-Mills Theory in Polyakov Gauge

OpenAIRE

Quandt, M.; Reinhardt, H.; Schafke, A.

1998-01-01

We express the Pontryagin index in Polyakov gauge completely in terms of magnetically charged gauge fixing defects, namely magnetic monopoles, lines, and domain walls. Open lines and domain walls are topologically equivalent to monopoles, which are the genuine defects. The emergence of non-genuine magnetically charged closed domain walls can be avoided by choosing the temporal gauge field smoothly. The Pontryagin index is then exclusively determined by the magnetic monopoles.

Green-Schwarz superstring theory in two dimensions and topological field theories

International Nuclear Information System (INIS)

Igarashi, Yuji; Kubo, Jisuke

1991-01-01

It is shown that the algebra associated with the local Κ-supersymmetry in the Green-Schwarz superstring theory in d=2 dimensions closes of shell. We quantize the theory in a Lorentz covariant fashion by using the generalized hamiltonian method of Batalin, Fradkin and Vilkovisky and derive a quantum mechanically consistent, gauge-fixed theory, which can be interpreted as a Κ-supersymmetric extension of conformal topological gravity. (orig.)

What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

Directory of Open Access Journals (Sweden)

Talavera Gerard

2011-10-01

Full Text Available Abstract Background Efforts to solve higher-level evolutionary relationships within the class Insecta by using mitochondrial genomic data are hindered due to fast sequence evolution of several groups, most notably Hymenoptera, Strepsiptera, Phthiraptera, Hemiptera and Thysanoptera. Accelerated rates of substitution on their sequences have been shown to have negative consequences in phylogenetic inference. In this study, we tested several methodological approaches to recover phylogenetic signal from whole mitochondrial genomes. As a model, we used two classical problems in insect phylogenetics: The relationships within Paraneoptera and within Holometabola. Moreover, we assessed the mitochondrial phylogenetic signal limits in the deeper Eumetabola dataset, and we studied the contribution of individual genes. Results Long-branch attraction (LBA artefacts were detected in all the datasets. Methods using Bayesian inference outperformed maximum likelihood approaches, and LBA was avoided in Paraneoptera and Holometabola when using protein sequences and the site-heterogeneous mixture model CAT. The better performance of this method was evidenced by resulting topologies matching generally accepted hypotheses based on nuclear and/or morphological data, and was confirmed by cross-validation and simulation analyses. Using the CAT model, the order Strepsiptera was recovered as sister to Coleoptera for the first time using mitochondrial sequences, in agreement with recent results based on large nuclear and morphological datasets. Also the Hymenoptera-Mecopterida association was obtained, leaving Coleoptera and Strepsiptera as the basal groups of the holometabolan insects, which coincides with one of the two main competing hypotheses. For the Paraneroptera, the currently accepted non-monophyly of Homoptera was documented as a phylogenetic novelty for mitochondrial data. However, results were not satisfactory when exploring the entire Eumetabola, revealing the

Feedback topology and XOR-dynamics in Boolean networks with varying input structure.

Science.gov (United States)

Ciandrini, L; Maffi, C; Motta, A; Bassetti, B; Cosentino Lagomarsino, M

2009-08-01

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the parameter gamma. We investigate analytically and numerically the dynamics of graphs under a parallel XOR updating scheme. This scheme is interesting because it is accessible analytically and its phenomenology is at the same time under control and as rich as the one of general Boolean networks. We give analytical formulas for the dynamics on general graphs, showing that with a XOR-type evolution rule, dynamic features are direct consequences of the topological feedback structure, in analogy with the role of relevant components in Kauffman networks. Considering graphs with fixed in-degree, we characterize analytically and numerically the feedback regions using graph decimation algorithms (Leaf Removal). With varying gamma , this graph ensemble shows a phase transition that separates a treelike graph region from one in which feedback components emerge. Networks near the transition point have feedback components made of disjoint loops, in which each node has exactly one incoming and one outgoing link. Using this fact, we provide analytical estimates of the maximum period starting from topological considerations.

Feedback topology and XOR-dynamics in Boolean networks with varying input structure

Science.gov (United States)

Ciandrini, L.; Maffi, C.; Motta, A.; Bassetti, B.; Cosentino Lagomarsino, M.

2009-08-01

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the parameter γ . We investigate analytically and numerically the dynamics of graphs under a parallel XOR updating scheme. This scheme is interesting because it is accessible analytically and its phenomenology is at the same time under control and as rich as the one of general Boolean networks. We give analytical formulas for the dynamics on general graphs, showing that with a XOR-type evolution rule, dynamic features are direct consequences of the topological feedback structure, in analogy with the role of relevant components in Kauffman networks. Considering graphs with fixed in-degree, we characterize analytically and numerically the feedback regions using graph decimation algorithms (Leaf Removal). With varying γ , this graph ensemble shows a phase transition that separates a treelike graph region from one in which feedback components emerge. Networks near the transition point have feedback components made of disjoint loops, in which each node has exactly one incoming and one outgoing link. Using this fact, we provide analytical estimates of the maximum period starting from topological considerations.

Exploring 4D quantum Hall physics with a 2D topological charge pump.

Science.gov (United States)

Lohse, Michael; Schweizer, Christian; Price, Hannah M; Zilberberg, Oded; Bloch, Immanuel

2018-01-03

The discovery of topological states of matter has greatly improved our understanding of phase transitions in physical systems. Instead of being described by local order parameters, topological phases are described by global topological invariants and are therefore robust against perturbations. A prominent example is the two-dimensional (2D) integer quantum Hall effect: it is characterized by the first Chern number, which manifests in the quantized Hall response that is induced by an external electric field. Generalizing the quantum Hall effect to four-dimensional (4D) systems leads to the appearance of an additional quantized Hall response, but one that is nonlinear and described by a 4D topological invariant-the second Chern number. Here we report the observation of a bulk response with intrinsic 4D topology and demonstrate its quantization by measuring the associated second Chern number. By implementing a 2D topological charge pump using ultracold bosonic atoms in an angled optical superlattice, we realize a dynamical version of the 4D integer quantum Hall effect. Using a small cloud of atoms as a local probe, we fully characterize the nonlinear response of the system via in situ imaging and site-resolved band mapping. Our findings pave the way to experimentally probing higher-dimensional quantum Hall systems, in which additional strongly correlated topological phases, exotic collective excitations and boundary phenomena such as isolated Weyl fermions are predicted.

Exploring 4D quantum Hall physics with a 2D topological charge pump

Science.gov (United States)

Lohse, Michael; Schweizer, Christian; Price, Hannah M.; Zilberberg, Oded; Bloch, Immanuel

2018-01-01

The discovery of topological states of matter has greatly improved our understanding of phase transitions in physical systems. Instead of being described by local order parameters, topological phases are described by global topological invariants and are therefore robust against perturbations. A prominent example is the two-dimensional (2D) integer quantum Hall effect: it is characterized by the first Chern number, which manifests in the quantized Hall response that is induced by an external electric field. Generalizing the quantum Hall effect to four-dimensional (4D) systems leads to the appearance of an additional quantized Hall response, but one that is nonlinear and described by a 4D topological invariant—the second Chern number. Here we report the observation of a bulk response with intrinsic 4D topology and demonstrate its quantization by measuring the associated second Chern number. By implementing a 2D topological charge pump using ultracold bosonic atoms in an angled optical superlattice, we realize a dynamical version of the 4D integer quantum Hall effect. Using a small cloud of atoms as a local probe, we fully characterize the nonlinear response of the system via in situ imaging and site-resolved band mapping. Our findings pave the way to experimentally probing higher-dimensional quantum Hall systems, in which additional strongly correlated topological phases, exotic collective excitations and boundary phenomena such as isolated Weyl fermions are predicted.

Inverse participation ratio and localization in topological insulator phase transitions

International Nuclear Information System (INIS)

Calixto, M; Romera, E

2015-01-01

Fluctuations of Hamiltonian eigenfunctions, measured by the inverse participation ratio (IPR), turn out to characterize topological-band insulator transitions occurring in 2D Dirac materials like silicene, which is isostructural with graphene but with a strong spin–orbit interaction. Using monotonic properties of the IPR, as a function of a perpendicular electric field (which provides a tunable band gap), we define topological-like quantum numbers that take different values in the topological-insulator and band-insulator phases. (paper)

Effect of Topology Structures on Synchronization Transition in Coupled Neuron Cells System

International Nuclear Information System (INIS)

Liang Li-Si; Zhang Ji-Qian; Xu Gui-Xia; Liu Le-Zhu; Huang Shou-Fang

2013-01-01

In this paper, by the help of evolutionary algorithm and using Hindmarsh—Rose (HR) neuron model, we investigate the effect of topology structures on synchronization transition between different states in coupled neuron cells system. First, we build different coupling structure with N cells, and found the effect of synchronized transition contact not only closely with the topology of the system, but also with whether there exist the ring structures in the system. In particular, both the size and the number of rings have greater effects on such transition behavior. Secondly, we introduce synchronization error to qualitative analyze the effect of the topology structure. Furthermore, by fitting the simulation results, we find that with the increment of the neurons number, there always exist the optimization structures which have the minimum number of connecting edges in the coupling systems. Above results show that the topology structures have a very crucial role on synchronization transition in coupled neuron system. Biological system may gradually acquire such efficient topology structures through the long-term evolution, thus the systems' information process may be optimized by this scheme. (interdisciplinary physics and related areas of science and technology)

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales.

