Dual simulation of the massless lattice Schwinger model with topological term and non-zero chemical potential

NASA Astrophysics Data System (ADS)

Göschl, Daniel

2018-03-01

We discuss simulation strategies for the massless lattice Schwinger model with a topological term and finite chemical potential. The simulation is done in a dual representation where the complex action problem is solved and the partition function is a sum over fermion loops, fermion dimers and plaquette-occupation numbers. We explore strategies to update the fermion loops coupled to the gauge degrees of freedom and check our results with conventional simulations (without topological term and at zero chemical potential), as well as with exact summation on small volumes. Some physical implications of the results are discussed.

The Vertex on a Strip

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashani-Poor, A.

2004-11-03

We demonstrate that for a broad class of local Calabi-Yau geometries built around a string of IP{sup 1}s--those whose toric diagrams are given by triangulations of a strip--we can derive simple rules, based on the topological vertex, for obtaining expressions for the topological string partition function in which the sums over Young tableaux have been performed. By allowing non-trivial tableaux on the external legs of the corresponding web diagrams, these strips can be used as building blocks for more general geometries. As applications of our result, we study the behavior of topological string amplitudes under flops, as well as checkmore » Nekrasov's conjecture in its most general form.« less

Elliptic CY3folds and non-perturbative modular transformation

NASA Astrophysics Data System (ADS)

Iqbal, Amer; Shabbir, Khurram

2016-03-01

We study the refined topological string partition function of a class of toric elliptically fibered Calabi-Yau threefolds. These Calabi-Yau threefolds give rise to five dimensional quiver gauge theories and are dual to configurations of M5-M2-branes. We determine the Gopakumar-Vafa invariants for these threefolds and show that the genus g free energy is given by the weight 2 g Eisenstein series. We also show that although the free energy at all genera are modular invariant, the full partition function satisfies the non-perturbative modular transformation property discussed by Lockhart and Vafa in arXiv:1210.5909 and therefore the modularity of free energy is up to non-perturbative corrections.

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

PubMed

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.

Automation of Space Station module power management and distribution system

NASA Technical Reports Server (NTRS)

Bechtel, Robert; Weeks, Dave; Walls, Bryan

1990-01-01

Viewgraphs on automation of space station module (SSM) power management and distribution (PMAD) system are presented. Topics covered include: reasons for power system automation; SSM/PMAD approach to automation; SSM/PMAD test bed; SSM/PMAD topology; functional partitioning; SSM/PMAD control; rack level autonomy; FRAMES AI system; and future technology needs for power system automation.

Donaldson-Witten theory and indefinite theta functions

NASA Astrophysics Data System (ADS)

Korpas, Georgios; Manschot, Jan

2017-11-01

We consider partition functions with insertions of surface operators of topologically twisted N=2 , SU(2) supersymmetric Yang-Mills theory, or Donaldson-Witten theory for short, on a four-manifold. If the metric of the compact four-manifold has positive scalar curvature, Moore and Witten have shown that the partition function is completely determined by the integral over the Coulomb branch parameter a, while more generally the Coulomb branch integral captures the wall-crossing behavior of both Donaldson polynomials and Seiberg-Witten invariants. We show that after addition of a \\overlineQ -exact surface operator to the Moore-Witten integrand, the integrand can be written as a total derivative to the anti-holomorphic coordinate ā using Zwegers' indefinite theta functions. In this way, we reproduce Göttsche's expressions for Donaldson invariants of rational surfaces in terms of indefinite theta functions for any choice of metric.

ABJM Wilson loops in arbitrary representations

NASA Astrophysics Data System (ADS)

Hatsuda, Yasuyuki; Honda, Masazumi; Moriyama, Sanefumi; Okuyama, Kazumi

2013-10-01

We study vacuum expectation values (VEVs) of circular half BPS Wilson loops in arbitrary representations in ABJM theory. We find that those in hook representations are reduced to elementary integrations thanks to the Fermi gas formalism, which are accessible from the numerical studies similar to the partition function in the previous studies. For non-hook representations, we show that the VEVs in the grand canonical formalism can be exactly expressed as determinants of those in the hook representations. Using these facts, we can study the instanton effects of the VEVs in various representations. Our results are consistent with the worldsheet instanton effects studied from the topological string and a prescription to include the membrane instanton effects by shifting the chemical potential, which has been successful for the partition function.

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference

PubMed Central

Minh, Bui Quang; von Haeseler, Arndt

2015-01-01

Abstract 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. PMID:26448206

Topological structures in the equities market network

PubMed Central

Leibon, Gregory; Pauls, Scott; Rockmore, Daniel; Savell, Robert

2008-01-01

We present a new method for articulating scale-dependent topological descriptions of the network structure inherent in many complex systems. The technique is based on “partition decoupled null models,” a new class of null models that incorporate the interaction of clustered partitions into a random model and generalize the Gaussian ensemble. As an application, we analyze a correlation matrix derived from 4 years of close prices of equities in the New York Stock Exchange (NYSE) and National Association of Securities Dealers Automated Quotation (NASDAQ). In this example, we expose (i) a natural structure composed of 2 interacting partitions of the market that both agrees with and generalizes standard notions of scale (e.g., sector and industry) and (ii) structure in the first partition that is a topological manifestation of a well-known pattern of capital flow called “sector rotation.” Our approach gives rise to a natural form of multiresolution analysis of the underlying time series that naturally decomposes the basic data in terms of the effects of the different scales at which it clusters. We support our conclusions and show the robustness of the technique with a successful analysis on a simulated network with an embedded topological structure. The equities market is a prototypical complex system, and we expect that our approach will be of use in understanding a broad class of complex systems in which correlation structures are resident.

Aggregation models on hypergraphs

NASA Astrophysics Data System (ADS)

Alberici, Diego; Contucci, Pierluigi; Mingione, Emanuele; Molari, Marco

2017-01-01

Following a newly introduced approach by Rasetti and Merelli we investigate the possibility to extract topological information about the space where interacting systems are modelled. From the statistical datum of their observable quantities, like the correlation functions, we show how to reconstruct the activities of their constitutive parts which embed the topological information. The procedure is implemented on a class of polymer models on hypergraphs with hard-core interactions. We show that the model fulfils a set of iterative relations for the partition function that generalise those introduced by Heilmann and Lieb for the monomer-dimer case. After translating those relations into structural identities for the correlation functions we use them to test the precision and the robustness of the inverse problem. Finally the possible presence of a further interaction of peer-to-peer type is considered and a criterion to discover it is identified.

Topologically Diverse Human Membrane Proteins Partition to Liquid-Disordered Domains in Phase-Separated Lipid Vesicles.

PubMed

Schlebach, Jonathan P; Barrett, Paul J; Day, Charles A; Kim, Ji Hun; Kenworthy, Anne K; Sanders, Charles R

2016-02-23

The integration of membrane proteins into "lipid raft" membrane domains influences many biochemical processes. The intrinsic structural properties of membrane proteins are thought to mediate their partitioning between membrane domains. However, whether membrane topology influences the targeting of proteins to rafts remains unclear. To address this question, we examined the domain preference of three putative raft-associated membrane proteins with widely different topologies: human caveolin-3, C99 (the 99 residue C-terminal domain of the amyloid precursor protein), and peripheral myelin protein 22. We find that each of these proteins are excluded from the ordered domains of giant unilamellar vesicles containing coexisting liquid-ordered and liquid-disordered phases. Thus, the intrinsic structural properties of these three topologically distinct disease-linked proteins are insufficient to confer affinity for synthetic raft-like domains.

Topology driven modeling: the IS metaphor.

PubMed

Merelli, Emanuela; Pettini, Marco; Rasetti, Mario

In order to define a new method for analyzing the immune system within the realm of Big Data, we bear on the metaphor provided by an extension of Parisi's model, based on a mean field approach. The novelty is the multilinearity of the couplings in the configurational variables. This peculiarity allows us to compare the partition function [Formula: see text] with a particular functor of topological field theory-the generating function of the Betti numbers of the state manifold of the system-which contains the same global information of the system configurations and of the data set representing them. The comparison between the Betti numbers of the model and the real Betti numbers obtained from the topological analysis of phenomenological data, is expected to discover hidden n-ary relations among idiotypes and anti-idiotypes. The data topological analysis will select global features, reducible neither to a mere subgraph nor to a metric or vector space. How the immune system reacts, how it evolves, how it responds to stimuli is the result of an interaction that took place among many entities constrained in specific configurations which are relational. Within this metaphor, the proposed method turns out to be a global topological application of the S[B] paradigm for modeling complex systems.

Classification of topological insulators and superconductors in three spatial dimensions

NASA Astrophysics Data System (ADS)

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

2008-11-01

We systematically study topological phases of insulators and superconductors (or superfluids) in three spatial dimensions. We find that there exist three-dimensional (3D) topologically nontrivial insulators or superconductors in five out of ten symmetry classes introduced in seminal work by Altland and Zirnbauer within the context of random matrix theory, more than a decade ago. One of these is the recently introduced Z2 topological insulator in the symplectic (or spin-orbit) symmetry class. We show that there exist precisely four more topological insulators. For these systems, all of which are time-reversal invariant in three dimensions, the space of insulating ground states satisfying certain discrete symmetry properties is partitioned into topological sectors that are separated by quantum phase transitions. Three of the above five topologically nontrivial phases can be realized as time-reversal invariant superconductors. In these the different topological sectors are characterized by an integer winding number defined in momentum space. When such 3D topological insulators are terminated by a two-dimensional surface, they support a number (which may be an arbitrary nonvanishing even number for singlet pairing) of Dirac fermion (Majorana fermion when spin-rotation symmetry is completely broken) surface modes which remain gapless under arbitrary perturbations of the Hamiltonian that preserve the characteristic discrete symmetries, including disorder. In particular, these surface modes completely evade Anderson localization from random impurities. These topological phases can be thought of as three-dimensional analogs of well-known paired topological phases in two spatial dimensions such as the spinless chiral (px±ipy) -wave superconductor (or Moore-Read Pfaffian state). In the corresponding topologically nontrivial (analogous to “weak pairing”) and topologically trivial (analogous to “strong pairing”) 3D phases, the wave functions exhibit markedly distinct behavior. When an electromagnetic U(1) gauge field and fluctuations of the gap functions are included in the dynamics, the superconducting phases with nonvanishing winding number possess nontrivial topological ground-state degeneracies.

Aggregation models on hypergraphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alberici, Diego, E-mail: diego.alberici2@unibo.it; Contucci, Pierluigi, E-mail: pierluigi.contucci@unibo.it; Mingione, Emanuele, E-mail: emanuele.mingione2@unibo.it

2017-01-15

Following a newly introduced approach by Rasetti and Merelli we investigate the possibility to extract topological information about the space where interacting systems are modelled. From the statistical datum of their observable quantities, like the correlation functions, we show how to reconstruct the activities of their constitutive parts which embed the topological information. The procedure is implemented on a class of polymer models on hypergraphs with hard-core interactions. We show that the model fulfils a set of iterative relations for the partition function that generalise those introduced by Heilmann and Lieb for the monomer–dimer case. After translating those relations intomore » structural identities for the correlation functions we use them to test the precision and the robustness of the inverse problem. Finally the possible presence of a further interaction of peer-to-peer type is considered and a criterion to discover it is identified.« less

Non-perturbative effects and wall-crossing from topological strings

NASA Astrophysics Data System (ADS)

Collinucci, Andrés; Soler, Pablo; Uranga, Angel M.

2009-11-01

We argue that the Gopakumar-Vafa interpretation of the topological string partition function can be used to compute and resum certain non-perturbative brane instanton effects of type II CY compactifications. In particular the topological string A-model encodes the non-perturbative corrections to the hypermultiplet moduli space metric from general D1/D(-1)-brane instantons in 4d Script N = 2 IIB models. We also discuss the reduction to 4d Script N = 1 by fluxes and/or orientifolds and/or D-branes, and the prospects to resum brane instanton contributions to non-perturbative superpotentials. We argue that the connection between non-perturbative effects and the topological string underlies the continuity of non-perturbative effects across lines of BPS stability. We also confirm this statement in mirror B-model matrix model examples, relating matrix model instantons to non-perturbative D-brane instantons. The computation of non-perturbative effects from the topological string requires a 3d circle compactification and T-duality, relating effects from particles and instantons, reminiscent of that involved in the physical derivation of the Kontsevich-Soibelmann wall-crossing formula.

A universal counting of black hole microstates in AdS4

NASA Astrophysics Data System (ADS)

Azzurli, Francesco; Bobev, Nikolay; Crichigno, P. Marcos; Min, Vincent S.; Zaffaroni, Alberto

2018-02-01

Many three-dimensional N=2 SCFTs admit a universal partial topological twist when placed on hyperbolic Riemann surfaces. We exploit this fact to derive a universal formula which relates the planar limit of the topologically twisted index of these SCFTs and their three-sphere partition function. We then utilize this to account for the entropy of a large class of supersymmetric asymptotically AdS4 magnetically charged black holes in M-theory and massive type IIA string theory. In this context we also discuss novel AdS2 solutions of eleven-dimensional supergravity which describe the near horizon region of large new families of supersymmetric black holes arising from M2-branes wrapping Riemann surfaces.

Multi-scale modularity and motif distributional effect in metabolic networks.

PubMed

Gao, Shang; Chen, Alan; Rahmani, Ali; Zeng, Jia; Tan, Mehmet; Alhajj, Reda; Rokne, Jon; Demetrick, Douglas; Wei, Xiaohui

2016-01-01

Metabolism is a set of fundamental processes that play important roles in a plethora of biological and medical contexts. It is understood that the topological information of reconstructed metabolic networks, such as modular organization, has crucial implications on biological functions. Recent interpretations of modularity in network settings provide a view of multiple network partitions induced by different resolution parameters. Here we ask the question: How do multiple network partitions affect the organization of metabolic networks? Since network motifs are often interpreted as the super families of evolved units, we further investigate their impact under multiple network partitions and investigate how the distribution of network motifs influences the organization of metabolic networks. We studied Homo sapiens, Saccharomyces cerevisiae and Escherichia coli metabolic networks; we analyzed the relationship between different community structures and motif distribution patterns. Further, we quantified the degree to which motifs participate in the modular organization of metabolic networks.

Estimating Bayesian Phylogenetic Information Content

PubMed Central

Lewis, Paul O.; Chen, Ming-Hui; Kuo, Lynn; Lewis, Louise A.; Fučíková, Karolina; Neupane, Suman; Wang, Yu-Bo; Shi, Daoyuan

2016-01-01

Measuring the phylogenetic information content of data has a long history in systematics. Here we explore a Bayesian approach to information content estimation. The entropy of the posterior distribution compared with the entropy of the prior distribution provides a natural way to measure information content. If the data have no information relevant to ranking tree topologies beyond the information supplied by the prior, the posterior and prior will be identical. Information in data discourages consideration of some hypotheses allowed by the prior, resulting in a posterior distribution that is more concentrated (has lower entropy) than the prior. We focus on measuring information about tree topology using marginal posterior distributions of tree topologies. We show that both the accuracy and the computational efficiency of topological information content estimation improve with use of the conditional clade distribution, which also allows topological information content to be partitioned by clade. We explore two important applications of our method: providing a compelling definition of saturation and detecting conflict among data partitions that can negatively affect analyses of concatenated data. [Bayesian; concatenation; conditional clade distribution; entropy; information; phylogenetics; saturation.] PMID:27155008

ESTimating plant phylogeny: lessons from partitioning

PubMed Central

de la Torre, Jose EB; Egan, Mary G; Katari, Manpreet S; Brenner, Eric D; Stevenson, Dennis W; Coruzzi, Gloria M; DeSalle, Rob

2006-01-01

Background While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. Results A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. Conclusion Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products. PMID:16776834

Minimal gravity and Frobenius manifolds: bulk correlation on sphere and disk

NASA Astrophysics Data System (ADS)

Aleshkin, Konstantin; Belavin, Vladimir; Rim, Chaiho

2017-11-01

There are two alternative approaches to the minimal gravity — direct Liouville approach and matrix models. Recently there has been a certain progress in the matrix model approach, growing out of presence of a Frobenius manifold (FM) structure embedded in the theory. The previous studies were mainly focused on the spherical topology. Essentially, it was shown that the action principle of Douglas equation allows to define the free energy and to compute the correlation numbers if the resonance transformations are properly incorporated. The FM structure allows to find the explicit form of the resonance transformation as well as the closed expression for the partition function. In this paper we elaborate on the case of gravitating disk. We focus on the bulk correlators and show that in the similar way as in the closed topology the generating function can be formulated using the set of flat coordinates on the corresponding FM. Moreover, the resonance transformations, which follow from the spherical topology consideration, are exactly those needed to reproduce FZZ result of the Liouville gravity approach.

RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology

PubMed Central

Elmetwaly, Shereef; Schlick, Tamar

2014-01-01

Graph representations have been widely used to analyze and design various economic, social, military, political, and biological networks. In systems biology, networks of cells and organs are useful for understanding disease and medical treatments and, in structural biology, structures of molecules can be described, including RNA structures. In our RNA-As-Graphs (RAG) framework, we represent RNA structures as tree graphs by translating unpaired regions into vertices and helices into edges. Here we explore the modularity of RNA structures by applying graph partitioning known in graph theory to divide an RNA graph into subgraphs. To our knowledge, this is the first application of graph partitioning to biology, and the results suggest a systematic approach for modular design in general. The graph partitioning algorithms utilize mathematical properties of the Laplacian eigenvector (µ2) corresponding to the second eigenvalues (λ2) associated with the topology matrix defining the graph: λ2 describes the overall topology, and the sum of µ2′s components is zero. The three types of algorithms, termed median, sign, and gap cuts, divide a graph by determining nodes of cut by median, zero, and largest gap of µ2′s components, respectively. We apply these algorithms to 45 graphs corresponding to all solved RNA structures up through 11 vertices (∼220 nucleotides). While we observe that the median cut divides a graph into two similar-sized subgraphs, the sign and gap cuts partition a graph into two topologically-distinct subgraphs. We find that the gap cut produces the best biologically-relevant partitioning for RNA because it divides RNAs at less stable connections while maintaining junctions intact. The iterative gap cuts suggest basic modules and assembly protocols to design large RNA structures. Our graph substructuring thus suggests a systematic approach to explore the modularity of biological networks. In our applications to RNA structures, subgraphs also suggest design strategies for novel RNA motifs. PMID:25188578

Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution.

PubMed

Galupa, Rafael; Heard, Edith

2018-04-23

The packaging of genetic material into chromatin and chromosomes has been recognized for more than a century, thanks to microscopy and biochemical approaches. This was followed by the progressive realization that chromatin organization is critical for genome functions such as transcription and DNA replication and repair. The recent discovery that chromosomes are partitioned at the submegabase scale into topologically associating domains (TADs) has implications for our understanding of gene regulation during developmental processes such as X-chromosome inactivation, as well as for evolution and for the search for disease-associated loci. Here we discuss our current knowledge about this recently recognized level of mammalian chromosome organization, with a special emphasis on the potential role of TADs as a structural basis for the function and evolution of mammalian regulatory landscapes. © 2017 Galupa and Heard; Published by Cold Spring Harbor Laboratory Press.

Field-theory representation of gauge-gravity symmetry-protected topological invariants, group cohomology, and beyond.

PubMed

Wang, Juven C; Gu, Zheng-Cheng; Wen, Xiao-Gang

2015-01-23

The challenge of identifying symmetry-protected topological states (SPTs) is due to their lack of symmetry-breaking order parameters and intrinsic topological orders. For this reason, it is impossible to formulate SPTs under Ginzburg-Landau theory or probe SPTs via fractionalized bulk excitations and topology-dependent ground state degeneracy. However, the partition functions from path integrals with various symmetry twists are universal SPT invariants, fully characterizing SPTs. In this work, we use gauge fields to represent those symmetry twists in closed spacetimes of any dimensionality and arbitrary topology. This allows us to express the SPT invariants in terms of continuum field theory. We show that SPT invariants of pure gauge actions describe the SPTs predicted by group cohomology, while the mixed gauge-gravity actions describe the beyond-group-cohomology SPTs. We find new examples of mixed gauge-gravity actions for U(1) SPTs in (4+1)D via the gravitational Chern-Simons term. Field theory representations of SPT invariants not only serve as tools for classifying SPTs, but also guide us in designing physical probes for them. In addition, our field theory representations are independently powerful for studying group cohomology within the mathematical context.

Multiflavor string-net models

NASA Astrophysics Data System (ADS)

Lin, Chien-Hung

2017-05-01

We generalize the string-net construction to multiple flavors of strings, each of which is labeled by the elements of an Abelian group Gi. The same flavor of strings can branch, while different flavors of strings can cross one another and thus they form intersecting string nets. We systematically construct the exactly soluble lattice Hamiltonians and the ground-state wave functions for the intersecting string-net condensed phases. We analyze the braiding statistics of the low-energy quasiparticle excitations and find that our model can realize all the topological phases as the string-net model with group G =∏iGi . In this respect, our construction provides various ways of building lattice models which realize topological order G , corresponding to different partitions of G and thus different flavors of string nets. In fact, our construction concretely demonstrates the Künneth formula by constructing various lattice models with the same topological order. As an example, we construct the G =Z2×Z2×Z2 string-net model which realizes a non-Abelian topological phase by properly intersecting three copies of toric codes.

Weights and topology: a study of the effects of graph construction on 3D image segmentation.

PubMed

Grady, Leo; Jolly, Marie-Pierre

2008-01-01

Graph-based algorithms have become increasingly popular for medical image segmentation. The fundamental process for each of these algorithms is to use the image content to generate a set of weights for the graph and then set conditions for an optimal partition of the graph with respect to these weights. To date, the heuristics used for generating the weighted graphs from image intensities have largely been ignored, while the primary focus of attention has been on the details of providing the partitioning conditions. In this paper we empirically study the effects of graph connectivity and weighting function on the quality of the segmentation results. To control for algorithm-specific effects, we employ both the Graph Cuts and Random Walker algorithms in our experiments.

Trophic groups and modules: two levels of group detection in food webs

PubMed Central

Gauzens, Benoit; Thébault, Elisa; Lacroix, Gérard; Legendre, Stéphane

2015-01-01

Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups (TGs), which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group concepts remains unknown in empirical food webs. While recent developments in network theory have led to efficient methods for detecting modules in food webs, the determination of TGs (groups of species that are functionally similar) is largely based on subjective expert knowledge. We develop a novel algorithm for TG detection. We apply this method to empirical food webs and show that aggregation into TGs allows for the simplification of food webs while preserving their information content. Furthermore, we reveal a two-level hierarchical structure where modules partition food webs into large bottom–top trophic pathways, whereas TGs further partition these pathways into groups of species with similar trophic connections. This provides new perspectives for the study of dynamical and functional consequences of food-web structure, bridging topological and dynamical analysis. TGs have a clear ecological meaning and are found to provide a trade-off between network complexity and information loss. PMID:25878127

Thermodynamics. [algebraic structure

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.

1976-01-01

The fundamental structure of thermodynamics is purely algebraic, in the sense of atopological, and it is also independent of partitions, composite systems, the zeroth law, and entropy. The algebraic structure requires the notion of heat, but not the first law. It contains a precise definition of entropy and identifies it as a purely mathematical concept. It also permits the construction of an entropy function from heat measurements alone when appropriate conditions are satisfied. Topology is required only for a discussion of the continuity of thermodynamic properties, and then the weak topology is the relevant topology. The integrability of the differential form of the first law can be examined independently of Caratheodory's theorem and his inaccessibility axiom. Criteria are established by which one can determine when an integrating factor can be made intensive and the pseudopotential extensive and also an entropy. Finally, a realization of the first law is constructed which is suitable for all systems whether they are solids or fluids, whether they do or do not exhibit chemical reactions, and whether electromagnetic fields are or are not present.

The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

PubMed

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

Supersymmetric attractors, topological strings, and the M5-brane CFT

NASA Astrophysics Data System (ADS)

Guica, Monica M.

One of the purposes of this thesis is to present the consistent and unifying picture that emerges in string and M-theory with eight supercharges. On one hand, this involves classifying and relating supersymmetric objects that occur in N = 2 compactifications of string and M-theory on a Calabi-Yau manifold. These come in a surprisingly wide variety of four and five-dimensional black holes, black rings and their sometimes very complicated bound states. On the other hand, the topological string also makes its appearance in theories with eight supercharges, and turns out to compute certain black hole degeneracies. We dedicate the introduction and the first chapter to summarizing and reviewing the beautiful relationships between black holes, black rings, their dual conformal field theory and the topological string, and we also outline the remaining puzzles and issues. Some of the black holes in question can be obtained by multiply-wrapping an M-theory M5-brane on a self-intersecting four-cycle in the Calabi-Yau manifold. Their dual microscopic description is known, and consists of a two-dimensional conformal field theory (CFT) which is the low-energy limit of the gauge theory that resides on the worldvolume of the M5 brane. We show that in a certain limit the M5-brane CFT is - perhaps surprisingly - able to reproduce the entropy of a completely different type of black holes, those obtained from wrapped M2-branes, whose microscopic description has not yet been understood. We also argue that certain black hole bound states should also be described by the same CFT, which suggests a unifying description of the various black objects in eight-supercharge supergravity theories. Finally, we describe and present a proof of the so-called OSV conjecture, which states that the mixed partition function of N = 2 four-dimensional BPS black holes equals the modulus square of the type A topological string partition function. We also attempt to use this relationship to better understand corrections to the entropy of supersymmetric black holes and rings in five dimensions.

Effect of video server topology on contingency capacity requirements

NASA Astrophysics Data System (ADS)

Kienzle, Martin G.; Dan, Asit; Sitaram, Dinkar; Tetzlaff, William H.

1996-03-01

Video servers need to assign a fixed set of resources to each video stream in order to guarantee on-time delivery of the video data. If a server has insufficient resources to guarantee the delivery, it must reject the stream request rather than slowing down all existing streams. Large scale video servers are being built as clusters of smaller components, so as to be economical, scalable, and highly available. This paper uses a blocking model developed for telephone systems to evaluate video server cluster topologies. The goal is to achieve high utilization of the components and low per-stream cost combined with low blocking probability and high user satisfaction. The analysis shows substantial economies of scale achieved by larger server images. Simple distributed server architectures can result in partitioning of resources with low achievable resource utilization. By comparing achievable resource utilization of partitioned and monolithic servers, we quantify the cost of partitioning. Next, we present an architecture for a distributed server system that avoids resource partitioning and results in highly efficient server clusters. Finally, we show how, in these server clusters, further optimizations can be achieved through caching and batching of video streams.

DNA Gyrase Is Involved in Chloroplast Nucleoid Partitioning

PubMed Central

Cho, Hye Sun; Lee, Sang Sook; Kim, Kwang Dong; Hwang, Inhwan; Lim, Jong-Seok; Park, Youn-Il; Pai, Hyun-Sook

2004-01-01

DNA gyrase, which catalyzes topological transformation of DNA, plays an essential role in replication and transcription in prokaryotes. Virus-induced gene silencing of NbGyrA or NbGyrB, which putatively encode DNA gyrase subunits A and B, respectively, resulted in leaf yellowing phenotypes in Nicotiana benthamiana. NbGyrA and NbGyrB complemented the gyrA and gyrB temperature-sensitive mutations of Escherichia coli, respectively, which indicates that the plant and bacterial subunits are functionally similar. NbGyrA and NbGyrB were targeted to both chloroplasts and mitochondria, and depletion of these subunits affected both organelles by reducing chloroplast numbers and inducing morphological and physiological abnormalities in both organelles. Flow cytometry analysis revealed that the average DNA content in the affected chloroplasts and mitochondria was significantly higher than in the control organelles. Furthermore, 4′,6-diamidino-2-phenylindole staining revealed that the abnormal chloroplasts contained one or a few large nucleoids instead of multiple small nucleoids dispersed throughout the stroma. Pulse-field gel electrophoresis analyses of chloroplasts demonstrated that the sizes and/or structure of the DNA molecules in the abnormal chloroplast nucleoids are highly aberrant. Based on these results, we propose that DNA gyrase plays a critical role in chloroplast nucleoid partitioning by regulating DNA topology. PMID:15367714

Reflection states in Ding-Iohara-Miki algebra and brane-web for D-type quiver

NASA Astrophysics Data System (ADS)

Bourgine, J.-E.; Fukuda, M.; Matsuo, Y.; Zhu, R.-D.

2017-12-01

Reflection states are introduced in the vertical and horizontal modules of the Ding-Iohara-Miki (DIM) algebra (quantum toroidal gl_1 ). Webs of DIM representations are in correspondence with ( p, q)-web diagrams of type IIB string theory, under the identification of the algebraic intertwiner of Awata, Feigin and Shiraishi with the refined topological vertex. Extending the correspondence to the vertical reflection states, it is possible to engineer the N=1 quiver gauge theory of D-type (with unitary gauge groups). In this way, the Nekrasov instanton partition function is reproduced from the evaluation of expectation values of intertwiners. This computation leads to the identification of the vertical reflection state with the orientifold plane of string theory. We also provide a translation of this construction in the Iqbal-Kozcaz-Vafa refined topological vertex formalism.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jing-Yuan; Son, Jun Ho; Wang, Chao

The idea of statistical transmutation plays a crucial role in descriptions of the fractional quantum Hall effect. However, a recently conjectured duality between a critical boson and a massless two-component Dirac fermion extends this notion to gapless systems. This duality sheds light on highly nontrivial problems such as the half-filled Landau level, the superconductor-insulator transition, and surface states of strongly coupled topological insulators. Although this boson-fermion duality has undergone many consistency checks, it has remained unproven. Here, we describe the duality in a nonperturbative fashion using an exact UV mapping of partition functions on a 3D Euclidean lattice.

Trophic groups and modules: two levels of group detection in food webs.

PubMed

Gauzens, Benoit; Thébault, Elisa; Lacroix, Gérard; Legendre, Stéphane

2015-05-06

Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups (TGs), which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group concepts remains unknown in empirical food webs. While recent developments in network theory have led to efficient methods for detecting modules in food webs, the determination of TGs (groups of species that are functionally similar) is largely based on subjective expert knowledge. We develop a novel algorithm for TG detection. We apply this method to empirical food webs and show that aggregation into TGs allows for the simplification of food webs while preserving their information content. Furthermore, we reveal a two-level hierarchical structure where modules partition food webs into large bottom-top trophic pathways, whereas TGs further partition these pathways into groups of species with similar trophic connections. This provides new perspectives for the study of dynamical and functional consequences of food-web structure, bridging topological and dynamical analysis. TGs have a clear ecological meaning and are found to provide a trade-off between network complexity and information loss. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Black hole meiosis

NASA Astrophysics Data System (ADS)

van Herck, Walter; Wyder, Thomas

2010-04-01

The enumeration of BPS bound states in string theory needs refinement. Studying partition functions of particles made from D-branes wrapped on algebraic Calabi-Yau 3-folds, and classifying states using split attractor flow trees, we extend the method for computing a refined BPS index, [1]. For certain D-particles, a finite number of microstates, namely polar states, exclusively realized as bound states, determine an entire partition function (elliptic genus). This underlines their crucial importance: one might call them the ‘chromosomes’ of a D-particle or a black hole. As polar states also can be affected by our refinement, previous predictions on elliptic genera are modified. This can be metaphorically interpreted as ‘crossing-over in the meiosis of a D-particle’. Our results improve on [2], provide non-trivial evidence for a strong split attractor flow tree conjecture, and thus suggest that we indeed exhaust the BPS spectrum. In the D-brane description of a bound state, the necessity for refinement results from the fact that tachyonic strings split up constituent states into ‘generic’ and ‘special’ states. These are enumerated separately by topological invariants, which turn out to be partitions of Donaldson-Thomas invariants. As modular predictions provide a check on many of our results, we have compelling evidence that our computations are correct.

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

PubMed Central

Burke, Sean V.; Wysocki, William P.; Clark, Lynn G.

2018-01-01

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity. PMID:29416954

A multicolour graph as a complete topological invariant for \\Omega-stable flows without periodic trajectories on surfaces

NASA Astrophysics Data System (ADS)

Kruglov, V. E.; Malyshev, D. S.; Pochinka, O. V.

2018-01-01

Studying the dynamics of a flow on surfaces by partitioning the phase space into cells with the same limit behaviour of trajectories within a cell goes back to the classical papers of Andronov, Pontryagin, Leontovich and Maier. The types of cells (the number of which is finite) and how the cells adjoin one another completely determine the topological equivalence class of a flow with finitely many special trajectories. If one trajectory is chosen in every cell of a rough flow without periodic orbits, then the cells are partitioned into so-called triangular regions of the same type. A combinatorial description of such a partition gives rise to the three-colour Oshemkov-Sharko graph, the vertices of which correspond to the triangular regions, and the edges to separatrices connecting them. Oshemkov and Sharko proved that such flows are topologically equivalent if and only if the three-colour graphs of the flows are isomorphic, and described an algorithm of distinguishing three-colour graphs. But their algorithm is not efficient with respect to graph theory. In the present paper, we describe the dynamics of Ω-stable flows without periodic trajectories on surfaces in the language of four-colour graphs, present an efficient algorithm for distinguishing such graphs, and develop a realization of a flow from some abstract graph. Bibliography: 17 titles.

Large scale genomic reorganization of topological domains at the HoxD locus.

PubMed

Fabre, Pierre J; Leleu, Marion; Mormann, Benjamin H; Lopez-Delisle, Lucille; Noordermeer, Daan; Beccari, Leonardo; Duboule, Denis

2017-08-07

The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts. To assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH. We assessed the robustness of the TAD architecture by using a series of genomic deletions and inversions that impact the integrity of this chromatin domain and that remodel long-range contacts. We report multi-partite associations between HoxD genes and up to three enhancers. We find that the loss of native chromatin topology leads to the remodeling of TAD structure following distinct parameters. Our results reveal that the recomposition of TAD architectures after large genomic re-arrangements is dependent on a boundary-selection mechanism in which CTCF mediates the gating of long-range contacts in combination with genomic distance and sequence specificity. Accordingly, the building of a recomposed TAD at this locus depends on distinct functional and constitutive parameters.