Science.gov (United States)

Purschke, Oliver; Michalski, Stefan G; Bruelheide, Helge; Durka, Walter

2017-12-01

Although spatial and temporal patterns of phylogenetic community structure during succession are inherently interlinked and assembly processes vary with environmental and phylogenetic scales, successional studies of community assembly have yet to integrate spatial and temporal components of community structure, while accounting for scaling issues. To gain insight into the processes that generate biodiversity after disturbance, we combine analyses of spatial and temporal phylogenetic turnover across phylogenetic scales, accounting for covariation with environmental differences. We compared phylogenetic turnover, at the species- and individual-level, within and between five successional stages, representing woody plant communities in a subtropical forest chronosequence. We decomposed turnover at different phylogenetic depths and assessed its covariation with between-plot abiotic differences. Phylogenetic turnover between stages was low relative to species turnover and was not explained by abiotic differences. However, within the late-successional stages, there was high presence-/absence-based turnover (clustering) that occurred deep in the phylogeny and covaried with environmental differentiation. Our results support a deterministic model of community assembly where (i) phylogenetic composition is constrained through successional time, but (ii) toward late succession, species sorting into preferred habitats according to niche traits that are conserved deep in phylogeny, becomes increasingly important.

Study on the fixed point in crustal deformation before strong earthquake

Science.gov (United States)

Niu, A.; Li, Y.; Yan, W. Mr

2017-12-01

Usually, scholars believe that the fault pre-sliding or expansion phenomenon will be observed near epicenter area before strong earthquake, but more and more observations show that the crust deformation nearby epicenter area is smallest(Zhou, 1997; Niu,2009,2012;Bilham, 2005; Amoruso et al., 2010). The theory of Fixed point t is a branch of mathematics that arises from the theory of topological transformation and has important applications in obvious model analysis. An important precursory was observed by two tilt-meter sets, installed at Wenchuan Observatory in the epicenter area, that the tilt changes were the smallest compared with the other 8 stations around them in one year before the Wenchuan earthquake. To subscribe the phenomenon, we proposed the minimum annual variation range that used as a topological transformation. The window length is 1 year, and the sliding length is 1 day. The convergence of points with minimum annual change in the 3 years before the Wenchuan earthquake is studied. And the results show that the points with minimum deformation amplitude basically converge to the epicenter region before the earthquake. The possible mechanism of fixed point of crustal deformation was explored. Concerning the fixed point of crust deformation, the liquidity of lithospheric medium and the isostasy theory are accepted by many scholars (Bott &Dean, 1973; Merer et al.1988; Molnar et al., 1975,1978; Tapponnier et al., 1976; Wang et al., 2001). To explain the fixed point of crust deformation before earthquakes, we study the plate bending model (Bai, et al., 2003). According to plate bending model and real deformation data, we have found that the earthquake rupture occurred around the extreme point of plate bending, where the velocities of displacement, tilt, strain, gravity and so on are close to zero, and the fixed points are located around the epicenter.The phenomenon of fixed point of crust deformation is different from former understandings about the

Driving protocol for a Floquet topological phase without static counterpart

Science.gov (United States)

Quelle, A.; Weitenberg, C.; Sengstock, K.; Morais Smith, C.

2017-11-01

Periodically driven systems play a prominent role in optical lattices. In these ultracold atomic systems, driving is used to create a variety of interesting behaviours, of which an important example is provided by topological states of matter. Such Floquet topological phases have a richer classification than their equilibrium counterparts. Although there exist analogues of the equilibrium topological phases that are characterised by a Chern number, the corresponding Hall conductivity, and protected edge states, there is an additional possibility. This is a phase that has a vanishing Chern number and no Hall conductivity, but nevertheless hosts anomalous topological edge states (Rudner et al (2013 Phys. Rev. X 3 031005)). Due to experimental difficulties associated with the observation of such a phase, it has not been experimentally realised in optical lattices so far. In this paper, we show that optical lattices prove to be a good candidate for its realisation and observation, because they can be driven in a controlled manner. Specifically, we present a simple shaking protocol that serves to realise this special Floquet phase, discuss the specific properties that it has, and propose a method to experimentally detect this fascinating topological phase that has no counterpart in equilibrium systems.

Critical exponents for square lattice trails with a fixed number of vertices of degree 4

International Nuclear Information System (INIS)

James, E W; Soteros, C E

2002-01-01

We prove several previously conjectured results about the number of n-edge trails and n-edge embeddings of Eulerian graphs, each with a fixed number, k, of degree 4 vertices, in the lattice Z 2 . In particular, under the assumption that the relevant critical exponents exist, we prove that the difference between the critical exponent for closed trails (Eulerian graph embeddings) and that for self-avoiding circuits (polygons) is exactly k, the number of degree 4 vertices. Similarly, we prove that the difference between the critical exponent for either open trails or open Eulerian graph embeddings and that for self-avoiding walks is also k. These results are proved by establishing upper and lower bounds for the number of n-edge embeddings of closed (open) Eulerian graphs with k vertices of degree 4 in terms of the number of n-edge self-avoiding polygons (walks). The lower bounds are proved using a Kesten pattern theorem argument and the upper bounds are established by developing (based on a detailed case analysis) a method for removing vertices of degree 4 from an embedding by altering at most a constant (independent of n) number of vertices and edges of the embedding. The work presented here extends and improves the arguments first given in the work of Zhao and Lookman (1993 J. Phys. A: Math. Gen. 26 1067-76)

Topological Quantization of Instantons in SU(2) Yang–Mills Theory

International Nuclear Information System (INIS)

Wo-Jun, Zhong; Yi-Shi, Duan

2008-01-01

By decomposing SU(2) gauge potential in four-dimensional Euclidean SU(2) Yang–Mills theory in a new way, we find that the instanton number related to the isospin defects of a doublet order parameter can be topologically quantized by the Hopf index and Brouwer degree. It is also shown that the instanton number is just the sum of the topological charges of the isospin defects in the non-trivial sector of Yang–Mills theory. (general)

Molecular phylogenetics of finches and sparrows: consequences of character state removal in cytochrome b sequences.

Science.gov (United States)

Groth, J G

1998-12-01

The complete mitochondrial cytochrome b genes of 53 genera of oscine passerine birds representing the major groups of finches and some allies were compared. Phylogenetic trees resulting from three levels of character partition removal (no data removed, transitions at third positions of codons removed, and all transitions removed [transversion parsimony]) were generally concordant, and all supported several basic statements regarding relationships of finches and finch-like birds, including: (1) larks (Alaudidae) show no close relationship to any finch group; (2) Peucedramus (olive warbler) is phylogenetically far removed from true wood warblers; (3) a clade consisting of fringillids, passerids, motacillids, and emberizids is supported, and this clade is characterized by evolution of a vestigial 10th wing primary; and (4) Hawaiian honeycreepers are derived from within the cardueline finches. Excluding transition substitutions at third positions of codons resulted in phylogenetic trees similar to, but with greater bootstrap nodal support than, trees derived using either all data (equally weighted) or transversion parsimony. Relative to the shortest trees obtained using all data, the topologies obtained after elimination of third-position transitions showed only slight increases in realized treelength and homoplasy. These increases were negligable compared to increases in overall nodal support; therefore, this partition removal scheme may enhance recovery of deep phylogenetic signal in protein-coding DNA datasets. Copyright 1998 Academic Press.

p-topological Cauchy completions

Directory of Open Access Journals (Sweden)

J. Wig

1999-01-01

Full Text Available The duality between “regular” and “topological” as convergence space properties extends in a natural way to the more general properties “p-regular” and “p-topological.” Since earlier papers have investigated regular, p-regular, and topological Cauchy completions, we hereby initiate a study of p-topological Cauchy completions. A p-topological Cauchy space has a p-topological completion if and only if it is “cushioned,” meaning that each equivalence class of nonconvergent Cauchy filters contains a smallest filter. For a Cauchy space allowing a p-topological completion, it is shown that a certain class of Reed completions preserve the p-topological property, including the Wyler and Kowalsky completions, which are, respectively, the finest and the coarsest p-topological completions. However, not all p-topological completions are Reed completions. Several extension theorems for p-topological completions are obtained. The most interesting of these states that any Cauchy-continuous map between Cauchy spaces allowing p-topological and p′-topological completions, respectively, can always be extended to a θ-continuous map between any p-topological completion of the first space and any p′-topological completion of the second.

Emerging Trends in Topological Insulators and Topological ...

Indian Academy of Sciences (India)

/fulltext/reso/022/08/0787-0800. Keywords. Superconductor, quantum Hall effect, topological insulator, Majorana fermions. Abstract. Topological insulators are new class of materials which arecharacterized by a bulk band gap like ordinary ...

Topological string theory, modularity and non-perturbative physics

Energy Technology Data Exchange (ETDEWEB)

Rauch, Marco

2011-09-15

In this thesis the holomorphic anomaly of correlators in topological string theory, matrix models and supersymmetric gauge theories is investigated. In the first part it is shown how the techniques of direct integration known from topological string theory can be used to solve the closed amplitudes of Hermitian multi-cut matrix models with polynomial potentials. In the case of the cubic matrix model, explicit expressions for the ring of non-holomorphic modular forms that are needed to express all closed matrix model amplitudes are given. This allows to integrate the holomorphic anomaly equation up to holomorphic modular terms that are fixed by the gap condition up to genus four. There is an one-dimensional submanifold of the moduli space in which the spectral curve becomes the Seiberg-Witten curve and the ring reduces to the non-holomorphic modular ring of the group {gamma}(2). On that submanifold, the gap conditions completely fix the holomorphic ambiguity and the model can be solved explicitly to very high genus. Using these results it is possible to make precision tests of the connection between the large order behavior of the 1/N expansion and non-perturbative effects due to instantons. Finally, it is argued that a full understanding of the large genus asymptotics in the multi-cut case requires a new class of non-perturbative sectors in the matrix model. In the second part a holomorphic anomaly equation for the modified elliptic genus of two M5-branes wrapping a rigid divisor inside a Calabi-Yau manifold is derived using wall-crossing formulae and the theory of mock modular forms. The anomaly originates from restoring modularity of an indefinite theta-function capturing the wall-crossing of BPS invariants associated to D4- D2-D0 brane systems. The compatibility of this equation with anomaly equations previously observed in the context of N=4 topological Yang-Mills theory on P{sup 2} and E-strings obtained from wrapping M5-branes on a del Pezzo surface which in

Topological string theory, modularity and non-perturbative physics

International Nuclear Information System (INIS)

Rauch, Marco

2011-09-01

In this thesis the holomorphic anomaly of correlators in topological string theory, matrix models and supersymmetric gauge theories is investigated. In the first part it is shown how the techniques of direct integration known from topological string theory can be used to solve the closed amplitudes of Hermitian multi-cut matrix models with polynomial potentials. In the case of the cubic matrix model, explicit expressions for the ring of non-holomorphic modular forms that are needed to express all closed matrix model amplitudes are given. This allows to integrate the holomorphic anomaly equation up to holomorphic modular terms that are fixed by the gap condition up to genus four. There is an one-dimensional submanifold of the moduli space in which the spectral curve becomes the Seiberg-Witten curve and the ring reduces to the non-holomorphic modular ring of the group Γ(2). On that submanifold, the gap conditions completely fix the holomorphic ambiguity and the model can be solved explicitly to very high genus. Using these results it is possible to make precision tests of the connection between the large order behavior of the 1/N expansion and non-perturbative effects due to instantons. Finally, it is argued that a full understanding of the large genus asymptotics in the multi-cut case requires a new class of non-perturbative sectors in the matrix model. In the second part a holomorphic anomaly equation for the modified elliptic genus of two M5-branes wrapping a rigid divisor inside a Calabi-Yau manifold is derived using wall-crossing formulae and the theory of mock modular forms. The anomaly originates from restoring modularity of an indefinite theta-function capturing the wall-crossing of BPS invariants associated to D4- D2-D0 brane systems. The compatibility of this equation with anomaly equations previously observed in the context of N=4 topological Yang-Mills theory on P 2 and E-strings obtained from wrapping M5-branes on a del Pezzo surface which in turn is

PhyDesign: an online application for profiling phylogenetic informativeness

Directory of Open Access Journals (Sweden)

Townsend Jeffrey P

2011-05-01

Full Text Available Abstract Background The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007 phylogenetic informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic informativeness metric has been available. Results Here, we present PhyDesign, a platform-independent online application that implements the Townsend (2007 phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest. Conclusions By providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu.

Streamline topology of steady axisymmetric vortex breakdown in a cylinder with co- and counter-rotating end-covers

DEFF Research Database (Denmark)

Brøns, Morten; Voigt, Lars Peter Kølgaard; Sørensen, Jens Nørkær

1999-01-01

Using a combination of bifurcation theory for two-dimensional dynamical systems and numerical simulations, we systematically determine the possible flow topologies of the steady vortex breakdown in axisymmetric flow in a cylindrical container with rotating end-covers. For fixed values of the ratio...

Amorphous topological insulators constructed from random point sets

Science.gov (United States)

Mitchell, Noah P.; Nash, Lisa M.; Hexner, Daniel; Turner, Ari M.; Irvine, William T. M.

2018-04-01

The discovery that the band structure of electronic insulators may be topologically non-trivial has revealed distinct phases of electronic matter with novel properties1,2. Recently, mechanical lattices have been found to have similarly rich structure in their phononic excitations3,4, giving rise to protected unidirectional edge modes5-7. In all of these cases, however, as well as in other topological metamaterials3,8, the underlying structure was finely tuned, be it through periodicity, quasi-periodicity or isostaticity. Here we show that amorphous Chern insulators can be readily constructed from arbitrary underlying structures, including hyperuniform, jammed, quasi-crystalline and uniformly random point sets. While our findings apply to mechanical and electronic systems alike, we focus on networks of interacting gyroscopes as a model system. Local decorations control the topology of the vibrational spectrum, endowing amorphous structures with protected edge modes—with a chirality of choice. Using a real-space generalization of the Chern number, we investigate the topology of our structures numerically, analytically and experimentally. The robustness of our approach enables the topological design and self-assembly of non-crystalline topological metamaterials on the micro and macro scale.

Quintessential quartic quasi-topological quartet

Energy Technology Data Exchange (ETDEWEB)

Ahmed, Jamil [Department of Physics and Astronomy, University of Waterloo,200 University Avenue West, Waterloo, ON, N2L 3G1 (Canada); Department of Mathematics, Quaid-i-Azam University,Islamabad (Pakistan); Hennigar, Robie A. [Department of Physics and Astronomy, University of Waterloo,200 University Avenue West, Waterloo, ON, N2L 3G1 (Canada); Mann, Robert B. [Department of Physics and Astronomy, University of Waterloo,200 University Avenue West, Waterloo, ON, N2L 3G1 (Canada); Perimeter Institute,31 Caroline Street North, Waterloo, ON, N2L 2Y5 (Canada); Mir, Mozhgan [Department of Physics and Astronomy, University of Waterloo,200 University Avenue West, Waterloo, ON, N2L 3G1 (Canada); School of Physics, Institute for Research in Fundamental Sciences (IPM),P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)

2017-05-25

We construct the quartic version of generalized quasi-topological gravity, which was recently constructed to cubic order in https://arxiv.org/abs/1703.01631. This class of theories includes Lovelock gravity and a known form of quartic quasi-topological gravity as special cases and possess a number of remarkable properties: (i) In vacuum, or in the presence of suitable matter, there is a single independent field equation which is a total derivative. (ii) At the linearized level, the equations of motion on a maximally symmetric background are second order, coinciding with the linearized Einstein equations up to a redefinition of Newton’s constant. Therefore, these theories propagate only the massless, transverse graviton on a maximally symmetric background. (iii) While the Lovelock and quasi-topological terms are trivial in four dimensions, there exist four new generalized quasi-topological terms (the quartet) that are nontrivial, leading to interesting higher curvature theories in d≥4 dimensions that appear well suited for holographic study. We construct four dimensional black hole solutions to the theory and study their properties. A study of black brane solutions in arbitrary dimensions reveals that these solutions are modified from the ‘universal’ properties they possess in other higher curvature theories, which may lead to interesting consequences for the dual CFTs.

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees

Directory of Open Access Journals (Sweden)

Kedzierska Anna M

2012-08-01

Full Text Available Abstract Background A number of software packages are available to generate DNA multiple sequence alignments (MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages. Results We present the first package designed to generate MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site, the algorithm produces DNA alignments of desired length. GenNon-h is publicly available for download. Conclusion The software presented here is an efficient tool to generate DNA MSAs on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.