Entanglement entropy of ABJM theory and entropy of topological black hole

NASA Astrophysics Data System (ADS)

Nian, Jun; Zhang, Xinyu

2017-07-01

In this paper we discuss the supersymmetric localization of the 4D N = 2 offshell gauged supergravity on the background of the AdS4 neutral topological black hole, which is the gravity dual of the ABJM theory defined on the boundary {S}^1× H^2 . We compute the large- N expansion of the supergravity partition function. The result gives the black hole entropy with the logarithmic correction, which matches the previous result of the entanglement entropy of the ABJM theory up to some stringy effects. Our result is consistent with the previous on-shell one-loop computation of the logarithmic correction to black hole entropy. It provides an explicit example of the identification of the entanglement entropy of the boundary conformal field theory with the bulk black hole entropy beyond the leading order given by the classical Bekenstein-Hawking formula, which consequently tests the AdS/CFT correspondence at the subleading order.

Efficient Deterministic Finite Automata Minimization Based on Backward Depth Information.

PubMed

Liu, Desheng; Huang, Zhiping; Zhang, Yimeng; Guo, Xiaojun; Su, Shaojing

2016-01-01

Obtaining a minimal automaton is a fundamental issue in the theory and practical implementation of deterministic finite automatons (DFAs). A minimization algorithm is presented in this paper that consists of two main phases. In the first phase, the backward depth information is built, and the state set of the DFA is partitioned into many blocks. In the second phase, the state set is refined using a hash table. The minimization algorithm has a lower time complexity O(n) than a naive comparison of transitions O(n2). Few states need to be refined by the hash table, because most states have been partitioned by the backward depth information in the coarse partition. This method achieves greater generality than previous methods because building the backward depth information is independent of the topological complexity of the DFA. The proposed algorithm can be applied not only to the minimization of acyclic automata or simple cyclic automata, but also to automata with high topological complexity. Overall, the proposal has three advantages: lower time complexity, greater generality, and scalability. A comparison to Hopcroft's algorithm demonstrates experimentally that the algorithm runs faster than traditional algorithms.

Classification of topological insulators and superconductors in three spatial dimensions

NASA Astrophysics Data System (ADS)

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

2009-03-01

We systematically study topological phases of insulators and superconductors (or superfluids) in 3D. We find that there exist 3D topologically non-trivial insulators or superconductors in five out of ten symmetry classes introduced in seminal work by Altland and Zirnbauer within the context of random matrix theory, more than a decade ago. One of these is the recently introduced Z2 topological insulator in the symplectic (or spin-orbit) symmetry class. We show there exist precisely four more topological insulators. For these systems, all of which are time-reversal invariant in 3D, the space of insulating ground states satisfying certain discrete symmetry properties is partitioned into topological sectors that are separated by quantum phase transitions. Three of the above five topologically non-trivial phases can be realized as time-reversal invariant superconductors, and in these the different topological sectors are characterized by an integer winding number defined in momentum space. When such 3D topological insulators are terminated by a 2D surface, they support stable surface Dirac (Majorana) fermion modes.

Scheduling applications for execution on a plurality of compute nodes of a parallel computer to manage temperature of the nodes during execution

DOEpatents

Archer, Charles J; Blocksome, Michael A; Peters, Amanda E; Ratterman, Joseph D; Smith, Brian E

2012-10-16

Methods, apparatus, and products are disclosed for scheduling applications for execution on a plurality of compute nodes of a parallel computer to manage temperature of the plurality of compute nodes during execution that include: identifying one or more applications for execution on the plurality of compute nodes; creating a plurality of physically discontiguous node partitions in dependence upon temperature characteristics for the compute nodes and a physical topology for the compute nodes, each discontiguous node partition specifying a collection of physically adjacent compute nodes; and assigning, for each application, that application to one or more of the discontiguous node partitions for execution on the compute nodes specified by the assigned discontiguous node partitions.

Continuously differentiable PIC shape functions for triangular meshes

DOE PAGES

Barnes, D. C.

2018-03-21

In this study, a new class of continuously-differentiable shape functions is developed and applied to two-dimensional electrostatic PIC simulation on an unstructured simplex (triangle) mesh. It is shown that troublesome aliasing instabilities are avoided for cold plasma simulation in which the Debye length is as small as 0.01 cell sizes. These new shape functions satisfy all requirements for PIC particle shape. They are non-negative, have compact support, and partition unity. They are given explicitly by cubic expressions in the usual triangle logical (areal) coordinates. The shape functions are not finite elements because their structure depends on the topology of themore » mesh, in particular, the number of triangles neighboring each mesh vertex. Nevertheless, they may be useful as approximations to solution of other problems in which continuity of derivatives is required or desired.« less

Continuously differentiable PIC shape functions for triangular meshes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnes, D. C.

In this study, a new class of continuously-differentiable shape functions is developed and applied to two-dimensional electrostatic PIC simulation on an unstructured simplex (triangle) mesh. It is shown that troublesome aliasing instabilities are avoided for cold plasma simulation in which the Debye length is as small as 0.01 cell sizes. These new shape functions satisfy all requirements for PIC particle shape. They are non-negative, have compact support, and partition unity. They are given explicitly by cubic expressions in the usual triangle logical (areal) coordinates. The shape functions are not finite elements because their structure depends on the topology of themore » mesh, in particular, the number of triangles neighboring each mesh vertex. Nevertheless, they may be useful as approximations to solution of other problems in which continuity of derivatives is required or desired.« less

Black holes, anti de Sitter space, and topological strings

NASA Astrophysics Data System (ADS)

Yin, Xi

This thesis is devoted to the study of black holes in string theory, their connection to two and three dimensional anti de-Sitter space, and topological strings. We start by proposing a relation between supersymmetric black holes in four and five dimensions, as well as connections between multi-centered black holes in four dimensions and black rings in five dimensions. This connection is then applied to counting supersymmetric dyonic black holes in four dimensional string compactifications with 16 and 32 supersymmetries, respectively. We then turn to the near horizon attractor geometry AdS 2 x S2 x CY 3, and study the classical supersymmetric D-branes in this background. We also find supersymmetric black hole solutions in supergravity in AdS2 x S2, although the solutions have regions of closed timelike curves. Finally we consider the M-theory attractor geometry AdS3 x S2 x CY3, and compute the elliptic genus of the dual (0, 4) CFT by counting wrapped M2-brane states in the bulk in a dilute gas approximation. This leads to a derivation of the conjectured relation between black hole partition function and topological string amplitudes.

DTN routing in body sensor networks with dynamic postural partitioning.

PubMed

Quwaider, Muhannad; Biswas, Subir

2010-11-01

This paper presents novel store-and-forward packet routing algorithms for Wireless Body Area Networks ( WBAN ) with frequent postural partitioning. A prototype WBAN has been constructed for experimentally characterizing on-body topology disconnections in the presence of ultra short range radio links, unpredictable RF attenuation, and human postural mobility. On-body DTN routing protocols are then developed using a stochastic link cost formulation, capturing multi-scale topological localities in human postural movements. Performance of the proposed protocols are evaluated experimentally and via simulation, and are compared with a number of existing single-copy DTN routing protocols and an on-body packet flooding mechanism that serves as a performance benchmark with delay lower-bound. It is shown that via multi-scale modeling of the spatio-temporal locality of on-body link disconnection patterns, the proposed algorithms can provide better routing performance compared to a number of existing probabilistic, opportunistic, and utility-based DTN routing protocols in the literature.

Influence of homology and node age on the growth of protein-protein interaction networks

NASA Astrophysics Data System (ADS)

Bottinelli, Arianna; Bassetti, Bruno; Lagomarsino, Marco Cosentino; Gherardi, Marco

2012-10-01

Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so the dynamics of the two objects are intrinsically linked. Here we first introduce a statistical model describing the joint growth of the network and the partitioning of nodes into classes, which is studied through a combined mean-field and simulation approach. We then employ this unified framework to address the specific issue of the age dependence of protein interactions through the definition of three different node wiring or divergence schemes. A comparison with empirical data indicates that an age-dependent divergence move is necessary in order to reproduce the basic topological observables together with the age correlation between interacting nodes visible in empirical data. We also discuss the possibility of nontrivial joint partition and topology observables.

Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation

PubMed Central

Phillips, James C.; Sun, Yanhua; Jain, Nikhil; Bohm, Eric J.; Kalé, Laxmikant V.

2014-01-01

Currently deployed petascale supercomputers typically use toroidal network topologies in three or more dimensions. While these networks perform well for topology-agnostic codes on a few thousand nodes, leadership machines with 20,000 nodes require topology awareness to avoid network contention for communication-intensive codes. Topology adaptation is complicated by irregular node allocation shapes and holes due to dedicated input/output nodes or hardware failure. In the context of the popular molecular dynamics program NAMD, we present methods for mapping a periodic 3-D grid of fixed-size spatial decomposition domains to 3-D Cray Gemini and 5-D IBM Blue Gene/Q toroidal networks to enable hundred-million atom full machine simulations, and to similarly partition node allocations into compact domains for smaller simulations using multiple-copy algorithms. Additional enabling techniques are discussed and performance is reported for NCSA Blue Waters, ORNL Titan, ANL Mira, TACC Stampede, and NERSC Edison. PMID:25594075

Efficient Deterministic Finite Automata Minimization Based on Backward Depth Information

PubMed Central

Liu, Desheng; Huang, Zhiping; Zhang, Yimeng; Guo, Xiaojun; Su, Shaojing

2016-01-01

Obtaining a minimal automaton is a fundamental issue in the theory and practical implementation of deterministic finite automatons (DFAs). A minimization algorithm is presented in this paper that consists of two main phases. In the first phase, the backward depth information is built, and the state set of the DFA is partitioned into many blocks. In the second phase, the state set is refined using a hash table. The minimization algorithm has a lower time complexity O(n) than a naive comparison of transitions O(n2). Few states need to be refined by the hash table, because most states have been partitioned by the backward depth information in the coarse partition. This method achieves greater generality than previous methods because building the backward depth information is independent of the topological complexity of the DFA. The proposed algorithm can be applied not only to the minimization of acyclic automata or simple cyclic automata, but also to automata with high topological complexity. Overall, the proposal has three advantages: lower time complexity, greater generality, and scalability. A comparison to Hopcroft’s algorithm demonstrates experimentally that the algorithm runs faster than traditional algorithms. PMID:27806102

A novel partitioning method for block-structured adaptive meshes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Lin, E-mail: lin.fu@tum.de; Litvinov, Sergej, E-mail: sergej.litvinov@aer.mw.tum.de; Hu, Xiangyu Y., E-mail: xiangyu.hu@tum.de

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtainmore » the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.« less

A novel partitioning method for block-structured adaptive meshes

NASA Astrophysics Data System (ADS)

Fu, Lin; Litvinov, Sergej; Hu, Xiangyu Y.; Adams, Nikolaus A.

2017-07-01

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtain the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.

Lagrangian statistics and flow topology in forced two-dimensional turbulence.

PubMed

Kadoch, B; Del-Castillo-Negrete, D; Bos, W J T; Schneider, K

2011-03-01

A study of the relationship between Lagrangian statistics and flow topology in fluid turbulence is presented. The topology is characterized using the Weiss criterion, which provides a conceptually simple tool to partition the flow into topologically different regions: elliptic (vortex dominated), hyperbolic (deformation dominated), and intermediate (turbulent background). The flow corresponds to forced two-dimensional Navier-Stokes turbulence in doubly periodic and circular bounded domains, the latter with no-slip boundary conditions. In the double periodic domain, the probability density function (pdf) of the Weiss field exhibits a negative skewness consistent with the fact that in periodic domains the flow is dominated by coherent vortex structures. On the other hand, in the circular domain, the elliptic and hyperbolic regions seem to be statistically similar. We follow a Lagrangian approach and obtain the statistics by tracking large ensembles of passively advected tracers. The pdfs of residence time in the topologically different regions are computed introducing the Lagrangian Weiss field, i.e., the Weiss field computed along the particles' trajectories. In elliptic and hyperbolic regions, the pdfs of the residence time have self-similar algebraic decaying tails. In contrast, in the intermediate regions the pdf has exponential decaying tails. The conditional pdfs (with respect to the flow topology) of the Lagrangian velocity exhibit Gaussian-like behavior in the periodic and in the bounded domains. In contrast to the freely decaying turbulence case, the conditional pdfs of the Lagrangian acceleration in forced turbulence show a comparable level of intermittency in both the periodic and the bounded domains. The conditional pdfs of the Lagrangian curvature are characterized, in all cases, by self-similar power-law behavior with a decay exponent of order -2.

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain.

PubMed

Albuixech-Crespo, Beatriz; López-Blanch, Laura; Burguera, Demian; Maeso, Ignacio; Sánchez-Arrones, Luisa; Moreno-Bravo, Juan Antonio; Somorjai, Ildiko; Pascual-Anaya, Juan; Puelles, Eduardo; Bovolenta, Paola; Garcia-Fernàndez, Jordi; Puelles, Luis; Irimia, Manuel; Ferran, José Luis

2017-04-01

All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still unclear how this Bauplan originated during evolution. We studied the relative expression of 48 genes with key roles in vertebrate neural patterning in a representative amphioxus embryonic stage. Unlike nonchordates, amphioxus develops its central nervous system (CNS) from a neural plate that is homologous to that of vertebrates, allowing direct topological comparisons. The resulting genoarchitectonic model revealed that the amphioxus incipient neural tube is unexpectedly complex, consisting of several AP and DV molecular partitions. Strikingly, comparison with vertebrates indicates that the vertebrate thalamus, pretectum, and midbrain domains jointly correspond to a single amphioxus region, which we termed Di-Mesencephalic primordium (DiMes). This suggests that these domains have a common developmental and evolutionary origin, as supported by functional experiments manipulating secondary organizers in zebrafish and mice.

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

PubMed Central

Albuixech-Crespo, Beatriz; Maeso, Ignacio; Sánchez-Arrones, Luisa; Moreno-Bravo, Juan Antonio; Somorjai, Ildiko; Pascual-Anaya, Juan; Puelles, Eduardo; Bovolenta, Paola; Garcia-Fernàndez, Jordi; Puelles, Luis; Ferran, José Luis

2017-01-01

All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still unclear how this Bauplan originated during evolution. We studied the relative expression of 48 genes with key roles in vertebrate neural patterning in a representative amphioxus embryonic stage. Unlike nonchordates, amphioxus develops its central nervous system (CNS) from a neural plate that is homologous to that of vertebrates, allowing direct topological comparisons. The resulting genoarchitectonic model revealed that the amphioxus incipient neural tube is unexpectedly complex, consisting of several AP and DV molecular partitions. Strikingly, comparison with vertebrates indicates that the vertebrate thalamus, pretectum, and midbrain domains jointly correspond to a single amphioxus region, which we termed Di-Mesencephalic primordium (DiMes). This suggests that these domains have a common developmental and evolutionary origin, as supported by functional experiments manipulating secondary organizers in zebrafish and mice. PMID:28422959

Exact Boson-Fermion Duality on a 3D Euclidean Lattice

DOE PAGES

Chen, Jing-Yuan; Son, Jun Ho; Wang, Chao; ...

2018-01-05

The idea of statistical transmutation plays a crucial role in descriptions of the fractional quantum Hall effect. However, a recently conjectured duality between a critical boson and a massless two-component Dirac fermion extends this notion to gapless systems. This duality sheds light on highly nontrivial problems such as the half-filled Landau level, the superconductor-insulator transition, and surface states of strongly coupled topological insulators. Although this boson-fermion duality has undergone many consistency checks, it has remained unproven. Here, we describe the duality in a nonperturbative fashion using an exact UV mapping of partition functions on a 3D Euclidean lattice.

Exact Boson-Fermion Duality on a 3D Euclidean Lattice.

PubMed

Chen, Jing-Yuan; Son, Jun Ho; Wang, Chao; Raghu, S

2018-01-05

The idea of statistical transmutation plays a crucial role in descriptions of the fractional quantum Hall effect. However, a recently conjectured duality between a critical boson and a massless two-component Dirac fermion extends this notion to gapless systems. This duality sheds light on highly nontrivial problems such as the half-filled Landau level, the superconductor-insulator transition, and surface states of strongly coupled topological insulators. Although this boson-fermion duality has undergone many consistency checks, it has remained unproven. We describe the duality in a nonperturbative fashion using an exact UV mapping of partition functions on a 3D Euclidean lattice.

Exact Boson-Fermion Duality on a 3D Euclidean Lattice

NASA Astrophysics Data System (ADS)

Chen, Jing-Yuan; Son, Jun Ho; Wang, Chao; Raghu, S.