Reduced order modeling in topology optimization of vibroacoustic problems

DEFF Research Database (Denmark)

Creixell Mediante, Ester; Jensen, Jakob Søndergaard; Brunskog, Jonas

2017-01-01

complex 3D parts. The optimization process can therefore become highly time consuming due to the need to solve a large system of equations at each iteration. Projection-based parametric Model Order Reduction (pMOR) methods have successfully been applied for reducing the computational cost of material......There is an interest in introducing topology optimization techniques in the design process of structural-acoustic systems. In topology optimization, the design space must be finely meshed in order to obtain an accurate design, which results in large numbers of degrees of freedom when designing...... or size optimization in large vibroacoustic models; however, new challenges are encountered when dealing with topology optimization. Since a design parameter per element is considered, the total number of design variables becomes very large; this poses a challenge to most existing pMOR techniques, which...

Topology

CERN Document Server

Manetti, Marco

2015-01-01

This is an introductory textbook on general and algebraic topology, aimed at anyone with a basic knowledge of calculus and linear algebra. It provides full proofs and includes many examples and exercises. The covered topics include: set theory and cardinal arithmetic; axiom of choice and Zorn's lemma; topological spaces and continuous functions; connectedness and compactness; Alexandrov compactification; quotient topologies; countability and separation axioms; prebasis and Alexander's theorem; the Tychonoff theorem and paracompactness; complete metric spaces and function spaces; Baire spaces; homotopy of maps; the fundamental group; the van Kampen theorem; covering spaces; Brouwer and Borsuk's theorems; free groups and free product of groups; and basic category theory. While it is very concrete at the beginning, abstract concepts are gradually introduced. It is suitable for anyone needing a basic, comprehensive introduction to general and algebraic topology and its applications.

Beginning topology

CERN Document Server

Goodman, Sue E

2009-01-01

Beginning Topology is designed to give undergraduate students a broad notion of the scope of topology in areas of point-set, geometric, combinatorial, differential, and algebraic topology, including an introduction to knot theory. A primary goal is to expose students to some recent research and to get them actively involved in learning. Exercises and open-ended projects are placed throughout the text, making it adaptable to seminar-style classes. The book starts with a chapter introducing the basic concepts of point-set topology, with examples chosen to captivate students' imaginations while i

Topologically protected bound states in one-dimensional Floquet acoustic waveguide systems

Science.gov (United States)

Peng, Yu-Gui; Geng, Zhi-Guo; Zhu, Xue-Feng

2018-03-01

Topological manipulation of sound has recently been a hot spot in acoustics due to the fascinating property of defect immune transport. To the best of our knowledge, the studies on one-dimensional (1D) topological acoustic systems hitherto mainly focus on the case of the Su-Schrieffer-Heeger model. Here, we show that topologically protected bound states may also exist in 1D periodically modulated acoustic waveguide systems, viz., 1D Floquet topological insulators. The results show that tuning the coupling strength in a waveguide lattice could trigger topological phase transition, which gives rise to topologically protected interface states as we put together two waveguide lattices featured with different topological phases or winding numbers. However, for the combined lattice, input at the waveguides other than the interfacial ones will excite bulk states. We have further verified the robustness of interface bound states against the variation of coupling strengths between the two distinct waveguide lattices. This work extends the scope of topological acoustics and may promote potential applications for acoustic devices with topological functionalities.

Topological Gyroscopic Metamaterials

Science.gov (United States)

Nash, Lisa Michelle

Topological materials are generally insulating in their bulk, with protected conducting states on their boundaries that are robust against disorder and perturbation of material property. The existence of these conducting edge states is characterized by an integer topological invariant. Though the phenomenon was first discovered in electronic systems, recent years have shown that topological states exist in classical systems as well. In this thesis we are primarily concerned with the topological properties of gyroscopic materials, which are created by coupling networks of fast-spinning objects. Through a series of simulations, numerical calculations, and experiments, we show that these materials can support topological edge states. We find that edge states in these gyroscopic metamaterials bear the hallmarks of topology related to broken time reversal symmetry: they transmit excitations unidirectionally and are extremely robust against experimental disorder. We also explore requirements for topology by studying several lattice configurations and find that topology emerges naturally in gyroscopic systems.A simple prescription can be used to create many gyroscopic lattices. Though many of our gyroscopic networks are periodic, we explore amorphous point-sets and find that topology also emerges in these networks.

Orthology prediction at scalable resolution by phylogenetic tree analysis

Directory of Open Access Journals (Sweden)

Huynen Martijn A

2007-03-01

Full Text Available Abstract Background Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. Results We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable. Conclusion The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website http://www.cmbi.ru.nl/LOFT.

On the information content of discrete phylogenetic characters.

Science.gov (United States)

Bordewich, Magnus; Deutschmann, Ina Maria; Fischer, Mareike; Kasbohm, Elisa; Semple, Charles; Steel, Mike

2017-12-16

Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a particular type of data, which contain information on how the species should be grouped together. However, it has long been known that some characters contain more information than others. For instance, a character that assigns the same state to each species groups all of them together and so provides no insight into the relationships of the species considered. At the other extreme, a character that assigns a different state to each species also conveys no phylogenetic signal. In this manuscript, we study a natural combinatorial measure of the information content of an individual character and analyse properties of characters that provide the maximum phylogenetic information, particularly, the number of states such a character uses and how the different states have to be distributed among the species or taxa of the phylogenetic tree.

DendroPy: a Python library for phylogenetic computing.

Science.gov (United States)

Sukumaran, Jeet; Holder, Mark T

2010-06-15

DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

Detecting Network Communities: An Application to Phylogenetic Analysis

Science.gov (United States)

Andrade, Roberto F. S.; Rocha-Neto, Ivan C.; Santos, Leonardo B. L.; de Santana, Charles N.; Diniz, Marcelo V. C.; Lobão, Thierry Petit; Goés-Neto, Aristóteles; Pinho, Suani T. R.; El-Hani, Charbel N.

2011-01-01

This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis. PMID:21573202

Topological crystalline superconductivity and second-order topological superconductivity in nodal-loop materials

Science.gov (United States)

Shapourian, Hassan; Wang, Yuxuan; Ryu, Shinsei

2018-03-01

We study the intrinsic fully gapped odd-parity superconducting order in doped nodal-loop materials with a torus-shaped Fermi surface. We show that the mirror symmetry, which protects the nodal loop in the normal state, also protects the superconducting state as a topological crystalline superconductor. As a result, the surfaces preserving the mirror symmetry host gapless Majorana cones. Moreover, for a Weyl-loop system (twofold degenerate at the nodal loop), the surfaces that break the mirror symmetry (those parallel to the bulk nodal loop) contribute a Chern (winding) number to the quasi-two-dimensional system in a slab geometry, which leads to a quantized thermal Hall effect and a single Majorana zero mode bound at a vortex line penetrating the system. This Chern number can be viewed as a higher-order topological invariant, which supports hinge modes in a cubic sample when mirror symmetry is broken. For a Dirac-loop system (fourfold degenerate at the nodal loop), the fully gapped odd-parity state can be either time-reversal symmetry-breaking or symmetric, similar to the A and B phases of 3He. In a slab geometry, the A phase has a Chern number two, while the B phase carries a nontrivial Z2 invariant. We discuss the experimental relevance of our results to nodal-loop materials such as CaAgAs.

Topological inversion for solution of geodesy-constrained geophysical problems

Science.gov (United States)

Saltogianni, Vasso; Stiros, Stathis

2015-04-01

Geodetic data, mostly GPS observations, permit to measure displacements of selected points around activated faults and volcanoes, and on the basis of geophysical models, to model the underlying physical processes. This requires inversion of redundant systems of highly non-linear equations with >3 unknowns; a situation analogous to the adjustment of geodetic networks. However, in geophysical problems inversion cannot be based on conventional least-squares techniques, and is based on numerical inversion techniques (a priori fixing of some variables, optimization in steps with values of two variables each time to be regarded fixed, random search in the vicinity of approximate solutions). Still these techniques lead to solutions trapped in local minima, to correlated estimates and to solutions with poor error control (usually sampling-based approaches). To overcome these problems, a numerical-topological, grid-search based technique in the RN space is proposed (N the number of unknown variables). This technique is in fact a generalization and refinement of techniques used in lighthouse positioning and in some cases of low-accuracy 2-D positioning using Wi-Fi etc. The basic concept is to assume discrete possible ranges of each variable, and from these ranges to define a grid G in the RN space, with some of the gridpoints to approximate the true solutions of the system. Each point of hyper-grid G is then tested whether it satisfies the observations, given their uncertainty level, and successful grid points define a sub-space of G containing the true solutions. The optimal (minimal) space containing one or more solutions is obtained using a trial-and-error approach, and a single optimization factor. From this essentially deterministic identification of the set of gridpoints satisfying the system of equations, at a following step, a stochastic optimal solution is computed corresponding to the center of gravity of this set of gridpoints. This solution corresponds to a

Simulating a topological transition in a superconducting phase qubit by fast adiabatic trajectories

Science.gov (United States)

Wang, Tenghui; Zhang, Zhenxing; Xiang, Liang; Gong, Zhihao; Wu, Jianlan; Yin, Yi

2018-04-01

The significance of topological phases has been widely recognized in the community of condensed matter physics. The well controllable quantum systems provide an artificial platform to probe and engineer various topological phases. The adiabatic trajectory of a quantum state describes the change of the bulk Bloch eigenstates with the momentum, and this adiabatic simulation method is however practically limited due to quantum dissipation. Here we apply the "shortcut to adiabaticity" (STA) protocol to realize fast adiabatic evolutions in the system of a superconducting phase qubit. The resulting fast adiabatic trajectories illustrate the change of the bulk Bloch eigenstates in the Su-Schrieffer-Heeger (SSH) model. A sharp transition is experimentally determined for the topological invariant of a winding number. Our experiment helps identify the topological Chern number of a two-dimensional toy model, suggesting the applicability of the fast adiabatic simulation method for topological systems.

Phylogenetically-informed priorities for amphibian conservation.

Science.gov (United States)

Isaac, Nick J B; Redding, David W; Meredith, Helen M; Safi, Kamran

2012-01-01

The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species' threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list) for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species' phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our 'top 100' list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history.

Phylogenetically-informed priorities for amphibian conservation.

Directory of Open Access Journals (Sweden)

Nick J B Isaac

Full Text Available The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species' threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species' phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our 'top 100' list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history.

Quantum algorithms for topological and geometric analysis of data

Science.gov (United States)

Lloyd, Seth; Garnerone, Silvano; Zanardi, Paolo

2016-01-01

Extracting useful information from large data sets can be a daunting task. Topological methods for analysing data sets provide a powerful technique for extracting such information. Persistent homology is a sophisticated tool for identifying topological features and for determining how such features persist as the data is viewed at different scales. Here we present quantum machine learning algorithms for calculating Betti numbers—the numbers of connected components, holes and voids—in persistent homology, and for finding eigenvectors and eigenvalues of the combinatorial Laplacian. The algorithms provide an exponential speed-up over the best currently known classical algorithms for topological data analysis. PMID:26806491

Non metrizable topologies on Z with countable dual group.

Directory of Open Access Journals (Sweden)

Daniel de la Barrera Mayoral

2017-04-01

Full Text Available In this paper we give two families of non-metrizable topologies on the group of the integers having a countable dual group which is isomorphic to a infinite torsion subgroup of the unit circle in the complex plane. Both families are related to D-sequences, which are sequences of natural numbers such that each term divides the following. The first family consists of locally quasi-convex group topologies. The second consists of complete topologies which are not locally quasi-convex. In order to study the dual groups for both families we need to make numerical considerations of independent interest.

Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)

Science.gov (United States)

Abu Salim, Kamariah; Chase, Mark W.; Dexter, Kyle G.; Pennington, R. Toby; Tan, Sylvester; Kaye, Maria Ellen; Samuel, Rosabelle

2017-01-01

DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses

Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo.

Directory of Open Access Journals (Sweden)

Jacqueline Heckenhauer

Full Text Available DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia. The combined matrix (rbcL + matK comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016, making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI and nearest taxon index (NTI. In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals

Monopole Solutions in Topologically Massive Gauge Theory

International Nuclear Information System (INIS)

Teh, Rosy; Wong, Khai-Ming; Koh, Pin-Wai

2010-01-01

Monopoles in topologically massive SU(2) Yang-Mils-Higgs gauge theory in 2+1 dimensions with a Chern-Simon mass term have been studied by Pisarski some years ago. He argued that there is a monopole solution that is regular everywhere, but found that it does not possess finite action. There were no exact or numerical solutions being presented by him. Hence it is our purpose to further investigate this solution in more detail. We obtained numerical regular solutions that smoothly interpolates between the behavior at small and large distances for different values of Chern-Simon term strength and for several fixed values of Higgs field strength.

Topological social choice

CERN Document Server

1997-01-01

The origins of this volume can be traced back to a conference on "Ethics, Economic and Business" organized by Columbia Busi­ ness School in March of 1993, and held in the splendid facilities of Columbia's Casa Italiana. Preliminary versions of several of the papers were presented at that meeting. In July 1994 the Fields Institute of Mathematical Sciences sponsored a workshop on "Geometry, Topology and Markets": additional papers and more refined versions of the original papers were presented there. They were published in their present versions in Social Choice and Wel­ fare, volume 14, number 2, 1997. The common aim of these workshops and this volume is to crystallize research in an area which has emerged rapidly in the last fifteen years, the area of topological approaches to social choice and the theory of games. The area is attracting increasing interest from social choice theorists, game theorists, mathematical econ­ omists and mathematicians, yet there is no authoritative collection of papers in the a...

Topology with applications topological spaces via near and far

CERN Document Server

Naimpally, Somashekhar A

2013-01-01

The principal aim of this book is to introduce topology and its many applications viewed within a framework that includes a consideration of compactness, completeness, continuity, filters, function spaces, grills, clusters and bunches, hyperspace topologies, initial and final structures, metric spaces, metrization, nets, proximal continuity, proximity spaces, separation axioms, and uniform spaces. This book provides a complete framework for the study of topology with a variety of applications in science and engineering that include camouflage filters, classification, digital image processing, forgery detection, Hausdorff raster spaces, image analysis, microscopy, paleontology, pattern recognition, population dynamics, stem cell biology, topological psychology, and visual merchandising. It is the first complete presentation on topology with applications considered in the context of proximity spaces, and the nearness and remoteness of sets of objects. A novel feature throughout this book is the use of near and...

Topology and slowing down of high energy ion orbits

Energy Technology Data Exchange (ETDEWEB)

Eriksson, L G [Commission of the European Communities, Abingdon (United Kingdom). JET Joint Undertaking; Porcelli, F [Politecnico di Torino, Turin (Italy); Berk, H L [Texas Univ., Austin, TX (United States). Inst. for Fusion Studies

1994-07-01

An analysis of nonstandard guiding centre orbits is presented, which is relevant to MeV ions in a Tokamak. The orbit equation has been simplified from the start, allowing to present an analytic classification of the possible orbits. The topological transitions of the orbits during collisional slowing down are described. In particular, the characteristic equations reveal the existence of a single fixed point in the relevant phase plane, and the presence of a bifurcation curve corresponding to the locus of the pinch orbits. A significant particle inward pinch has been discovered. (authors). 7 figs.

Asymptotically optimal load balancing topologies

NARCIS (Netherlands)

Mukherjee, D.; Borst, S.C.; van Leeuwaarden, J.S.H.

2017-01-01

We consider a system of N servers inter-connected by some underlying graph topology G N . Tasks arrive at the various servers as independent Poisson processes of rate λ . Each incoming task is irrevocably assigned to whichever server has the smallest number of tasks among the one where it appears

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study [version 1; referees: 1 approved, 2 approved with reservations

Directory of Open Access Journals (Sweden)

John A. Lees

2018-03-01

Full Text Available Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes.

Science.gov (United States)

Urantowka, Adam Dawid; Kroczak, Aleksandra; Mackiewicz, Paweł

2017-07-14

Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the 'true' Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots' phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods. Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in

Maximum Parsimony on Phylogenetic networks

Science.gov (United States)

2012-01-01

Background Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past. Results In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores. Conclusion The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are

Topological Quantum Phase Transitions in Two-Dimensional Hexagonal Lattice Bilayers

Science.gov (United States)

Zhai, Xuechao; Jin, Guojun

2013-09-01

Since the successful fabrication of graphene, two-dimensional hexagonal lattice structures have become a research hotspot in condensed matter physics. In this short review, we theoretically focus on discussing the possible realization of a topological insulator (TI) phase in systems of graphene bilayer (GBL) and boron nitride bilayer (BNBL), whose band structures can be experimentally modulated by an interlayer bias voltage. Under the bias, a band gap can be opened in AB-stacked GBL but is still closed in AA-stacked GBL and significantly reduced in AA- or AB-stacked BNBL. In the presence of spin-orbit couplings (SOCs), further demonstrations indicate whether the topological quantum phase transition can be realized strongly depends on the stacking orders and symmetries of structures. It is observed that a bulk band gap can be first closed and then reopened when the Rashba SOC increases for gated AB-stacked GBL or when the intrinsic SOC increases for gated AA-stacked BNBL. This gives a distinct signal for a topological quantum phase transition, which is further characterized by a jump of the ℤ2 topological invariant. At fixed SOCs, the TI phase can be well switched by the interlayer bias and the phase boundaries are precisely determined. For AA-stacked GBL and AB-stacked BNBL, no strong TI phase exists, regardless of the strength of the intrinsic or Rashba SOCs. At last, a brief overview is given on other two-dimensional hexagonal materials including silicene and molybdenum disulfide bilayers.