2018-01-01

The idea of statistical transmutation plays a crucial role in descriptions of the fractional quantum Hall effect. However, a recently conjectured duality between a critical boson and a massless two-component Dirac fermion extends this notion to gapless systems. This duality sheds light on highly nontrivial problems such as the half-filled Landau level, the superconductor-insulator transition, and surface states of strongly coupled topological insulators. Although this boson-fermion duality has undergone many consistency checks, it has remained unproven. We describe the duality in a nonperturbative fashion using an exact UV mapping of partition functions on a 3D Euclidean lattice.

The connection between BRG1, CTCF and topoisomerases at TAD boundaries.

PubMed

Barutcu, A Rasim; Lian, Jane B; Stein, Janet L; Stein, Gary S; Imbalzano, Anthony N

2017-03-04

The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries. In this review, we elaborate on our findings and speculate that BRG1 may contribute to the regulation of the structural and functional properties of chromatin at TAD boundaries by affecting the function or the recruitment of CTCF and DNA topoisomerase complexes.

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

PubMed

Barrett, Craig F; Specht, Chelsea D; Leebens-Mack, Jim; Stevenson, Dennis Wm; Zomlefer, Wendy B; Davis, Jerrold I

2014-01-01

Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life. Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support. Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies. Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations.

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

PubMed Central

Barrett, Craig F.; Specht, Chelsea D.; Leebens-Mack, Jim; Stevenson, Dennis Wm.; Zomlefer, Wendy B.; Davis, Jerrold I.

2014-01-01

Background and Aims Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life. Methods Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support. Key Results Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies. Conclusions Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations. PMID:24280362

Tunneling topological vacua via extended operators: (Spin-)TQFT spectra and boundary deconfinement in various dimensions

NASA Astrophysics Data System (ADS)

Wang, Juven; Ohmori, Kantaro; Putrov, Pavel; Zheng, Yunqin; Wan, Zheyan; Guo, Meng; Lin, Hai; Gao, Peng; Yau, Shing-Tung

2018-05-01

Distinct quantum vacua of topologically ordered states can be tunneled into each other via extended operators. The possible applications include condensed matter and quantum cosmology. We present a straightforward approach to calculate the partition function on various manifolds and ground state degeneracy (GSD), mainly based on continuum/cochain topological quantum field theories (TQFTs), in any dimension. This information can be related to the counting of extended operators of bosonic/fermionic TQFTs. On the lattice scale, anyonic particles/strings live at the ends of line/surface operators. Certain systems in different dimensions are related to each other through dimensional reduction schemes, analogous to (de)categorification. Examples include spin TQFTs derived from gauging the interacting fermionic symmetry-protected topological states (with fermion parity {Z}_2^f) of symmetry groups {Z}_4× {Z}_2 and ({Z}_4)^2 in 3+1D, also {Z}_2 and ({Z}_2)^2 in 2+1D. Gauging the last three cases begets non-Abelian spin TQFTs (fermionic topological order). We consider situations where a TQFT lives on (1) a closed spacetime or (2) a spacetime with a boundary, such that the bulk and boundary are fully gapped and short- or long-range entangled (SRE/LRE). Anyonic excitations can be deconfined on the boundary. We introduce new exotic topological interfaces on which neither particle nor string excitations alone condense, but only fuzzy-composite objects of extended operators can end (e.g., a string-like composite object formed by a set of particles can end on a special 2+1D boundary of 3+1D bulk). We explore the relations between group extension constructions and partially breaking constructions (e.g., 0-form/higher-form/"composite" breaking) of topological boundaries, after gauging. We comment on the implications of entanglement entropy for some such LRE systems.

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

PubMed Central

Flower, Rosalyn; Choo, Siew Woh

2017-01-01

It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries. While we have not demonstrated causality, we suggest that the D domain chromatin state, characterised by very low or absent H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome. PMID:28282436

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

PubMed Central

Jost, Daniel; Carrivain, Pascal; Cavalli, Giacomo; Vaillant, Cédric

2014-01-01

Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domains tend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the general mechanisms behind such compartmentalization including the contribution of epigenetic regulation remain unclear. Here, we address the question of the coupling between chromatin folding and epigenome. Using polymer physics, we analyze the properties of a block copolymer model that accounts for local epigenomic information. Considering copolymers build from the epigenomic landscape of Drosophila, we observe a very good agreement with the folding patterns observed in chromosome conformation capture experiments. Moreover, this model provides a physical basis for the existence of multistability in epigenome folding at sub-chromosomal scale. We show how experiments are fully consistent with multistable conformations where topologically associated domains of the same epigenomic state interact dynamically with each other. Our approach provides a general framework to improve our understanding of chromatin folding during cell cycle and differentiation and its relation to epigenetics. PMID:25092923

Generalized Knizhnik-Zamolodchikov equation for Ding-Iohara-Miki algebra

NASA Astrophysics Data System (ADS)

Awata, Hidetoshi; Kanno, Hiroaki; Mironov, Andrei; Morozov, Alexei; Morozov, Andrey; Ohkubo, Yusuke; Zenkevich, Yegor

2017-07-01

We derive the generalization of the Knizhnik-Zamolodchikov equation (KZE) associated with the Ding-Iohara-Miki algebra Uq ,t(gl^ ^ 1) . We demonstrate that certain refined topological string amplitudes satisfy these equations and find that the braiding transformations are performed by the R matrix of Uq ,t(gl^ ^ 1) . The resulting system is the uplifting of the u^1 Wess-Zumino-Witten model. The solutions to the (q ,t ) KZE are identified with the (spectral dual of) building blocks of the Nekrasov partition function for five-dimensional linear quiver gauge theories. We also construct an elliptic version of the KZE and discuss its modular and monodromy properties, the latter being related to a dual version of the KZE.

A string realisation of Ω-deformed Abelian N =2* theory

NASA Astrophysics Data System (ADS)

Angelantonj, Carlo; Antoniadis, Ignatios; Samsonyan, Marine

2017-10-01

The N =2* supersymmetric gauge theory is a massive deformation of N = 4, in which the adjoint hypermultiplet gets a mass. We present a D-brane realisation of the (non-)Abelian N =2* theory, and compute suitable topological amplitudes, which are expressed as a double series expansion. The coefficients determine couplings of higher-dimensional operators in the effective supergravity action that involve powers of the anti-self-dual N = 2 chiral Weyl superfield and of self-dual gauge field strengths superpartners of the D5-brane coupling modulus. In the field theory limit, the result reproduces the Nekrasov partition function in the two-parameter Ω-background, in agreement with a recent proposal.

5-brane webs for 5d N = 1 G 2 gauge theories

NASA Astrophysics Data System (ADS)

Hayashi, Hirotaka; Kim, Sung-Soo; Lee, Kimyeong; Yagi, Futoshi

2018-03-01

We propose 5-brane webs for 5d N = 1 G 2 gauge theories. From a Higgsing of the SO(7) gauge theory with a hypermultiplet in the spinor representation, we construct two types of 5-brane web configurations for the pure G 2 gauge theory using an O5-plane or an \\tilde{O5} -plane. Adding flavors to the 5-brane web for the pure G 2 gauge theory is also discussed. Based on the obtained 5-brane webs, we compute the partition functions for the 5d G 2 gauge theories using the recently suggested topological vertex formulation with an O5-plane, and we find agreement with known results.

Development of Thread-compatible Open Source Stack

NASA Astrophysics Data System (ADS)

Zimmermann, Lukas; Mars, Nidhal; Schappacher, Manuel; Sikora, Axel

2017-07-01

The Thread protocol is a recent development based on 6LoWPAN (IPv6 over IEEE 802.15.4), but with extensions regarding a more media independent approach, which - additionally - also promises true interoperability. To evaluate and analyse the operation of a Thread network a given open source 6LoWPAN stack for embedded devices (emb::6) has been extended in order to comply with the Thread specification. The implementation covers Mesh Link Establishment (MLE) and network layer functionality as well as 6LoWPAN mesh under routing mechanism based on MAC short addresses. The development has been verified on a virtualization platform and allows dynamical establishment of network topologies based on Thread’s partitioning algorithm.

Mining the modular structure of protein interaction networks.

PubMed

Berenstein, Ariel José; Piñero, Janet; Furlong, Laura Inés; Chernomoretz, Ariel

2015-01-01

Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis. We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera's cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns. As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge.

Volumetric data analysis using Morse-Smale complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Natarajan, V; Pascucci, V

2005-10-13

The 3D Morse-Smale complex is a fundamental topological construct that partitions the domain of a real-valued function into regions having uniform gradient flow behavior. In this paper, we consider the construction and selective presentation of cells of the Morse-Smale complex and their use in the analysis and visualization of scientific datasets. We take advantage of the fact that cells of different dimension often characterize different types of features present in the data. For example, critical points pinpoint changes in topology by showing where components of the level sets are created, destroyed or modified in genus. Edges of the Morse-Smale complexmore » extract filament-like features that are not explicitly modeled in the original data. Interactive selection and rendering of portions of the Morse-Smale complex introduces fundamental data management challenges due to the unstructured nature of the complex even for structured inputs. We describe a data structure that stores the Morse-Smale complex and allows efficient selective traversal of regions of interest. Finally, we illustrate the practical use of this approach by applying it to cryo-electron microscopy data of protein molecules.« less

Reconstruction of Energy Surfaces from Friction Force Microscopy Measurements with the Jarzynski Equality

NASA Astrophysics Data System (ADS)

Berkovich, Ronen; Klafter, Joseph; Urbakh, Michael

Free energy is one of the most fundamental thermodynamic functions, determining relative phase stability and serving as a generating function for other thermodynamic quantities. The calculation of free energies is a challenging enterprise. In equilibrium statistical mechanics, the free energy is related to the canonical partition function. The partition function itself involves integrations over all degrees of freedom in the system and, in most cases, cannot be easily calculated directly. In 1997, Jarzynski proved a remarkable equality that allows computing the equilibrium free-energy difference between two states from the probability distribution of the nonequilibrium work done on the system to switch between the two states. The Jarzynski equality provides a powerful free-energy difference estimator from a set of irreversible experiments. This method is closely related to free-energy perturbation approach, which is also a computational technique for estimating free-energy differences. The ability to map potential profiles and topologies is of major significance to areas as diverse as biological recognition and nanoscale friction. This capability has been demonstrated for frictional studies where a force between the tip of the scanning force microscope and the surface is probed. The surface free-energy corrugation produces a detectable friction forces. Thus, friction force microscopy (FFM) should be able to discriminate between energetically different areas on the probed surface. Here, we apply the Jarzynski equality for the analysis of FFM measurements and thus obtain a variation of the free energy along a surface.

A statistical mechanical approach to restricted integer partition functions

NASA Astrophysics Data System (ADS)

Zhou, Chi-Chun; Dai, Wu-Sheng

2018-05-01

The main aim of this paper is twofold: (1) suggesting a statistical mechanical approach to the calculation of the generating function of restricted integer partition functions which count the number of partitions—a way of writing an integer as a sum of other integers under certain restrictions. In this approach, the generating function of restricted integer partition functions is constructed from the canonical partition functions of various quantum gases. (2) Introducing a new type of restricted integer partition functions corresponding to general statistics which is a generalization of Gentile statistics in statistical mechanics; many kinds of restricted integer partition functions are special cases of this restricted integer partition function. Moreover, with statistical mechanics as a bridge, we reveal a mathematical fact: the generating function of restricted integer partition function is just the symmetric function which is a class of functions being invariant under the action of permutation groups. Using this approach, we provide some expressions of restricted integer partition functions as examples.

A multiscale restriction-smoothed basis method for high contrast porous media represented on unstructured grids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Møyner, Olav, E-mail: olav.moyner@sintef.no; Lie, Knut-Andreas, E-mail: knut-andreas.lie@sintef.no

2016-01-01

A wide variety of multiscale methods have been proposed in the literature to reduce runtime and provide better scaling for the solution of Poisson-type equations modeling flow in porous media. We present a new multiscale restricted-smoothed basis (MsRSB) method that is designed to be applicable to both rectilinear grids and unstructured grids. Like many other multiscale methods, MsRSB relies on a coarse partition of the underlying fine grid and a set of local prolongation operators (multiscale basis functions) that map unknowns associated with the fine grid cells to unknowns associated with blocks in the coarse partition. These mappings are constructedmore » by restricted smoothing: Starting from a constant, a localized iterative scheme is applied directly to the fine-scale discretization to compute prolongation operators that are consistent with the local properties of the differential operators. The resulting method has three main advantages: First of all, both the coarse and the fine grid can have general polyhedral geometry and unstructured topology. This means that partitions and good prolongation operators can easily be constructed for complex models involving high media contrasts and unstructured cell connections introduced by faults, pinch-outs, erosion, local grid refinement, etc. In particular, the coarse partition can be adapted to geological or flow-field properties represented on cells or faces to improve accuracy. Secondly, the method is accurate and robust when compared to existing multiscale methods and does not need expensive recomputation of local basis functions to account for transient behavior: Dynamic mobility changes are incorporated by continuing to iterate a few extra steps on existing basis functions. This way, the cost of updating the prolongation operators becomes proportional to the amount of change in fluid mobility and one reduces the need for expensive, tolerance-based updates. Finally, since the MsRSB method is formulated on top of a cell-centered, conservative, finite-volume method, it is applicable to any flow model in which one can isolate a pressure equation. Herein, we only discuss single and two-phase incompressible models. Compressible flow, e.g., as modeled by the black-oil equations, is discussed in a separate paper.« less

One-dimensional Ising model with multispin interactions

NASA Astrophysics Data System (ADS)

Turban, Loïc

2016-09-01

We study the spin-1/2 Ising chain with multispin interactions K involving the product of m successive spins, for general values of m. Using a change of spin variables the zero-field partition function of a finite chain is obtained for free and periodic boundary conditions and we calculate the two-spin correlation function. When placed in an external field H the system is shown to be self-dual. Using another change of spin variables the one-dimensional Ising model with multispin interactions in a field is mapped onto a zero-field rectangular Ising model with first-neighbour interactions K and H. The 2D system, with size m × N/m, has the topology of a cylinder with helical BC. In the thermodynamic limit N/m\\to ∞ , m\\to ∞ , a 2D critical singularity develops on the self-duality line, \\sinh 2K\\sinh 2H=1.

A Collaborative Recommend Algorithm Based on Bipartite Community

PubMed Central

Fu, Yuchen; Liu, Quan; Cui, Zhiming

2014-01-01

The recommendation algorithm based on bipartite network is superior to traditional methods on accuracy and diversity, which proves that considering the network topology of recommendation systems could help us to improve recommendation results. However, existing algorithms mainly focus on the overall topology structure and those local characteristics could also play an important role in collaborative recommend processing. Therefore, on account of data characteristics and application requirements of collaborative recommend systems, we proposed a link community partitioning algorithm based on the label propagation and a collaborative recommendation algorithm based on the bipartite community. Then we designed numerical experiments to verify the algorithm validity under benchmark and real database. PMID:24955393

Instantons on ALE spaces and orbifold partitions

NASA Astrophysics Data System (ADS)

Dijkgraaf, Robbert; Sułkowski, Piotr

2008-03-01

We consider Script N = 4 theories on ALE spaces of Ak-1 type. As is well known, their partition functions coincide with Ak-1 affine characters. We show that these partition functions are equal to the generating functions of some peculiar classes of partitions which we introduce under the name 'orbifold partitions'. These orbifold partitions turn out to be related to the generalized Frobenius partitions introduced by G. E. Andrews some years ago. We relate the orbifold partitions to the blended partitions and interpret explicitly in terms of a free fermion system.

Artificial Epigenetic Networks: Automatic Decomposition of Dynamical Control Tasks Using Topological Self-Modification.

PubMed

Turner, Alexander P; Caves, Leo S D; Stepney, Susan; Tyrrell, Andy M; Lones, Michael A

2017-01-01

This paper describes the artificial epigenetic network, a recurrent connectionist architecture that is able to dynamically modify its topology in order to automatically decompose and solve dynamical problems. The approach is motivated by the behavior of gene regulatory networks, particularly the epigenetic process of chromatin remodeling that leads to topological change and which underlies the differentiation of cells within complex biological organisms. We expected this approach to be useful in situations where there is a need to switch between different dynamical behaviors, and do so in a sensitive and robust manner in the absence of a priori information about problem structure. This hypothesis was tested using a series of dynamical control tasks, each requiring solutions that could express different dynamical behaviors at different stages within the task. In each case, the addition of topological self-modification was shown to improve the performance and robustness of controllers. We believe this is due to the ability of topological changes to stabilize attractors, promoting stability within a dynamical regime while allowing rapid switching between different regimes. Post hoc analysis of the controllers also demonstrated how the partitioning of the networks could provide new insights into problem structure.

ClueNet: Clustering a temporal network based on topological similarity rather than denseness.