Quantum computation with topological codes from qubit to topological fault-tolerance

CERN Document Server

Fujii, Keisuke

2015-01-01

This book presents a self-consistent review of quantum computation with topological quantum codes. The book covers everything required to understand topological fault-tolerant quantum computation, ranging from the definition of the surface code to topological quantum error correction and topological fault-tolerant operations. The underlying basic concepts and powerful tools, such as universal quantum computation, quantum algorithms, stabilizer formalism, and measurement-based quantum computation, are also introduced in a self-consistent way. The interdisciplinary fields between quantum information and other fields of physics such as condensed matter physics and statistical physics are also explored in terms of the topological quantum codes. This book thus provides the first comprehensive description of the whole picture of topological quantum codes and quantum computation with them.

Topological BF field theory description of topological insulators

International Nuclear Information System (INIS)

Cho, Gil Young; Moore, Joel E.

2011-01-01

Research highlights: → We show that a BF theory is the effective theory of 2D and 3D topological insulators. → The non-gauge-invariance of the bulk theory yields surface terms for a bosonized Dirac fermion. → The 'axion' term in electromagnetism is correctly obtained from gapped surfaces. → Generalizations to possible fractional phases are discussed in closing. - Abstract: Topological phases of matter are described universally by topological field theories in the same way that symmetry-breaking phases of matter are described by Landau-Ginzburg field theories. We propose that topological insulators in two and three dimensions are described by a version of abelian BF theory. For the two-dimensional topological insulator or quantum spin Hall state, this description is essentially equivalent to a pair of Chern-Simons theories, consistent with the realization of this phase as paired integer quantum Hall effect states. The BF description can be motivated from the local excitations produced when a π flux is threaded through this state. For the three-dimensional topological insulator, the BF description is less obvious but quite versatile: it contains a gapless surface Dirac fermion when time-reversal-symmetry is preserved and yields 'axion electrodynamics', i.e., an electromagnetic E . B term, when time-reversal symmetry is broken and the surfaces are gapped. Just as changing the coefficients and charges of 2D Chern-Simons theory allows one to obtain fractional quantum Hall states starting from integer states, BF theory could also describe (at a macroscopic level) fractional 3D topological insulators with fractional statistics of point-like and line-like objects.

Topology and statistics in zero dimensions

International Nuclear Information System (INIS)

Aneziris, Charilaos.

1992-05-01

It has been suggested that space-time may be intrinsically not continuous, but discrete. Here we review some topological notions of discrete manifolds, in particular ones made out of final number of points, and discuss the possibilties for statistics in such spaces. (author)

TOPOLOGY OF RANDOM POINTS YOGESHWARAN. D.

Indian Academy of Sciences (India)

Balls grow at unit rate centred at the points of the point cloud/ process. ... Idea of persistence : Keep track of births and deaths of topological features. ..... holes, Betti numbers, etc., one will be more interested in the distribution of such objects on ...

Macroevolution of life-history traits in passerine birds: adaptation and phylogenetic inertia.

Science.gov (United States)

Pienaar, Jason; Ilany, Amiyaal; Geffen, Eli; Yom-Tov, Yoram

2013-05-01

We used a recent passerine phylogeny and comparative method to evaluate the macroevolution of body and egg mass, incubation and fledging periods, time to independence and time with parents of the main passerine lineages. We hypothesised that passerine reproductive traits are affected by adaptation to both past and present environmental factors and phenotypic attributes such as body mass. Our results suggest that the evolution of body and egg mass, time to independence, incubation and fledging times are affected by strong phylogenetic inertia and that these breeding traits are all affected by body mass. Time with parents, where major lineages exhibit their own fixed optima and body mass does not have an effect, and clutch size which is affected by body mass and additionally by climate regimes, do not exhibit any phylogenetic inertia. © 2013 Blackwell Publishing Ltd/CNRS.

Barcoding and Phylogenetic Inferences in Nine Mugilid Species (Pisces, Mugiliformes

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Neonila Polyakova

2013-10-01

Full Text Available Accurate identification of fish and fish products, from eggs to adults, is important in many areas. Grey mullets of the family Mugilidae are distributed worldwide and inhabit marine, estuarine, and freshwater environments in all tropical and temperate regions. Various Mugilid species are commercially important species in fishery and aquaculture of many countries. For the present study we have chosen two Mugilid genes with different phylogenetic signals: relatively variable mitochondrial cytochrome oxidase subunit I (COI and conservative nuclear rhodopsin (RHO. We examined their diversity within and among 9 Mugilid species belonging to 4 genera, many of which have been examined from multiple specimens, with the goal of determining whether DNA barcoding can achieve unambiguous species recognition of Mugilid species. The data obtained showed that information based on COI sequences was diagnostic not only for species-level identification but also for recognition of intraspecific units, e.g., allopatric populations of circumtropical Mugil cephalus, or even native and acclimatized specimens of Chelon haematocheila. All RHO sequences appeared strictly species specific. Based on the data obtained, we conclude that COI, as well as RHO sequencing can be used to unambiguously identify fish species. Topologies of phylogeny based on RHO and COI sequences coincided with each other, while together they had a good phylogenetic signal.

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace

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Mao Li

2018-04-01

Full Text Available Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions, to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.

BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

Science.gov (United States)

Wang, Juan; Guo, Maozu; Xing, Linlin; Che, Kai; Liu, Xiaoyan; Wang, Chunyu

2013-09-15

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/. © 2013 Elsevier B.V. All rights reserved.

A-Soft Separation Axioms in Soft Topological Space

Directory of Open Access Journals (Sweden)

Luay Abd –Al-Hani Al-Sweedi

2018-01-01

Full Text Available The important science tools in a different kinds and  specialties , that considered the basic mainstay of ( the set theory and because of  huge development in all life fields. This causes great problems , that need solution and parallel tools for those developments , so the scientis become responsible to work on the development of number theory and open new horizons , that a new science had appeared  which is  ( soft figures theory which is considered the important tool to solve most difficult problems or overcome them ,in these sciences and their specific life specialization, economy, medicine , geometry and others. Also the theory of soft numbers had entered in general topology in power full and active way. The last years a new science has appeared is (soft topological space.              The main idea of this research is to define the separation axioms in  (soft topological space  and practically in certain point , and to study the most important  properties and results of it .

Topological Nodal Cooper Pairing in Doped Weyl Metals

Science.gov (United States)

Li, Yi; Haldane, F. D. M.

2018-02-01

We generalize the concept of Berry connection of the single-electron band structure to that of a two-particle Cooper pairing state between two Fermi surfaces with opposite Chern numbers. Because of underlying Fermi surface topology, the pairing Berry phase acquires nontrivial monopole structure. Consequently, pairing gap functions have topologically protected nodal structure as vortices in the momentum space with the total vorticity solely determined by the pair monopole charge qp. The nodes of gap function behave as the Weyl-Majorana points of the Bogoliubov-de Gennes pairing Hamiltonian. Their relation with the connection patterns of the surface modes from the Weyl band structure and the Majorana surface modes inside the pairing gap is also discussed. Under the approximation of spherical Fermi surfaces, the pairing symmetry are represented by monopole harmonic functions. The lowest possible pairing channel carries angular momentum number j =|qp|, and the corresponding gap functions are holomorphic or antiholomorphic functions on Fermi surfaces. After projected on the Fermi surfaces with nontrivial topology, all the partial-wave channels of pairing interactions acquire the monopole charge qp independent of concrete pairing mechanism.

Topological Aspects of Information Retrieval.

Science.gov (United States)

Egghe, Leo; Rousseau, Ronald

1998-01-01

Discusses topological aspects of theoretical information retrieval, including retrieval topology; similarity topology; pseudo-metric topology; document spaces as topological spaces; Boolean information retrieval as a subsystem of any topological system; and proofs of theorems. (LRW)

Propagation of optical vortices with fractional topological charge in free space

Science.gov (United States)

Ali, Tamelia; Kreminska, Liubov; Golovin, Andrii B.; Crouse, David T.

2014-10-01

The behavior of the optical vortices with fractional topological charges in the far-field is assessed through numerical modeling and confirmed by experimental results. The generation of fractional topological charge variations of the phase within a Gaussian beam was achieved by using a liquid crystal spatial light modulator (LCoS SLM). It is shown that a laser beam carrying an optical vortex with a fractional topological charge evolves into a beam with a topological charge of integer value, specifically an integer value closer to the fractional number in the far field. A potential application of this work is for data transmission within optical telecommunication systems.

Enumeration of RNA complexes via random matrix theory.

Science.gov (United States)

Andersen, Jørgen E; Chekhov, Leonid O; Penner, Robert C; Reidys, Christian M; Sułkowski, Piotr

2013-04-01

In the present article, we review a derivation of the numbers of RNA complexes of an arbitrary topology. These numbers are encoded in the free energy of the Hermitian matrix model with potential V(x)=x2/2-stx/(1-tx), where s and t are respective generating parameters for the number of RNA molecules and hydrogen bonds in a given complex. The free energies of this matrix model are computed using the so-called topological recursion, which is a powerful new formalism arising from random matrix theory. These numbers of RNA complexes also have profound meaning in mathematics: they provide the number of chord diagrams of fixed genus with specified numbers of backbones and chords as well as the number of cells in Riemann's moduli spaces for bordered surfaces of fixed topological type.

The phylogenetic distribution of extrafloral nectaries in plants.

Science.gov (United States)

Weber, Marjorie G; Keeler, Kathleen H

2013-06-01

Understanding the evolutionary patterns of ecologically relevant traits is a central goal in plant biology. However, for most important traits, we lack the comprehensive understanding of their taxonomic distribution needed to evaluate their evolutionary mode and tempo across the tree of life. Here we evaluate the broad phylogenetic patterns of a common plant-defence trait found across vascular plants: extrafloral nectaries (EFNs), plant glands that secrete nectar and are located outside the flower. EFNs typically defend plants indirectly by attracting invertebrate predators who reduce herbivory. Records of EFNs published over the last 135 years were compiled. After accounting for changes in taxonomy, phylogenetic comparative methods were used to evaluate patterns of EFN evolution, using a phylogeny of over 55 000 species of vascular plants. Using comparisons of parametric and non-parametric models, the true number of species with EFNs likely to exist beyond the current list was estimated. To date, EFNs have been reported in 3941 species representing 745 genera in 108 families, about 1-2 % of vascular plant species and approx. 21 % of families. They are found in 33 of 65 angiosperm orders. Foliar nectaries are known in four of 36 fern families. Extrafloral nectaries are unknown in early angiosperms, magnoliids and gymnosperms. They occur throughout monocotyledons, yet most EFNs are found within eudicots, with the bulk of species with EFNs being rosids. Phylogenetic analyses strongly support the repeated gain and loss of EFNs across plant clades, especially in more derived dicot families, and suggest that EFNs are found in a minimum of 457 independent lineages. However, model selection methods estimate that the number of unreported cases of EFNs may be as high as the number of species already reported. EFNs are widespread and evolutionarily labile traits that have repeatedly evolved a remarkable number of times in vascular plants. Our current understanding of the

Spontaneous breaking of time-reversal symmetry in topological insulators

Energy Technology Data Exchange (ETDEWEB)

Karnaukhov, Igor N., E-mail: karnaui@yahoo.com

2017-06-21

Highlights: • Proposed a new approach for description of phase transitions in topological insulators. • Considered the mechanism of spontaneous breaking of time-reversal symmetry in topological insulators. • The Haldane model can be implemented in real compounds of the condensed matter physics. - Abstract: The system of spinless fermions on a hexagonal lattice is studied. We have considered tight-binding model with the hopping integrals between the nearest-neighbor and next-nearest-neighbor lattice sites, that depend on the direction of the link. The links are divided on three types depending on the direction, the hopping integrals are defined by different phases along the links. The energy of the system depends on the phase differences, the solutions for the phases, that correspond to the minimums of the energy, lead to a topological insulator state with the nontrivial Chern numbers. We have analyzed distinct topological states and phase transitions, the behavior of the chiral gapless edge modes, have defined the Chern numbers. The band structure of topological insulator (TI) is calculated, the ground-state phase diagram in the parameter space is obtained. We propose a novel mechanism of realization of TI, when the TI state is result of spontaneous breaking of time-reversal symmetry due to nontrivial stable solutions for the phases that determine the hopping integrals along the links and show that the Haldane model can be implemented in real compounds of the condensed matter physics.

Modelling low Reynolds number vortex-induced vibration problems with a fixed mesh fluid-solid interaction formulation

Science.gov (United States)

González Cornejo, Felipe A.; Cruchaga, Marcela A.; Celentano, Diego J.

2017-11-01

The present work reports a fluid-rigid solid interaction formulation described within the framework of a fixed-mesh technique. The numerical analysis is focussed on the study of a vortex-induced vibration (VIV) of a circular cylinder at low Reynolds number. The proposed numerical scheme encompasses the fluid dynamics computation in an Eulerian domain where the body is embedded using a collection of markers to describe its shape, and the rigid solid's motion is obtained with the well-known Newton's law. The body's velocity is imposed on the fluid domain through a penalty technique on the embedded fluid-solid interface. The fluid tractions acting on the solid are computed from the fluid dynamic solution of the flow around the body. The resulting forces are considered to solve the solid motion. The numerical code is validated by contrasting the obtained results with those reported in the literature using different approaches for simulating the flow past a fixed circular cylinder as a benchmark problem. Moreover, a mesh convergence analysis is also done providing a satisfactory response. In particular, a VIV problem is analyzed, emphasizing the description of the synchronization phenomenon.

Hannay angle. Yet another symmetry-protected topological order parameter in classical mechanics

International Nuclear Information System (INIS)

Kariyado, Toshikaze; Hatsugai, Yasuhiro

2016-01-01

The topological way of thinking now goes beyond quantum solids, and topological characters of classical mechanical systems obeying Newton's law are attracting current interest. To provide a physical insight into the topological numbers in mechanics, we demonstrate the use of the Hannay angle, a “classical” Berry phase, as a symmetry-protected topological order parameter. The Hannay angle is derived using a canonical transformation that maps Newton's equation to a Schrödinger-type equation, and the condition for the quantization is discussed in connection with the symmetry in mechanics. Also, we demonstrate the use of the Hannay angle for a topological characterization of a spring-mass model focusing on the bulk-edge correspondence. (author)

Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae).

Science.gov (United States)

Davis, Brian W; Li, Gang; Murphy, William J

2010-07-01

The pantherine lineage of cats diverged from the remainder of modern Felidae less than 11 million years ago and consists of the five big cats of the genus Panthera, the lion, tiger, jaguar, leopard, and snow leopard, as well as the closely related clouded leopard. A significant problem exists with respect to the precise phylogeny of these highly threatened great cats. Despite multiple publications on the subject, no two molecular studies have reconstructed Panthera with the same topology. These evolutionary relationships remain unresolved partially due to the recent and rapid radiation of pantherines in the Pliocene, individual speciation events occurring within less than 1 million years, and probable introgression between lineages following their divergence. We provide an alternative, highly supported interpretation of the evolutionary history of the pantherine lineage using novel and published DNA sequence data from the autosomes, both sex chromosomes and the mitochondrial genome. New sequences were generated for 39 single-copy regions of the felid Y chromosome, as well as four mitochondrial and four autosomal gene segments, totaling 28.7 kb. Phylogenetic analysis of these new data, combined with all published data in GenBank, highlighted the prevalence of phylogenetic disparities stemming either from the amplification of a mitochondrial to nuclear translocation event (numt), or errors in species identification. Our 47.6 kb combined dataset was analyzed as a supermatrix and with respect to individual partitions using maximum likelihood and Bayesian phylogenetic inference, in conjunction with Bayesian Estimation of Species Trees (BEST) which accounts for heterogeneous gene histories. Our results yield a robust consensus topology supporting the monophyly of lion and leopard, with jaguar sister to these species, as well as a sister species relationship of tiger and snow leopard. These results highlight new avenues for the study of speciation genomics and

Topological Phases in the Real World

Science.gov (United States)

Hsu, Yi-Ting

enhance the T c of the existing leading candidate Sr2RuO 4 and to propose new material candidates for topological superconductors. First, by carrying out perturbative renormalization group (RG) analysis, we predicted that straining the ruthenate films will maximize the T c for triplet pairing channel when the Fermi surface is close to van Hove singularities without tuning on to the singularity. Then with a similar RG approach and a self-consistent calculation for the gap equations, we investigated the repulsion-mediated intrinsic and proximity-induced superconductivity in a family of lightly hole-doped noncentrosymmetric semiconductors, monolayer transition metal dichalcogenides (TMDs). We found that thanks to the spin-valley locking in lightly hole-doped TMDs, two distinct topological pairing states are favored for the intrinsically superconducting case: an interpocket paired state with Chern number 2 and an intrapocket paired state with finite pair momentum. Moreover, nematic odd-parity pairing with a possibly high Tc can be induced when proximitized by a cuprate. A confirmation of our predictions will open up possibilities for manipulating unconventional and topological superconductivity at a higher temperature on the device-friendly platform of strained ruthenate films and monolayer TMDs. In the second part, I will discuss our studies on the stability of the Dirac surface states in 3D TIs in the presence of bulk states and in TI-ferromagnetic metal heterostructures. We constructed simple microscopic models with Fano-type couplings between localized and extended states for each situation. Then with ab initio calculations we investigated the fate of the Dirac surface states in terms of the spectrum, the spatial profile and the spin-texture. Based on our results, we proposed explanations for existing experimental spectroscopic and spin-torque results.