PubMed

Crawford, Joseph; Milenković, Tijana

2018-01-01

Network clustering is a very popular topic in the network science field. Its goal is to divide (partition) the network into groups (clusters or communities) of "topologically related" nodes, where the resulting topology-based clusters are expected to "correlate" well with node label information, i.e., metadata, such as cellular functions of genes/proteins in biological networks, or age or gender of people in social networks. Even for static data, the problem of network clustering is complex. For dynamic data, the problem is even more complex, due to an additional dimension of the data-their temporal (evolving) nature. Since the problem is computationally intractable, heuristic approaches need to be sought. Existing approaches for dynamic network clustering (DNC) have drawbacks. First, they assume that nodes should be in the same cluster if they are densely interconnected within the network. We hypothesize that in some applications, it might be of interest to cluster nodes that are topologically similar to each other instead of or in addition to requiring the nodes to be densely interconnected. Second, they ignore temporal information in their early steps, and when they do consider this information later on, they do so implicitly. We hypothesize that capturing temporal information earlier in the clustering process and doing so explicitly will improve results. We test these two hypotheses via our new approach called ClueNet. We evaluate ClueNet against six existing DNC methods on both social networks capturing evolving interactions between individuals (such as interactions between students in a high school) and biological networks capturing interactions between biomolecules in the cell at different ages. We find that ClueNet is superior in over 83% of all evaluation tests. As more real-world dynamic data are becoming available, DNC and thus ClueNet will only continue to gain importance.

Topology-function conservation in protein-protein interaction networks.

PubMed

Davis, Darren; Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Stojmirovic, Aleksandar; Pržulj, Nataša

2015-05-15

Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. © The Author 2015. Published by Oxford University Press.

Metrics for comparing neuronal tree shapes based on persistent homology.

PubMed

Li, Yanjie; Wang, Dingkang; Ascoli, Giorgio A; Mitra, Partha; Wang, Yusu

2017-01-01

As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching) typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures), by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max) of morphometric quantities-Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as points in a simple Euclidean feature space, which would be important for constructing efficient searching or indexing structures over them. We present preliminary experimental results to demonstrate the effectiveness of our persistence-based neuronal feature vectorization framework.

Metrics for comparing neuronal tree shapes based on persistent homology

PubMed Central

Li, Yanjie; Wang, Dingkang; Ascoli, Giorgio A.; Mitra, Partha

2017-01-01

As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching) typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures), by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max) of morphometric quantities—Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as points in a simple Euclidean feature space, which would be important for constructing efficient searching or indexing structures over them. We present preliminary experimental results to demonstrate the effectiveness of our persistence-based neuronal feature vectorization framework. PMID:28809960

Optimal steering for kinematic vehicles with applications to spatially distributed agents

NASA Astrophysics Data System (ADS)

Brown, Scott; Praeger, Cheryl E.; Giudici, Michael

While there is no universal method to address control problems involving networks of autonomous vehicles, there exist a few promising schemes that apply to different specific classes of problems, which have attracted the attention of many researchers from different fields. In particular, one way to extend techniques that address problems involving a single autonomous vehicle to those involving teams of autonomous vehicles is to use the concept of Voronoi diagram. The Voronoi diagram provides a spatial partition of the environment the team of vehicles operate in, where each element of this partition is associated with a unique vehicle from the team. The partition induces a graph abstraction of the operating space that is in an one-to-one correspondence with the network abstraction of the team of autonomous vehicles; a fact that can provide both conceptual and analytical advantages during mission planning and execution. In this dissertation, we propose the use of a new class of Voronoi-like partitioning schemes with respect to state-dependent proximity (pseudo-) metrics rather than the Euclidean distance or other generalized distance functions, which are typically used in the literature. An important nuance here is that, in contrast to the Euclidean distance, state-dependent metrics can succinctly capture system theoretic features of each vehicle from the team (e.g., vehicle kinematics), as well as the environment-vehicle interactions, which are induced, for example, by local winds/currents. We subsequently illustrate how the proposed concept of state-dependent Voronoi-like partition can induce local control schemes for problems involving networks of spatially distributed autonomous vehicles by examining a sequential pursuit problem of a maneuvering target by a group of pursuers distributed in the plane. The construction of generalized Voronoi diagrams with respect to state-dependent metrics poses some significant challenges. First, the generalized distance metric may be a function of the direction of motion of the vehicle (anisotropic pseudo-distance function) and/or may not be expressible in closed form. Second, such problems fall under the general class of partitioning problems for which the vehicles' dynamics must be taken into account. The topology of the vehicle's configuration space may be non-Euclidean, for example, it may be a manifold embedded in a Euclidean space. In other words, these problems may not be reducible to generalized Voronoi diagram problems for which efficient construction schemes, analytical and/or computational, exist in the literature. This research effort pursues three main objectives. First, we present the complete solution of different steering problems involving a single vehicle in the presence of motion constraints imposed by the maneuverability envelope of the vehicle and/or the presence of a drift field induced by winds/currents in its vicinity. The analysis of each steering problem involving a single vehicle provides us with a state-dependent generalized metric, such as the minimum time-to-go/come. We subsequently use these state-dependent generalized distance functions as the proximity metrics in the formulation of generalized Voronoi-like partitioning problems. The characterization of the solutions of these state-dependent Voronoi-like partitioning problems using either analytical or computational techniques constitutes the second main objective of this dissertation. The third objective of this research effort is to illustrate the use of the proposed concept of state-dependent Voronoi-like partition as a means for passing from control techniques that apply to problems involving a single vehicle to problems involving networks of spatially distributed autonomous vehicles. To this aim, we formulate the problem of sequential/relay pursuit of a maneuvering target by a group of spatially distributed pursuers and subsequently propose a distributed group pursuit strategy that directly derives from the solution of a state-dependent Voronoi-like partitioning problem. (Abstract shortened by UMI.)

From r-spin intersection numbers to Hodge integrals

NASA Astrophysics Data System (ADS)

Ding, Xiang-Mao; Li, Yuping; Meng, Lingxian

2016-01-01

Generalized Kontsevich Matrix Model (GKMM) with a certain given potential is the partition function of r-spin intersection numbers. We represent this GKMM in terms of fermions and expand it in terms of the Schur polynomials by boson-fermion correspondence, and link it with a Hurwitz partition function and a Hodge partition by operators in a widehat{GL}(∞) group. Then, from a W 1+∞ constraint of the partition function of r-spin intersection numbers, we get a W 1+∞ constraint for the Hodge partition function. The W 1+∞ constraint completely determines the Schur polynomials expansion of the Hodge partition function.

Bounds for the Eventual Positivity of Difference Functions of Partitions

NASA Astrophysics Data System (ADS)

Woodford, Roger

2007-01-01

In this paper we specialize work done by Bateman and Erdos concerning difference functions of partition functions. In particular, we are concerned with partitions into fixed powers of the primes. We show that any difference function of these partition functions is eventually increasing, and derive explicit bounds for when it will attain strictly positive values. From these bounds an asymptotic result is derived.

[Three-dimensional genome organization: a lesson from the Polycomb-Group proteins].

PubMed

Bantignies, Frédéric

2013-01-01

As more and more genomes are being explored and annotated, important features of three-dimensional (3D) genome organization are just being uncovered. In the light of what we know about Polycomb group (PcG) proteins, we will present the latest findings on this topic. The PcG proteins are well-conserved chromatin factors that repress transcription of numerous target genes. They bind the genome at specific sites, forming chromatin domains of associated histone modifications as well as higher-order chromatin structures. These 3D chromatin structures involve the interactions between PcG-bound regulatory regions at short- and long-range distances, and may significantly contribute to PcG function. Recent high throughput "Chromosome Conformation Capture" (3C) analyses have revealed many other higher order structures along the chromatin fiber, partitioning the genomes into well demarcated topological domains. This revealed an unprecedented link between linear epigenetic domains and chromosome architecture, which might be intimately connected to genome function. © Société de Biologie, 2013.

Path similarity skeleton graph matching.

PubMed

Bai, Xiang; Latecki, Longin Jan

2008-07-01

This paper presents a novel framework to for shape recognition based on object silhouettes. The main idea is to match skeleton graphs by comparing the shortest paths between skeleton endpoints. In contrast to typical tree or graph matching methods, we completely ignore the topological graph structure. Our approach is motivated by the fact that visually similar skeleton graphs may have completely different topological structures. The proposed comparison of shortest paths between endpoints of skeleton graphs yields correct matching results in such cases. The skeletons are pruned by contour partitioning with Discrete Curve Evolution, which implies that the endpoints of skeleton branches correspond to visual parts of the objects. The experimental results demonstrate that our method is able to produce correct results in the presence of articulations, stretching, and occlusion.

Computation of entropy and Lyapunov exponent by a shift transform.

PubMed

Matsuoka, Chihiro; Hiraide, Koichi

2015-10-01

We present a novel computational method to estimate the topological entropy and Lyapunov exponent of nonlinear maps using a shift transform. Unlike the computation of periodic orbits or the symbolic dynamical approach by the Markov partition, the method presented here does not require any special techniques in computational and mathematical fields to calculate these quantities. In spite of its simplicity, our method can accurately capture not only the chaotic region but also the non-chaotic region (window region) such that it is important physically but the (Lebesgue) measure zero and usually hard to calculate or observe. Furthermore, it is shown that the Kolmogorov-Sinai entropy of the Sinai-Ruelle-Bowen measure (the physical measure) coincides with the topological entropy.

Computation of entropy and Lyapunov exponent by a shift transform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsuoka, Chihiro, E-mail: matsuoka.chihiro.mm@ehime-u.ac.jp; Hiraide, Koichi

2015-10-15

We present a novel computational method to estimate the topological entropy and Lyapunov exponent of nonlinear maps using a shift transform. Unlike the computation of periodic orbits or the symbolic dynamical approach by the Markov partition, the method presented here does not require any special techniques in computational and mathematical fields to calculate these quantities. In spite of its simplicity, our method can accurately capture not only the chaotic region but also the non-chaotic region (window region) such that it is important physically but the (Lebesgue) measure zero and usually hard to calculate or observe. Furthermore, it is shown thatmore » the Kolmogorov-Sinai entropy of the Sinai-Ruelle-Bowen measure (the physical measure) coincides with the topological entropy.« less

Poincare recurrence theorem and the strong CP problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalloniatis, Alex C.; Nedelko, Sergei N.; Bogoliubov Laboratory of Theoretical Physics, JINR, 141980 Dubna

2006-02-01

The existence in the physical QCD vacuum of nonzero gluon condensates, such as , requires dominance of gluon fields with finite mean action density. This naturally allows any real number value for the unit 'topological charge' q characterizing the fields approximating the gluon configurations which should dominate the QCD partition function. If q is an irrational number then the critical values of the {theta} parameter for which CP is spontaneously broken are dense in R, which provides for a mechanism of resolving the strong CP problem simultaneously with a correct implementation of U{sub A}(1) symmetry. We present anmore » explicit realization of this mechanism within a QCD motivated domain model. Some model independent arguments are given that suggest the relevance of this mechanism also to genuine QCD.« less

A hop count based heuristic routing protocol for mobile delay tolerant networks.

PubMed

You, Lei; Li, Jianbo; Wei, Changjiang; Dai, Chenqu; Xu, Jixing; Hu, Lejuan

2014-01-01

Routing in delay tolerant networks (DTNs) is a challenge since it must handle network partitioning, long delays, and dynamic topology. Meanwhile, routing protocols of the traditional mobile ad hoc networks (MANETs) cannot work well due to the failure of its assumption that most network connections are available. In this paper, we propose a hop count based heuristic routing protocol by utilizing the information carried by the peripatetic packets in the network. A heuristic function is defined to help in making the routing decision. We formally define a custom operation for square matrices so as to transform the heuristic value calculation into matrix manipulation. Finally, the performance of our proposed algorithm is evaluated by the simulation results, which show the advantage of such self-adaptive routing protocol in the diverse circumstance of DTNs.

Fivebranes and 3-manifold homology

NASA Astrophysics Data System (ADS)

Gukov, Sergei; Putrov, Pavel; Vafa, Cumrun

2017-07-01

Motivated by physical constructions of homological knot invariants, we study their analogs for closed 3-manifolds. We show that fivebrane compactifications provide a universal description of various old and new homological invariants of 3-manifolds. In terms of 3d/3d correspondence, such invariants are given by the Q-cohomology of the Hilbert space of partially topologically twisted 3d N=2 theory T[ M 3] on a Riemann surface with defects. We demonstrate this by concrete and explicit calculations in the case of monopole/Heegaard Floer homology and a 3-manifold analog of Khovanov-Rozansky link homology. The latter gives a categorification of Chern-Simons partition function. Some of the new key elements include the explicit form of the S-transform and a novel connection between categorification and a previously mysterious role of Eichler integrals in Chern-Simons theory.

A Hop Count Based Heuristic Routing Protocol for Mobile Delay Tolerant Networks

PubMed Central

Wei, Changjiang; Dai, Chenqu; Xu, Jixing; Hu, Lejuan

2014-01-01

Routing in delay tolerant networks (DTNs) is a challenge since it must handle network partitioning, long delays, and dynamic topology. Meanwhile, routing protocols of the traditional mobile ad hoc networks (MANETs) cannot work well due to the failure of its assumption that most network connections are available. In this paper, we propose a hop count based heuristic routing protocol by utilizing the information carried by the peripatetic packets in the network. A heuristic function is defined to help in making the routing decision. We formally define a custom operation for square matrices so as to transform the heuristic value calculation into matrix manipulation. Finally, the performance of our proposed algorithm is evaluated by the simulation results, which show the advantage of such self-adaptive routing protocol in the diverse circumstance of DTNs. PMID:25110736

Functional determinants, index theorems, and exact quantum black hole entropy

NASA Astrophysics Data System (ADS)

Murthy, Sameer; Reys, Valentin

2015-12-01

The exact quantum entropy of BPS black holes can be evaluated using localization in supergravity. An important ingredient in this program, that has been lacking so far, is the one-loop effect arising from the quadratic fluctuations of the exact deformation (the QV operator). We compute the fluctuation determinant for vector multiplets and hyper multiplets around Q-invariant off-shell configurations in four-dimensional N=2 supergravity with AdS 2 × S 2 boundary conditions, using the Atiyah-Bott fixed-point index theorem and a subsequent zeta function regularization. Our results extend the large-charge on-shell entropy computations in the literature to a regime of finite charges. Based on our results, we present an exact formula for the quantum entropy of BPS black holes in N=2 supergravity. We explain cancellations concerning 1/8 -BPS black holes in N=8 supergravity that were observed in arXiv:1111.1161. We also make comments about the interpretation of a logarithmic term in the topological string partition function in the low energy supergravity theory.

Modeling On-Body DTN Packet Routing Delay in the Presence of Postural Disconnections.

PubMed

Quwaider, Muhannad; Taghizadeh, Mahmoud; Biswas, Subir

2011-01-01

This paper presents a stochastic modeling framework for store-and-forward packet routing in Wireless Body Area Networks ( WBAN ) with postural partitioning. A prototype WBANs has been constructed for experimentally characterizing and capturing on-body topology disconnections in the presence of ultrashort range radio links, unpredictable RF attenuation, and human postural mobility. Delay modeling techniques for evaluating single-copy on-body DTN routing protocols are then developed. End-to-end routing delay for a series of protocols including opportunistic, randomized, and two other mechanisms that capture multiscale topological localities in human postural movements have been evaluated. Performance of the analyzed protocols are then evaluated experimentally and via simulation to compare with the results obtained from the developed model. Finally, a mechanism for evaluating the topological importance of individual on-body sensor nodes is developed. It is shown that such information can be used for selectively reducing the on-body sensor-count without substantially sacrificing the packet delivery delay.

Modeling On-Body DTN Packet Routing Delay in the Presence of Postural Disconnections

PubMed Central

Quwaider, Muhannad; Taghizadeh, Mahmoud; Biswas, Subir

2014-01-01

This paper presents a stochastic modeling framework for store-and-forward packet routing in Wireless Body Area Networks (WBAN) with postural partitioning. A prototype WBANs has been constructed for experimentally characterizing and capturing on-body topology disconnections in the presence of ultrashort range radio links, unpredictable RF attenuation, and human postural mobility. Delay modeling techniques for evaluating single-copy on-body DTN routing protocols are then developed. End-to-end routing delay for a series of protocols including opportunistic, randomized, and two other mechanisms that capture multiscale topological localities in human postural movements have been evaluated. Performance of the analyzed protocols are then evaluated experimentally and via simulation to compare with the results obtained from the developed model. Finally, a mechanism for evaluating the topological importance of individual on-body sensor nodes is developed. It is shown that such information can be used for selectively reducing the on-body sensor-count without substantially sacrificing the packet delivery delay. PMID:25530749

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

PubMed Central

Ulianov, Sergey V.; Khrameeva, Ekaterina E.; Gavrilov, Alexey A.; Flyamer, Ilya M.; Kos, Pavel; Mikhaleva, Elena A.; Penin, Aleksey A.; Logacheva, Maria D.; Imakaev, Maxim V.; Chertovich, Alexander; Gelfand, Mikhail S.; Shevelyov, Yuri Y.; Razin, Sergey V.