Exploring the relationship between sequence similarity and accurate phylogenetic trees.

Science.gov (United States)

Cantarel, Brandi L; Morrison, Hilary G; Pearson, William

2006-11-01

We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein families were evolved over a range of 100-400 point accepted mutations; at these distances 63% of the families shared significant sequence similarity. Protein families were evolved using balanced and unbalanced trees, with ancient or recent radiations. In families sharing statistically significant similarity, about 60% of multiple sequence alignments were 95% identical to true alignments. To compare recovered topologies with true topologies, we used a score that reflects the fraction of clades that were correctly clustered. As expected, the accuracy of the phylogenies was greatest in the least divergent families. About 88% of phylogenies clustered over 80% of clades in families that shared significant sequence similarity, using Bayesian, parsimony, distance, and maximum likelihood methods. However, for protein families with short ancient branches (ancient radiation), only 30% of the most divergent (but statistically significant) families produced accurate phylogenies, and only about 70% of the second most highly conserved families, with median expectation values better than 10(-60), produced accurate trees. These values represent upper bounds on expected tree accuracy for sequences with a simple divergence history; proteins from 700 Giardia families, with a similar range of sequence similarities but considerably more gaps, produced much less accurate trees. For our simulated insertions and deletions, correct multiple sequence alignments did not perform much better than those produced by T-COFFEE, and including sequences with expressed sequence tag-like sequencing errors did not

Topology and Edge Modes in Quantum Critical Chains

Science.gov (United States)

Verresen, Ruben; Jones, Nick G.; Pollmann, Frank

2018-02-01

We show that topology can protect exponentially localized, zero energy edge modes at critical points between one-dimensional symmetry-protected topological phases. This is possible even without gapped degrees of freedom in the bulk—in contrast to recent work on edge modes in gapless chains. We present an intuitive picture for the existence of these edge modes in the case of noninteracting spinless fermions with time-reversal symmetry (BDI class of the tenfold way). The stability of this phenomenon relies on a topological invariant defined in terms of a complex function, counting its zeros and poles inside the unit circle. This invariant can prevent two models described by the same conformal field theory (CFT) from being smoothly connected. A full classification of critical phases in the noninteracting BDI class is obtained: Each phase is labeled by the central charge of the CFT, c ∈1/2 N , and the topological invariant, ω ∈Z . Moreover, c is determined by the difference in the number of edge modes between the phases neighboring the transition. Numerical simulations show that the topological edge modes of critical chains can be stable in the presence of interactions and disorder.

Quantum states with topological properties via dipolar interactions

Energy Technology Data Exchange (ETDEWEB)

Peter, David

2015-06-25

This thesis proposes conceptually new ways to realize materials with topological properties by using dipole-dipole interactions. First, we study a system of ultracold dipolar fermions, where the relaxation mechanism of dipolar spins can be used to reach the quantum Hall regime. Second, in a system of polar molecules in an optical lattice, dipole-dipole interactions induce spin-orbit coupling terms for the rotational excitations. In combination with time-reversal symmetry breaking this leads to topological bands with Chern numbers greater than one.

Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata).

Science.gov (United States)

Weisrock, David W; Macey, J Robert; Matsui, Masafumi; Mulcahy, Daniel G; Papenfuss, Theodore J

2013-01-01

The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylogenetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S-16S region (the 3' end of 12S rRNA, tRNA(VAI), and the 5' end of 16S rRNA), and a ND2-COI region (ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), the origin for light strand replication--O(L), tRNA(Cys), tRNAT(Tyr), and the 5' end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phylogenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger

Topological mirror superconductivity.

Science.gov (United States)

Zhang, Fan; Kane, C L; Mele, E J

2013-08-02

We demonstrate the existence of topological superconductors (SCs) protected by mirror and time-reversal symmetries. D-dimensional (D=1, 2, 3) crystalline SCs are characterized by 2(D-1) independent integer topological invariants, which take the form of mirror Berry phases. These invariants determine the distribution of Majorana modes on a mirror symmetric boundary. The parity of total mirror Berry phase is the Z(2) index of a class DIII SC, implying that a DIII topological SC with a mirror line must also be a topological mirror SC but not vice versa and that a DIII SC with a mirror plane is always time-reversal trivial but can be mirror topological. We introduce representative models and suggest experimental signatures in feasible systems. Advances in quantum computing, the case for nodal SCs, the case for class D, and topological SCs protected by rotational symmetries are pointed out.

Interactive Topology Optimization

DEFF Research Database (Denmark)

Nobel-Jørgensen, Morten

Interactivity is the continuous interaction between the user and the application to solve a task. Topology optimization is the optimization of structures in order to improve stiffness or other objectives. The goal of the thesis is to explore how topology optimization can be used in applications...... on theory of from human-computer interaction which is described in Chapter 2. Followed by a description of the foundations of topology optimization in Chapter 3. Our applications for topology optimization in 2D and 3D are described in Chapter 4 and a game which trains the human intuition of topology...... optimization is presented in Chapter 5. Topology optimization can also be used as an interactive modeling tool with local control which is presented in Chapter 6. Finally, Chapter 7 contains a summary of the findings and concludes the dissertation. Most of the presented applications of the thesis are available...

Short segment search method for phylogenetic analysis using nested sliding windows

Science.gov (United States)

Iskandar, A. A.; Bustamam, A.; Trimarsanto, H.

2017-10-01

To analyze phylogenetics in Bioinformatics, coding DNA sequences (CDS) segment is needed for maximal accuracy. However, analysis by CDS cost a lot of time and money, so a short representative segment by CDS, which is envelope protein segment or non-structural 3 (NS3) segment is necessary. After sliding window is implemented, a better short segment than envelope protein segment and NS3 is found. This paper will discuss a mathematical method to analyze sequences using nested sliding window to find a short segment which is representative for the whole genome. The result shows that our method can find a short segment which more representative about 6.57% in topological view to CDS segment than an Envelope segment or NS3 segment.

Common fixed point theorems for fuzzy mappings in metric space under φ-contraction condition

International Nuclear Information System (INIS)

Abu-Donia, H.M.

2007-01-01

Some common fixed point theorems for multi-valued mappings under φ-contraction condition have been studied by Rashwan [Rashwan RA, Ahmed MA. Fixed points for φ-contraction type multivalued mappings. J Indian Acad Math 1995;17(2):194-204]. Butnariu [Butnariu D. Fixed point for fuzzy mapping. Fuzzy Sets Syst 1982;7:191-207] and Helipern [Hilpern S. Fuzzy mapping and fixed point theorem. J Math Anal Appl 1981;83:566-9] also, discussed some fixed point theorems for fuzzy mappings in the category of metric spaces. In this paper, we discussed some common fixed point theorems for fuzzy mappings in metric space under φ-contraction condition. Our investigation are related to the fuzzy form of Hausdorff metric which is a basic tool for computing Hausdorff dimensions. These dimensions help in understanding ε ∞ -space [El-Naschie MS. On the unification of the fundamental forces and complex time in the ε ∞ -space. Chaos, Solitons and Fractals 2000;11:1149-62] and are used in high energy physics [El-Naschie MS. Wild topology hyperbolic geometry and fusion algebra of high energy particle physics. Chaos, Solitons and Fractals 2002;13:1935-45

Common fixed point theorems for fuzzy mappings in metric space under {phi}-contraction condition

Energy Technology Data Exchange (ETDEWEB)

Abu-Donia, H.M. [Department of Mathematics, Faculty of Science, Zagazig University, Zagazig (Egypt)

2007-10-15

Some common fixed point theorems for multi-valued mappings under {phi}-contraction condition have been studied by Rashwan [Rashwan RA, Ahmed MA. Fixed points for {phi}-contraction type multivalued mappings. J Indian Acad Math 1995;17(2):194-204]. Butnariu [Butnariu D. Fixed point for fuzzy mapping. Fuzzy Sets Syst 1982;7:191-207] and Helipern [Hilpern S. Fuzzy mapping and fixed point theorem. J Math Anal Appl 1981;83:566-9] also, discussed some fixed point theorems for fuzzy mappings in the category of metric spaces. In this paper, we discussed some common fixed point theorems for fuzzy mappings in metric space under {phi}-contraction condition. Our investigation are related to the fuzzy form of Hausdorff metric which is a basic tool for computing Hausdorff dimensions. These dimensions help in understanding {epsilon} {sup {infinity}}-space [El-Naschie MS. On the unification of the fundamental forces and complex time in the {epsilon} {sup {infinity}}-space. Chaos, Solitons and Fractals 2000;11:1149-62] and are used in high energy physics [El-Naschie MS. Wild topology hyperbolic geometry and fusion algebra of high energy particle physics. Chaos, Solitons and Fractals 2002;13:1935-45].