2016-01-01

Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)+ RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin. PMID:26518482

Partitioning in Avionics Architectures: Requirements, Mechanisms, and Assurance

NASA Technical Reports Server (NTRS)

Rushby, John

1999-01-01

Automated aircraft control has traditionally been divided into distinct "functions" that are implemented separately (e.g., autopilot, autothrottle, flight management); each function has its own fault-tolerant computer system, and dependencies among different functions are generally limited to the exchange of sensor and control data. A by-product of this "federated" architecture is that faults are strongly contained within the computer system of the function where they occur and cannot readily propagate to affect the operation of other functions. More modern avionics architectures contemplate supporting multiple functions on a single, shared, fault-tolerant computer system where natural fault containment boundaries are less sharply defined. Partitioning uses appropriate hardware and software mechanisms to restore strong fault containment to such integrated architectures. This report examines the requirements for partitioning, mechanisms for their realization, and issues in providing assurance for partitioning. Because partitioning shares some concerns with computer security, security models are reviewed and compared with the concerns of partitioning.

Geometry of complex networks and topological centrality

NASA Astrophysics Data System (ADS)

Ranjan, Gyan; Zhang, Zhi-Li

2013-09-01

We explore the geometry of complex networks in terms of an n-dimensional Euclidean embedding represented by the Moore-Penrose pseudo-inverse of the graph Laplacian (L). The squared distance of a node i to the origin in this n-dimensional space (lii+), yields a topological centrality index, defined as C∗(i)=1/lii+. In turn, the sum of reciprocals of individual node centralities, ∑i1/C∗(i)=∑ilii+, or the trace of L, yields the well-known Kirchhoff index (K), an overall structural descriptor for the network. To put into context this geometric definition of centrality, we provide alternative interpretations of the proposed indices that connect them to meaningful topological characteristics - first, as forced detour overheads and frequency of recurrences in random walks that has an interesting analogy to voltage distributions in the equivalent electrical network; and then as the average connectedness of i in all the bi-partitions of the graph. These interpretations respectively help establish the topological centrality (C∗(i)) of node i as a measure of its overall position as well as its overall connectedness in the network; thus reflecting the robustness of i to random multiple edge failures. Through empirical evaluations using synthetic and real world networks, we demonstrate how the topological centrality is better able to distinguish nodes in terms of their structural roles in the network and, along with Kirchhoff index, is appropriately sensitive to perturbations/re-wirings in the network.

A stochastic model of tree architecture and biomass partitioning: application to Mongolian Scots pines.

PubMed

Wang, Feng; Kang, Mengzhen; Lu, Qi; Letort, Véronique; Han, Hui; Guo, Yan; de Reffye, Philippe; Li, Baoguo

2011-04-01

Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal species used for windbreak and sand stabilization in arid and semi-arid areas in northern China. A model-assisted analysis of its canopy architectural development and functions is valuable for better understanding its behaviour and roles in fragile ecosystems. However, due to the intrinsic complexity and variability of trees, the parametric identification of such models is currently a major obstacle to their evaluation and their validation with respect to real data. The aim of this paper was to present the mathematical framework of a stochastic functional-structural model (GL2) and its parameterization for Mongolian Scots pines, taking into account inter-plant variability in terms of topological development and biomass partitioning. In GL2, plant organogenesis is determined by the realization of random variables representing the behaviour of axillary or apical buds. The associated probabilities are calibrated for Mongolian Scots pines using experimental data including means and variances of the numbers of organs per plant in each order-based class. The functional part of the model relies on the principles of source-sink regulation and is parameterized by direct observations of living trees and the inversion method using measured data for organ mass and dimensions. The final calibration accuracy satisfies both organogenetic and morphogenetic processes. Our hypothesis for the number of organs following a binomial distribution is found to be consistent with the real data. Based on the calibrated parameters, stochastic simulations of the growth of Mongolian Scots pines in plantations are generated by the Monte Carlo method, allowing analysis of the inter-individual variability of the number of organs and biomass partitioning. Three-dimensional (3D) architectures of young Mongolian Scots pines were simulated for 4-, 6- and 8-year-old trees. This work provides a new method for characterizing tree structures and biomass allocation that can be used to build a 3D virtual Mongolian Scots pine forest. The work paves the way for bridging the gap between a single-plant model and a stand model.

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

PubMed Central

Dietmann, Sabine; Park, Jong; Notredame, Cedric; Heger, Andreas; Lappe, Michael; Holm, Liisa

2001-01-01

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families. PMID:11125048

ClueNet: Clustering a temporal network based on topological similarity rather than denseness

PubMed Central

Milenković, Tijana

2018-01-01

Network clustering is a very popular topic in the network science field. Its goal is to divide (partition) the network into groups (clusters or communities) of “topologically related” nodes, where the resulting topology-based clusters are expected to “correlate” well with node label information, i.e., metadata, such as cellular functions of genes/proteins in biological networks, or age or gender of people in social networks. Even for static data, the problem of network clustering is complex. For dynamic data, the problem is even more complex, due to an additional dimension of the data—their temporal (evolving) nature. Since the problem is computationally intractable, heuristic approaches need to be sought. Existing approaches for dynamic network clustering (DNC) have drawbacks. First, they assume that nodes should be in the same cluster if they are densely interconnected within the network. We hypothesize that in some applications, it might be of interest to cluster nodes that are topologically similar to each other instead of or in addition to requiring the nodes to be densely interconnected. Second, they ignore temporal information in their early steps, and when they do consider this information later on, they do so implicitly. We hypothesize that capturing temporal information earlier in the clustering process and doing so explicitly will improve results. We test these two hypotheses via our new approach called ClueNet. We evaluate ClueNet against six existing DNC methods on both social networks capturing evolving interactions between individuals (such as interactions between students in a high school) and biological networks capturing interactions between biomolecules in the cell at different ages. We find that ClueNet is superior in over 83% of all evaluation tests. As more real-world dynamic data are becoming available, DNC and thus ClueNet will only continue to gain importance. PMID:29738568

Covalent bond orders and atomic valences from correlated wavefunctions

NASA Astrophysics Data System (ADS)

Ángyán, János G.; Rosta, Edina; Surján, Péter R.

1999-01-01

A comparison is made between two alternative definitions for covalent bond orders: one derived from the exchange part of the two-particle density matrix and the other expressed as the correlation of fluctuations (covariance) of the number of electrons between the atomic centers. Although these definitions lead to identical formulae for mono-determinantal SCF wavefunctions, they predict different bond orders for correlated wavefunctions. It is shown that, in this case, the fluctuation-based definition leads to slightly lower values of the bond order than does the exchange-based definition, provided one uses an appropriate space-partitioning technique like that of Bader's topological theory of atoms in a molecule; however, use of Mulliken partitioning in this context leads to unphysical behaviour. The example of H 2 is discussed in detail.

Canonical partition functions: ideal quantum gases, interacting classical gases, and interacting quantum gases

NASA Astrophysics Data System (ADS)

Zhou, Chi-Chun; Dai, Wu-Sheng

2018-02-01

In statistical mechanics, for a system with a fixed number of particles, e.g. a finite-size system, strictly speaking, the thermodynamic quantity needs to be calculated in the canonical ensemble. Nevertheless, the calculation of the canonical partition function is difficult. In this paper, based on the mathematical theory of the symmetric function, we suggest a method for the calculation of the canonical partition function of ideal quantum gases, including ideal Bose, Fermi, and Gentile gases. Moreover, we express the canonical partition functions of interacting classical and quantum gases given by the classical and quantum cluster expansion methods in terms of the Bell polynomial in mathematics. The virial coefficients of ideal Bose, Fermi, and Gentile gases are calculated from the exact canonical partition function. The virial coefficients of interacting classical and quantum gases are calculated from the canonical partition function by using the expansion of the Bell polynomial, rather than calculated from the grand canonical potential.

Functional and topological characteristics of mammalian regulatory domains

PubMed Central

Symmons, Orsolya; Uslu, Veli Vural; Tsujimura, Taro; Ruf, Sandra; Nassari, Sonya; Schwarzer, Wibke; Ettwiller, Laurence; Spitz, François

2014-01-01

Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene regulatory activities along the mouse genome, using hundreds of insertions of a regulatory sensor. We found that enhancers distribute their activities along broad regions and not in a gene-centric manner, defining large regulatory domains. Remarkably, these domains correlate strongly with the recently described TADs, which partition the genome into distinct self-interacting blocks. Different features, including specific repeats and CTCF-binding sites, correlate with the transition zones separating regulatory domains, and may help to further organize promiscuously distributed regulatory influences within large domains. These findings support a model of genomic organization where TADs confine regulatory activities to specific but large regulatory domains, contributing to the establishment of specific gene expression profiles. PMID:24398455

Fivebranes and 3-manifold homology

DOE PAGES

Gukov, Sergei; Putrov, Pavel; Vafa, Cumrun

2017-07-14

Motivated by physical constructions of homological knot invariants, we study their analogs for closed 3-manifolds. We show that vebrane compacti cations provide a universal description of various old and new homological invariants of 3-manifolds. In terms of 3d/3d correspondence, such invariants are given by the Q-cohomology of the Hilbert space of partially topologically twisted 3d N = 2 theory T[M 3] on a Riemann surface with defects. We demonstrate this by concrete and explicit calculations in the case of monopole/Heegaard Floer homology and a 3-manifold analog of Khovanov-Rozansky link homology. The latter gives a categori cation of Chern-Simons partition function.more » Finally, some of the new key elements include the explicit form of the S-transform and a novel connection between categori cation and a previously mysterious role of Eichler integrals in Chern-Simons theory.« less

Cylindric partitions, {{\\boldsymbol{ W }}}_{r} characters and the Andrews-Gordon-Bressoud identities

NASA Astrophysics Data System (ADS)

Foda, O.; Welsh, T. A.

2016-04-01

We study the Andrews-Gordon-Bressoud (AGB) generalisations of the Rogers-Ramanujan q-series identities in the context of cylindric partitions. We recall the definition of r-cylindric partitions, and provide a simple proof of Borodin’s product expression for their generating functions, that can be regarded as a limiting case of an unpublished proof by Krattenthaler. We also recall the relationships between the r-cylindric partition generating functions, the principal characters of {\\hat{{sl}}}r algebras, the {{\\boldsymbol{ M }}}r r,r+d minimal model characters of {{\\boldsymbol{ W }}}r algebras, and the r-string abaci generating functions, providing simple proofs for each. We then set r = 2, and use two-cylindric partitions to re-derive the AGB identities as follows. Firstly, we use Borodin’s product expression for the generating functions of the two-cylindric partitions with infinitely long parts, to obtain the product sides of the AGB identities, times a factor {(q;q)}∞ -1, which is the generating function of ordinary partitions. Next, we obtain a bijection from the two-cylindric partitions, via two-string abaci, into decorated versions of Bressoud’s restricted lattice paths. Extending Bressoud’s method of transforming between restricted paths that obey different restrictions, we obtain sum expressions with manifestly non-negative coefficients for the generating functions of the two-cylindric partitions which contains a factor {(q;q)}∞ -1. Equating the product and sum expressions of the same two-cylindric partitions, and canceling a factor of {(q;q)}∞ -1 on each side, we obtain the AGB identities.

A Study of the Thermal Environment Developed by a Traveling Slipper at High Velocity

DTIC Science & Technology

2013-03-01

Power Partition Function The next partition function takes the same formulation as the powered function but now the exponent is squared. The...function and note the squared term in the exponent . 66 Equation 4.27 (4.36) Thus far the three partition functions each give a predicted...hypothesized that the function would fall somewhere between the first exponential decay function and the power function. However, by squaring the exponent

Visibility graphs and symbolic dynamics

NASA Astrophysics Data System (ADS)

Lacasa, Lucas; Just, Wolfram

2018-07-01

Visibility algorithms are a family of geometric and ordering criteria by which a real-valued time series of N data is mapped into a graph of N nodes. This graph has been shown to often inherit in its topology nontrivial properties of the series structure, and can thus be seen as a combinatorial representation of a dynamical system. Here we explore in some detail the relation between visibility graphs and symbolic dynamics. To do that, we consider the degree sequence of horizontal visibility graphs generated by the one-parameter logistic map, for a range of values of the parameter for which the map shows chaotic behaviour. Numerically, we observe that in the chaotic region the block entropies of these sequences systematically converge to the Lyapunov exponent of the time series. Hence, Pesin's identity suggests that these block entropies are converging to the Kolmogorov-Sinai entropy of the physical measure, which ultimately suggests that the algorithm is implicitly and adaptively constructing phase space partitions which might have the generating property. To give analytical insight, we explore the relation k(x) , x ∈ [ 0 , 1 ] that, for a given datum with value x, assigns in graph space a node with degree k. In the case of the out-degree sequence, such relation is indeed a piece-wise constant function. By making use of explicit methods and tools from symbolic dynamics we are able to analytically show that the algorithm indeed performs an effective partition of the phase space and that such partition is naturally expressed as a countable union of subintervals, where the endpoints of each subinterval are related to the fixed point structure of the iterates of the map and the subinterval enumeration is associated with particular ordering structures that we called motifs.

Task-specific image partitioning.

PubMed

Kim, Sungwoong; Nowozin, Sebastian; Kohli, Pushmeet; Yoo, Chang D

2013-02-01

Image partitioning is an important preprocessing step for many of the state-of-the-art algorithms used for performing high-level computer vision tasks. Typically, partitioning is conducted without regard to the task in hand. We propose a task-specific image partitioning framework to produce a region-based image representation that will lead to a higher task performance than that reached using any task-oblivious partitioning framework and existing supervised partitioning framework, albeit few in number. The proposed method partitions the image by means of correlation clustering, maximizing a linear discriminant function defined over a superpixel graph. The parameters of the discriminant function that define task-specific similarity/dissimilarity among superpixels are estimated based on structured support vector machine (S-SVM) using task-specific training data. The S-SVM learning leads to a better generalization ability while the construction of the superpixel graph used to define the discriminant function allows a rich set of features to be incorporated to improve discriminability and robustness. We evaluate the learned task-aware partitioning algorithms on three benchmark datasets. Results show that task-aware partitioning leads to better labeling performance than the partitioning computed by the state-of-the-art general-purpose and supervised partitioning algorithms. We believe that the task-specific image partitioning paradigm is widely applicable to improving performance in high-level image understanding tasks.

Molecular phylogeny of the aquatic beetle family Noteridae (Coleoptera: Adephaga) with an emphasis on data partitioning strategies.

PubMed

Baca, Stephen M; Toussaint, Emmanuel F A; Miller, Kelly B; Short, Andrew E Z

2017-02-01

The first molecular phylogenetic hypothesis for the aquatic beetle family Noteridae is inferred using DNA sequence data from five gene fragments (mitochondrial and nuclear): COI, H3, 16S, 18S, and 28S. Our analysis is the most comprehensive phylogenetic reconstruction of Noteridae to date, and includes 53 species representing all subfamilies, tribes and 16 of the 17 genera within the family. We examine the impact of data partitioning on phylogenetic inference by comparing two different algorithm-based partitioning strategies: one using predefined subsets of the dataset, and another recently introduced method, which uses the k-means algorithm to iteratively divide the dataset into clusters of sites evolving at similar rates across sampled loci. We conducted both maximum likelihood and Bayesian inference analyses using these different partitioning schemes. Resulting trees are strongly incongruent with prior classifications of Noteridae. We recover variant tree topologies and support values among the implemented partitioning schemes. Bayes factors calculated with marginal likelihoods of Bayesian analyses support a priori partitioning over k-means and unpartitioned data strategies. Our study substantiates the importance of data partitioning in phylogenetic inference, and underscores the use of comparative analyses to determine optimal analytical strategies. Our analyses recover Noterini Thomson to be paraphyletic with respect to three other tribes. The genera Suphisellus Crotch and Hydrocanthus Say are also recovered as paraphyletic. Following the results of the preferred partitioning scheme, we here propose a revised classification of Noteridae, comprising two subfamilies, three tribes and 18 genera. The following taxonomic changes are made: Notomicrinae sensu n. (= Phreatodytinae syn. n.) is expanded to include the tribe Phreatodytini; Noterini sensu n. (= Neohydrocoptini syn. n., Pronoterini syn. n., Tonerini syn. n.) is expanded to include all genera of the Noterinae; The genus Suphisellus Crotch is expanded to include species of Pronoterus Sharp syn. n.; and the former subgenus Sternocanthus Guignot stat. rev. is resurrected from synonymy and elevated to genus rank. Copyright © 2016 Elsevier Inc. All rights reserved.

Combining in silico evolution and nonlinear dimensionality reduction to redesign responses of signaling networks

NASA Astrophysics Data System (ADS)

Prescott, Aaron M.; Abel, Steven M.

2016-12-01

The rational design of network behavior is a central goal of synthetic biology. Here, we combine in silico evolution with nonlinear dimensionality reduction to redesign the responses of fixed-topology signaling networks and to characterize sets of kinetic parameters that underlie various input-output relations. We first consider the earliest part of the T cell receptor (TCR) signaling network and demonstrate that it can produce a variety of input-output relations (quantified as the level of TCR phosphorylation as a function of the characteristic TCR binding time). We utilize an evolutionary algorithm (EA) to identify sets of kinetic parameters that give rise to: (i) sigmoidal responses with the activation threshold varied over 6 orders of magnitude, (ii) a graded response, and (iii) an inverted response in which short TCR binding times lead to activation. We also consider a network with both positive and negative feedback and use the EA to evolve oscillatory responses with different periods in response to a change in input. For each targeted input-output relation, we conduct many independent runs of the EA and use nonlinear dimensionality reduction to embed the resulting data for each network in two dimensions. We then partition the results into groups and characterize constraints placed on the parameters by the different targeted response curves. Our approach provides a way (i) to guide the design of kinetic parameters of fixed-topology networks to generate novel input-output relations and (ii) to constrain ranges of biological parameters using experimental data. In the cases considered, the network topologies exhibit significant flexibility in generating alternative responses, with distinct patterns of kinetic rates emerging for different targeted responses.

Contribution of Topology Determinants of a Viral Movement Protein to Its Membrane Association, Intracellular Traffic, and Viral Cell-to-Cell Movement▿†

PubMed Central

Genovés, A.; Pallás, V.; Navarro, J. A.

2011-01-01

The p7B movement protein (MP) of Melon necrotic spot virus (MNSV) is a single-pass membrane protein associated with the endoplasmic reticulum (ER), the Golgi apparatus (GA), and plasmodesmata (Pd). Experimental data presented here revealed that the p7B transmembrane domain (TMD) was sufficient to target the green fluorescent protein (GFP) to ER membranes. In addition, the short extramembrane regions of p7B were essential for subsequent ER export and transport to the GA and Pd. Microsomal partitioning and bimolecular fluorescence assays supported a type II topology of p7B in planta. Mutations affecting conventional determinants of p7B membrane topology, such as the TMD secondary structure, the overall hydrophobicity profile, the so-called “aromatic belt,” and the net charge distribution on either side of the TMD, were engineered into infectious RNAs to investigate the relationship between the MP structure and MNSV cell-to-cell movement. The results revealed that (i) the overall hydrophobic profile and the α-helix integrity of the TMD were relevant for virus movement, (ii) modification of the net charge balance of the regions flanking both TMD sides drastically reduced cell-to-cell movement, (iii) localization of p7B to the GA was necessary but not sufficient for virus movement, and (iv) membrane insertion was essential for p7B function in virus movement. Our results therefore indicate that MNSV cell-to-cell movement requires sequential transport of p7B from the ER via the GA to Pd, which is modulated by a combination of several signals with different strengths in the extramembrane regions and TMD of the MP. PMID:21593169

Intersecting surface defects and instanton partition functions

NASA Astrophysics Data System (ADS)

Pan, Yiwen; Peelaers, Wolfger

2017-07-01

We analyze intersecting surface defects inserted in interacting four-dimensional N=2 supersymmetric quantum field theories. We employ the realization of a class of such systems as the infrared fixed points of renormalization group flows from larger theories, triggered by perturbed Seiberg-Witten monopole-like configurations, to compute their partition functions. These results are cast into the form of a partition function of 4d/2d/0d coupled systems. Our computations provide concrete expressions for the instanton partition function in the presence of intersecting defects and we study the corresponding ADHM model.

Off-diagonal series expansion for quantum partition functions

NASA Astrophysics Data System (ADS)

Hen, Itay

2018-05-01

We derive an integral-free thermodynamic perturbation series expansion for quantum partition functions which enables an analytical term-by-term calculation of the series. The expansion is carried out around the partition function of the classical component of the Hamiltonian with the expansion parameter being the strength of the off-diagonal, or quantum, portion. To demonstrate the usefulness of the technique we analytically compute to third order the partition functions of the 1D Ising model with longitudinal and transverse fields, and the quantum 1D Heisenberg model.

Quantum corrections to Bekenstein-Hawking black hole entropy and gravity partition functions

NASA Astrophysics Data System (ADS)

Bytsenko, A. A.; Tureanu, A.

2013-08-01

Algebraic aspects of the computation of partition functions for quantum gravity and black holes in AdS3 are discussed. We compute the sub-leading quantum corrections to the Bekenstein-Hawking entropy. It is shown that the quantum corrections to the classical result can be included systematically by making use of the comparison with conformal field theory partition functions, via the AdS3/CFT2 correspondence. This leads to a better understanding of the role of modular and spectral functions, from the point of view of the representation theory of infinite-dimensional Lie algebras. Besides, the sum of known quantum contributions to the partition function can be presented in a closed form, involving the Patterson-Selberg spectral function. These contributions can be reproduced in a holomorphically factorized theory whose partition functions are associated with the formal characters of the Virasoro modules. We propose a spectral function formulation for quantum corrections to the elliptic genus from supergravity states.

Identifying essential proteins based on sub-network partition and prioritization by integrating subcellular localization information.

PubMed

Li, Min; Li, Wenkai; Wu, Fang-Xiang; Pan, Yi; Wang, Jianxin

2018-06-14

Essential proteins are important participants in various life activities and play a vital role in the survival and reproduction of living organisms. Identification of essential proteins from protein-protein interaction (PPI) networks has great significance to facilitate the study of human complex diseases, the design of drugs and the development of bioinformatics and computational science. Studies have shown that highly connected proteins in a PPI network tend to be essential. A series of computational methods have been proposed to identify essential proteins by analyzing topological structures of PPI networks. However, the high noise in the PPI data can degrade the accuracy of essential protein prediction. Moreover, proteins must be located in the appropriate subcellular localization to perform their functions, and only when the proteins are located in the same subcellular localization, it is possible that they can interact with each other. In this paper, we propose a new network-based essential protein discovery method based on sub-network partition and prioritization by integrating subcellular localization information, named SPP. The proposed method SPP was tested on two different yeast PPI networks obtained from DIP database and BioGRID database. The experimental results show that SPP can effectively reduce the effect of false positives in PPI networks and predict essential proteins more accurately compared with other existing computational methods DC, BC, CC, SC, EC, IC, NC. Copyright © 2018 Elsevier Ltd. All rights reserved.

Predicting crystal growth via a unified kinetic three-dimensional partition model

NASA Astrophysics Data System (ADS)

Anderson, Michael W.; Gebbie-Rayet, James T.; Hill, Adam R.; Farida, Nani; Attfield, Martin P.; Cubillas, Pablo; Blatov, Vladislav A.; Proserpio, Davide M.; Akporiaye, Duncan; Arstad, Bjørnar; Gale, Julian D.

2017-04-01

Understanding and predicting crystal growth is fundamental to the control of functionality in modern materials. Despite investigations for more than one hundred years, it is only recently that the molecular intricacies of these processes have been revealed by scanning probe microscopy. To organize and understand this large amount of new information, new rules for crystal growth need to be developed and tested. However, because of the complexity and variety of different crystal systems, attempts to understand crystal growth in detail have so far relied on developing models that are usually applicable to only one system. Such models cannot be used to achieve the wide scope of understanding that is required to create a unified model across crystal types and crystal structures. Here we describe a general approach to understanding and, in theory, predicting the growth of a wide range of crystal types, including the incorporation of defect structures, by simultaneous molecular-scale simulation of crystal habit and surface topology using a unified kinetic three-dimensional partition model. This entails dividing the structure into ‘natural tiles’ or Voronoi polyhedra that are metastable and, consequently, temporally persistent. As such, these units are then suitable for re-construction of the crystal via a Monte Carlo algorithm. We demonstrate our approach by predicting the crystal growth of a diverse set of crystal types, including zeolites, metal-organic frameworks, calcite, urea and L-cystine.

New approach to canonical partition functions computation in Nf=2 lattice QCD at finite baryon density

NASA Astrophysics Data System (ADS)

Bornyakov, V. G.; Boyda, D. L.; Goy, V. A.; Molochkov, A. V.; Nakamura, Atsushi; Nikolaev, A. A.; Zakharov, V. I.

2017-05-01

We propose and test a new approach to computation of canonical partition functions in lattice QCD at finite density. We suggest a few steps procedure. We first compute numerically the quark number density for imaginary chemical potential i μq I . Then we restore the grand canonical partition function for imaginary chemical potential using the fitting procedure for the quark number density. Finally we compute the canonical partition functions using high precision numerical Fourier transformation. Additionally we compute the canonical partition functions using the known method of the hopping parameter expansion and compare results obtained by two methods in the deconfining as well as in the confining phases. The agreement between two methods indicates the validity of the new method. Our numerical results are obtained in two flavor lattice QCD with clover improved Wilson fermions.

The Evolutionary History and Diverse Physiological Roles of the Grapevine Calcium-Dependent Protein Kinase Gene Family

PubMed Central

Chen, Fei; Fasoli, Marianna; Tornielli, Giovanni Battista; Dal Santo, Silvia; Pezzotti, Mario; Zhang, Liangsheng; Cai, Bin; Cheng, Zong-Ming

2013-01-01

Calcium-dependent protein kinases (CDPKs) are molecular switches that bind Ca2+, ATP, and protein substrates, acting as sensor relays and responders that convert Ca2+ signals, created by developmental processes and environmental stresses, into phosphorylation events. The precise functions of the CDPKs in grapevine (Vitis vinifera) are largely unknown. We therefore investigated the phylogenetic relationships and expression profiles of the 17 CDPK genes identified in the 12x grapevine genome sequence, resolving them into four subfamilies based on phylogenetic tree topology and gene structures. The origins of the CDPKs during grapevine evolution were characterized, involving 13 expansion events. Transcriptomic analysis using 54 tissues and developmental stages revealed three types of CDPK gene expression profiles: constitutive (housekeeping CDPKs), partitioned functions, and prevalent in pollen/stamen. We identified two duplicated CDPK genes that had evolved from housekeeping to pollen-prevalent functions and whose origin correlated with that of seed plants, suggesting neofunctionalization with an important role in pollen development and also potential value in the breeding of seedless varieties. We also found that CDPKs were involved in three abiotic stress signaling pathways and could therefore be used to investigate the crosstalk between stress responses. PMID:24324631

Optimality and self-organization in river deltas

NASA Astrophysics Data System (ADS)

Tejedor, A.; Longjas, A.; Edmonds, D. A.; Zaliapin, I. V.; Georgiou, T. T.; Rinaldo, A.; Foufoula-Georgiou, E.

2017-12-01

Deltas are nourished by channel networks, whose connectivity constrains, if not drives, the evolution, functionality and resilience of these systems. Understanding the coevolution of deltaic channels and their flux organization is crucial for guiding maintenance strategies of these highly stressed systems from a range of anthropogenic activities. However, in contrast to tributary channel networks, to date, no theory has been proposed to explain how deltas self-organize to distribute water and sediment to the delta top and the shoreline. Here, we hypothesize the existence of an optimality principle underlying the self-organized partition of fluxes in delta channel networks. Specifically, we hypothesize that deltas distribute water and sediment fluxes on a given delta topology such as to maximize the diversity of flux delivery to the shoreline. By introducing the concept of nonlocal Entropy Rate (nER) and analyzing ten field deltas in diverse environments, we present evidence that supports our hypothesis, suggesting that delta networks achieve dynamically accessible maxima of their nER. Furthermore, by analyzing six simulated deltas using the Delf3D model and following their topologic and flux re-organization before and after major avulsions, we further study the evolution of nER and confirm our hypothesis. We discuss how optimal flux distributions in terms of nER, when interpreted in terms of resilience, are configurations that reflect an increased ability to withstand perturbations.

Argyres–Douglas theories, S 1 reductions, and topological symmetries

DOE PAGES

Buican, Matthew; Nishinaka, Takahiro

2015-12-21

In a recent paper, we proposed closed-form expressions for the superconformal indices of the (A(1), A(2n-3)) and(A(1), D-2n) Argyres-Douglas (AD) superconformal field theories (SCFTs) in the Schur limit. Following up on our results, we turn our attention to the small S-1 regime of these indices. As expected on general grounds, our study reproduces the S-3 partition functions of the resulting dimensionally reduced theories. However, we show that in all cases-with the exception of the reduction of the (A(1), D-4) SCFTcertain imaginary partners of real mass terms are turned on in the corresponding mirror theories. We interpret these deformations as Rmore » symmetry mixing with the topological symmetries of the direct S-1 reductions. Moreover, we argue that these shifts occur in any of our theories whose four-dimensional N = 2 superconformal U(1)(R) symmetry does not obey an SU(2) quantization condition. We then use our R symmetry map to find the fourdimensional ancestors of certain three-dimensional operators. Somewhat surprisingly, this picture turns out to imply that the scaling dimensions of many of the chiral operators of the four-dimensional theory are encoded in accidental symmetries of the three-dimensional theory. We also comment on the implications of our work on the space of general N = 2 SCFTs.« less

Argyres–Douglas theories, S 1 reductions, and topological symmetries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buican, Matthew; Nishinaka, Takahiro

In a recent paper, we proposed closed-form expressions for the superconformal indices of the (A(1), A(2n-3)) and(A(1), D-2n) Argyres-Douglas (AD) superconformal field theories (SCFTs) in the Schur limit. Following up on our results, we turn our attention to the small S-1 regime of these indices. As expected on general grounds, our study reproduces the S-3 partition functions of the resulting dimensionally reduced theories. However, we show that in all cases-with the exception of the reduction of the (A(1), D-4) SCFTcertain imaginary partners of real mass terms are turned on in the corresponding mirror theories. We interpret these deformations as Rmore » symmetry mixing with the topological symmetries of the direct S-1 reductions. Moreover, we argue that these shifts occur in any of our theories whose four-dimensional N = 2 superconformal U(1)(R) symmetry does not obey an SU(2) quantization condition. We then use our R symmetry map to find the fourdimensional ancestors of certain three-dimensional operators. Somewhat surprisingly, this picture turns out to imply that the scaling dimensions of many of the chiral operators of the four-dimensional theory are encoded in accidental symmetries of the three-dimensional theory. We also comment on the implications of our work on the space of general N = 2 SCFTs.« less

Intersecting surface defects and instanton partition functions

DOE PAGES

Pan, Yiwen; Peelaers, Wolfger

2017-07-14

We analyze intersecting surface defects inserted in interacting four-dimensional N = 2 supersymmetric quantum field theories. We employ the realization of a class of such systems as the infrared xed points of renormalization group flows from larger theories, triggered by perturbed Seiberg-Witten monopole-like con gurations, to compute their partition functions. These results are cast into the form of a partition function of 4d/2d/0d coupled systems. In conclusion, our computations provide concrete expressions for the instanton partition function in the presence of intersecting defects and we study the corresponding ADHM model.

Intersecting surface defects and instanton partition functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Yiwen; Peelaers, Wolfger

We analyze intersecting surface defects inserted in interacting four-dimensional N = 2 supersymmetric quantum field theories. We employ the realization of a class of such systems as the infrared xed points of renormalization group flows from larger theories, triggered by perturbed Seiberg-Witten monopole-like con gurations, to compute their partition functions. These results are cast into the form of a partition function of 4d/2d/0d coupled systems. In conclusion, our computations provide concrete expressions for the instanton partition function in the presence of intersecting defects and we study the corresponding ADHM model.

Topological Landscapes: A Terrain Metaphor for ScientificData

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Gunther H.; Bremer, Peer-Timo; Pascucci, Valerio

2007-08-01

Scientific visualization and illustration tools are designed to help people understand the structure and complexity of scientific data with images that are as informative and intuitive as possible. In this context, the use of metaphors plays an important role, since they make complex information easily accessible by using commonly known concepts. In this paper we propose a new metaphor, called 'Topological Landscapes', which facilitates understanding the topological structure of scalar functions. The basic idea is to construct a terrain with the same topology as a given dataset and to display the terrain as an easily understood representation of the actualmore » input data. In this projection from an n-dimensional scalar function to a two-dimensional (2D) model we preserve function values of critical points, the persistence (function span) of topological features, and one possible additional metric property (in our examples volume). By displaying this topologically equivalent landscape together with the original data we harness the natural human proficiency in understanding terrain topography and make complex topological information easily accessible.« less

The partition function of the Bures ensemble as the τ-function of BKP and DKP hierarchies: continuous and discrete

NASA Astrophysics Data System (ADS)

Hu, Xing-Biao; Li, Shi-Hao

2017-07-01

The relationship between matrix integrals and integrable systems was revealed more than 20 years ago. As is known, matrix integrals over a Gaussian ensemble used in random matrix theory could act as the τ-function of several hierarchies of integrable systems. In this article, we will show that the time-dependent partition function of the Bures ensemble, whose measure has many interesting geometric properties, could act as the τ-function of BKP and DKP hierarchies. In addition, if discrete time variables are introduced, then this partition function could act as the τ-function of discrete BKP and DKP hierarchies. In particular, there are some links between the partition function of the Bures ensemble and Toda-type equations.

Analysis of red blood cell partitioning at bifurcations in simulated microvascular networks

NASA Astrophysics Data System (ADS)

Balogh, Peter; Bagchi, Prosenjit

2018-05-01

Partitioning of red blood cells (RBCs) at vascular bifurcations has been studied over many decades using in vivo, in vitro, and theoretical models. These studies have shown that RBCs usually do not distribute to the daughter vessels with the same proportion as the blood flow. Such disproportionality occurs, whereby the cell distribution fractions are either higher or lower than the flow fractions and have been referred to as classical partitioning and reverse partitioning, respectively. The current work presents a study of RBC partitioning based on, for the first time, a direct numerical simulation (DNS) of a flowing cell suspension through modeled vascular networks that are comprised of multiple bifurcations and have topological similarity to microvasculature in vivo. The flow of deformable RBCs at physiological hematocrits is considered through the networks, and the 3D dynamics of each individual cell are accurately resolved. The focus is on the detailed analysis of the partitioning, based on the DNS data, as it develops naturally in successive bifurcations, and the underlying mechanisms. We find that while the time-averaged partitioning at a bifurcation manifests in one of two ways, namely, the classical or reverse partitioning, the time-dependent behavior can cycle between these two types. We identify and analyze four different cellular-scale mechanisms underlying the time-dependent partitioning. These mechanisms arise, in general, either due to an asymmetry in the RBC distribution in the feeding vessels caused by the events at an upstream bifurcation or due to a temporary increase in cell concentration near capillary bifurcations. Using the DNS results, we show that a positive skewness in the hematocrit profile in the feeding vessel is associated with the classical partitioning, while a negative skewness is associated with the reverse one. We then present a detailed analysis of the two components of disproportionate partitioning as identified in prior studies, namely, plasma skimming and cell screening. The plasma skimming component is shown to under-predict the disproportionality, leaving the cell screening component to make up for the difference. The crossing of the separation surface by the cells is observed to be a dominant mechanism underlying the cell screening, which is shown to mitigate extreme heterogeneity in RBC distribution across the networks.

Inverse Scattering and Applications. Proceedings of Conference on Inverse Scattering on the Line, Held in Amherst, Massachusetts on June 7 - 13, 1990

DTIC Science & Technology

1990-01-01

J. Laurie Snell S. A. Amitsur, D. J. Saltman, and 2 Proceedings of the conference on G. B. Seligman , Editors integration, topology, and geometry in...Rational constructions of modules 17 Nonlinear partial differential equations. for simple Lie algebras, George B. Joel A. Smoller, Editor Seligman 18...number theory, Michael R. Stein and Linda Keen, Editor R. Keith Dennis, Editors 65 Logic and combinatorics, Stephen G. 84 Partition problems in

Structure-function relationships during segregated and integrated network states of human brain functional connectivity.

PubMed

Fukushima, Makoto; Betzel, Richard F; He, Ye; van den Heuvel, Martijn P; Zuo, Xi-Nian; Sporns, Olaf

2018-04-01

Structural white matter connections are thought to facilitate integration of neural information across functionally segregated systems. Recent studies have demonstrated that changes in the balance between segregation and integration in brain networks can be tracked by time-resolved functional connectivity derived from resting-state functional magnetic resonance imaging (rs-fMRI) data and that fluctuations between segregated and integrated network states are related to human behavior. However, how these network states relate to structural connectivity is largely unknown. To obtain a better understanding of structural substrates for these network states, we investigated how the relationship between structural connectivity, derived from diffusion tractography, and functional connectivity, as measured by rs-fMRI, changes with fluctuations between segregated and integrated states in the human brain. We found that the similarity of edge weights between structural and functional connectivity was greater in the integrated state, especially at edges connecting the default mode and the dorsal attention networks. We also demonstrated that the similarity of network partitions, evaluated between structural and functional connectivity, increased and the density of direct structural connections within modules in functional networks was elevated during the integrated state. These results suggest that, when functional connectivity exhibited an integrated network topology, structural connectivity and functional connectivity were more closely linked to each other and direct structural connections mediated a larger proportion of neural communication within functional modules. Our findings point out the possibility of significant contributions of structural connections to integrative neural processes underlying human behavior.

A topological hierarchy for functions on triangulated surfaces.

PubMed

Bremer, Peer-Timo; Edelsbrunner, Herbert; Hamann, Bernd; Pascucci, Valerio

2004-01-01

We combine topological and geometric methods to construct a multiresolution representation for a function over a two-dimensional domain. In a preprocessing stage, we create the Morse-Smale complex of the function and progressively simplify its topology by cancelling pairs of critical points. Based on a simple notion of dependency among these cancellations, we construct a hierarchical data structure supporting traversal and reconstruction operations similarly to traditional geometry-based representations. We use this data structure to extract topologically valid approximations that satisfy error bounds provided at runtime.

Topological defect clustering and plastic deformation mechanisms in functionalized graphene

NASA Astrophysics Data System (ADS)

Nunes, Ricardo; Araujo, Joice; Chacham, Helio

2011-03-01

We present ab initio results suggesting that strain plays a central role in the clustering of topological defects in strained and functionalized graphene models. We apply strain onto the topological-defect graphene networks from our previous work, and obtain topological-defect clustering patterns which are in excellent agreement with recent observations in samples of reduced graphene oxide. In our models, the graphene layer, containing an initial concentration of isolated topological defects, is covered by hydrogen or hydroxyl groups. Our results also suggest a rich variety of plastic deformation mechanism in functionalized graphene systems. We acknowledge support from the Brazilian agencies: CNPq, Fapemig, and INCT-Materiais de Carbono.

A parameter optimization approach to controller partitioning for integrated flight/propulsion control application

NASA Technical Reports Server (NTRS)

Schmidt, Phillip; Garg, Sanjay; Holowecky, Brian

1992-01-01

A parameter optimization framework is presented to solve the problem of partitioning a centralized controller into a decentralized hierarchical structure suitable for integrated flight/propulsion control implementation. The controller partitioning problem is briefly discussed and a cost function to be minimized is formulated, such that the resulting 'optimal' partitioned subsystem controllers will closely match the performance (including robustness) properties of the closed-loop system with the centralized controller while maintaining the desired controller partitioning structure. The cost function is written in terms of parameters in a state-space representation of the partitioned sub-controllers. Analytical expressions are obtained for the gradient of this cost function with respect to parameters, and an optimization algorithm is developed using modern computer-aided control design and analysis software. The capabilities of the algorithm are demonstrated by application to partitioned integrated flight/propulsion control design for a modern fighter aircraft in the short approach to landing task. The partitioning optimization is shown to lead to reduced-order subcontrollers that match the closed-loop command tracking and decoupling performance achieved by a high-order centralized controller.

A parameter optimization approach to controller partitioning for integrated flight/propulsion control application

NASA Technical Reports Server (NTRS)

Schmidt, Phillip H.; Garg, Sanjay; Holowecky, Brian R.

1993-01-01

A parameter optimization framework is presented to solve the problem of partitioning a centralized controller into a decentralized hierarchical structure suitable for integrated flight/propulsion control implementation. The controller partitioning problem is briefly discussed and a cost function to be minimized is formulated, such that the resulting 'optimal' partitioned subsystem controllers will closely match the performance (including robustness) properties of the closed-loop system with the centralized controller while maintaining the desired controller partitioning structure. The cost function is written in terms of parameters in a state-space representation of the partitioned sub-controllers. Analytical expressions are obtained for the gradient of this cost function with respect to parameters, and an optimization algorithm is developed using modern computer-aided control design and analysis software. The capabilities of the algorithm are demonstrated by application to partitioned integrated flight/propulsion control design for a modern fighter aircraft in the short approach to landing task. The partitioning optimization is shown to lead to reduced-order subcontrollers that match the closed-loop command tracking and decoupling performance achieved by a high-order centralized controller.

Use of JANAF Tables in Equilibrium Calculations and Partition Function Calculations for an Undergraduate Physical Chemistry Course

ERIC Educational Resources Information Center

Cleary, David A.

2014-01-01

The usefulness of the JANAF tables is demonstrated with specific equilibrium calculations. An emphasis is placed on the nature of standard chemical potential calculations. Also, the use of the JANAF tables for calculating partition functions is examined. In the partition function calculations, the importance of the zero of energy is highlighted.

Partition functions of thermally dissociating diatomic molecules and related momentum problem

NASA Astrophysics Data System (ADS)

Buchowiecki, Marcin

2017-11-01

The anharmonicity and ro-vibrational coupling in ro-vibrational partition functions of diatomic molecules are analyzed for the high temperatures of the thermal dissociation regime. The numerically exact partition functions and thermal energies are calculated. At the high temperatures the proper integration of momenta is important if the partition function of the molecule, understood as bounded system, is to be obtained. The problem of proper treatment of momentum is crucial for correctness of high temperature molecular simulations as the decomposition of simulated molecule have to be avoided; the analysis of O2, H2+, and NH3 molecules allows to show importance of βDe value.

Exact partition functions for gauge theories on Rλ3

NASA Astrophysics Data System (ADS)

Wallet, Jean-Christophe

2016-11-01

The noncommutative space Rλ3, a deformation of R3, supports a 3-parameter family of gauge theory models with gauge-invariant harmonic term, stable vacuum and which are perturbatively finite to all orders. Properties of this family are discussed. The partition function factorizes as an infinite product of reduced partition functions, each one corresponding to the reduced gauge theory on one of the fuzzy spheres entering the decomposition of Rλ3. For a particular sub-family of gauge theories, each reduced partition function is exactly expressible as a ratio of determinants. A relation with integrable 2-D Toda lattice hierarchy is indicated.

Orientifolding of the ABJ Fermi gas

NASA Astrophysics Data System (ADS)

Okuyama, Kazumi

2016-03-01

The grand partition functions of ABJ theory can be factorized into even and odd parts under the reflection of fermion coordinate in the Fermi gas approach. In some cases, the even/odd part of ABJ grand partition function is equal to that of {N}=5O(n)× USp({n}^') theory, hence it is natural to think of the even/odd projection of grand partition function as an orientifolding of ABJ Fermi gas system. By a systematic WKB analysis, we determine the coefficients in the perturbative part of grand potential of such orientifold ABJ theory. We also find the exact form of the first few "half-instanton" corrections coming from the twisted sector of the reflection of fermion coordinate. For the Chern-Simons level k = 2 ,4 ,8 we find closed form expressions of the grand partition functions of orientifold ABJ theory, and for k = 2 , 4 we prove the functional relations among the grand partition functions conjectured in arXiv:1410.7658.

Pore Space Partition in Metal-Organic Frameworks.

PubMed

Zhai, Quan-Guo; Bu, Xianhui; Zhao, Xiang; Li, Dong-Sheng; Feng, Pingyun

2017-02-21

Metal-organic framework (MOF) materials have emerged as one of the favorite crystalline porous materials (CPM) because of their compositional and geometric tunability and many possible applications. In efforts to develop better MOFs for gas storage and separation, a number of strategies including creation of open metal sites and implantation of Lewis base sites have been used to tune host-guest interactions. In addition to these chemical factors, the geometric features such as pore size and shape, surface area, and pore volume also play important roles in sorption energetics and uptake capacity. For efficient capture of small gas molecules such as carbon dioxide under ambient conditions, large surface area or high pore volume are often not needed. Instead, maximizing host-guest interactions or the density of binding sites by encaging gas molecules in snug pockets of pore space can be a fruitful approach. To put this concept into practice, the pore space partition (PSP) concept has been proposed and has achieved a great experimental success. In this account, we will highlight many efforts to implement PSP in MOFs and impact of PSP on gas uptake performance. In the synthetic design of PSP, it is helpful to distinguish between factors that contribute to the framework formation and factors that serve the purpose of PSP. Because of the need for complementary structural roles, the synthesis of MOFs with PSP often involves multicomponent systems including mixed ligands, mixed inorganic nodes, or both. It is possible to accomplish both framework formation and PSP with a single type of polyfunctional ligands that use some functional groups (called framework-forming group) for framework formation and the remaining functional groups (called pore-partition group) for PSP. Alternatively, framework formation and PSP can be shouldered by different chemical species. For example, in a mixed-ligand system, one ligand (called framework-forming agent) can play the role of the framework formation while the other type of ligand (called pore-partition agent) can assume the role of PSP. PSP is sensitive to the types of inorganic secondary building units (SBUs). The coexistence of SBUs complementary in charge, connectivity, and so on can promote PSP. The use of heterometallic systems can promote the diversity of SBUs coexistent under a given condition. Heterometallic system with metal ions of different oxidation states also provides the charge tunability of SBUs and the overall framework, providing an additional level of control in self-assembly and ultimately in the materials' properties. Of particular interest is the PSP in MIL-88 type (acs-type topology) structure, which has led to a huge family of CPMs (called pacs CPMs, pacs = partitioned acs) exhibiting low isosteric heat of adsorption and yet superior CO 2 uptake capacity.

Topological BF Theories

NASA Astrophysics Data System (ADS)

Sǎraru, Silviu-Constantin

Topological field theories originate in the papers of Schwarz and Witten. Initially, Schwarz shown that one of the topological invariants, namely the Ray-Singer torsion, can be represented as the partition function of a certain quantum field theory. Subsequently, Witten constructed a framework for understanding Morse theory in terms of supersymmetric quantum mechanics. These two constructions represent the prototypes of all topological field theories. The model used by Witten has been applied to classical index theorems and, moreover, suggested some generalizations that led to new mathematical results on holomorphic Morse inequalities. Starting with these results, further developments in the domain of topological field theories have been achieved. The Becchi-Rouet-Stora-Tyutin (BRST) symmetry allowed for a new definition of topological ...eld theories as theories whose BRST-invariant Hamiltonian is also BRST-exact. An important class of topological theories of Schwarz type is the class of BF models. This type of models describes three-dimensional quantum gravity and is useful at the study of four-dimensional quantum gravity in Ashtekar-Rovelli-Smolin formulation. Two-dimensional BF models are correlated to Poisson sigma models from various two-dimensional gravities. The analysis of Poisson sigma models, including their relationship to two-dimensional gravity and the study of classical solutions, has been intensively studied in the literature. In this thesis we approach the problem of construction of some classes of interacting BF models in the context of the BRST formalism. In view of this, we use the method of the deformation of the BRST charge and BRST-invariant Hamiltonian. Both methods rely on specific techniques of local BRST cohomology. The main hypotheses in which we construct the above mentioned interactions are: space-time locality, Poincare invariance, smoothness of deformations in the coupling constant and the preservation of the number of derivatives on each field. The first two hypotheses implies that the resulting interacting theory must be local in space-time and Poincare invariant. The smoothness of deformations means that the deformed objects that contribute to the construction of interactions must be smooth in the coupling constant and reduce to the objects corresponding to the free theory in the zero limit of the coupling constant. The preservation of the number of derivatives on each field imp! lies two aspects that must be simultaneously fulfilled: (i) the differential order of each free field equation must coincide with that of the corresponding interacting field equation; (ii) the maximum number of space-time derivatives from the interacting vertices cannot exceed the maximum number of derivatives from the free Lagrangian. The main results obtained can be synthesized into: obtaining self-interactions for certain classes of BF models; generation of couplings between some classes of BF theories and matter theories; construction of interactions between a class of BF models and a system of massless vector fields.

The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule.

PubMed

Martín Pendás, A; Hernández-Trujillo, J

2012-10-07

The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density.

Complete cpDNA genome sequence of Smilax china and phylogenetic placement of Liliales--influences of gene partitions and taxon sampling.

PubMed

Liu, Juan; Qi, Zhe-Chen; Zhao, Yun-Peng; Fu, Cheng-Xin; Jenny Xiang, Qiu-Yun

2012-09-01

The complete nucleotide sequence of the chloroplast genome (cpDNA) of Smilax china L. (Smilacaceae) is reported. It is the first complete cp genome sequence in Liliales. Genomic analyses were conducted to examine the rate and pattern of cpDNA genome evolution in Smilax relative to other major lineages of monocots. The cpDNA genomic sequences were combined with those available for Lilium to evaluate the phylogenetic position of Liliales and to investigate the influence of taxon sampling, gene sampling, gene function, natural selection, and substitution rate on phylogenetic inference in monocots. Phylogenetic analyses using sequence data of gene groups partitioned according to gene function, selection force, and total substitution rate demonstrated evident impacts of these factors on phylogenetic inference of monocots and the placement of Liliales, suggesting potential evolutionary convergence or adaptation of some cpDNA genes in monocots. Our study also demonstrated that reduced taxon sampling reduced the bootstrap support for the placement of Liliales in the cpDNA phylogenomic analysis. Analyses of sequences of 77 protein genes with some missing data and sequences of 81 genes (all protein genes plus the rRNA genes) support a sister relationship of Liliales to the commelinids-Asparagales clade, consistent with the APG III system. Analyses of 63 cpDNA protein genes for 32 taxa with few missing data, however, support a sister relationship of Liliales (represented by Smilax and Lilium) to Dioscoreales-Pandanales. Topology tests indicated that these two alignments do not significantly differ given any of these three cpDNA genomic sequence data sets. Furthermore, we found no saturation effect of the data, suggesting that the cpDNA genomic sequence data used in the study are appropriate for monocot phylogenetic study and long-branch attraction is unlikely to be the cause to explain the result of two well-supported, conflict placements of Liliales. Further analyses using sufficient nuclear data remain necessary to evaluate these two phylogenetic hypotheses regarding the position of Liliales and to address the causes of signal conflict among genes and partitions. Copyright © 2012 Elsevier Inc. All rights reserved.

A stochastic model of tree architecture and biomass partitioning: application to Mongolian Scots pines

PubMed Central

Wang, Feng; Kang, Mengzhen; Lu, Qi; Letort, Véronique; Han, Hui; Guo, Yan; de Reffye, Philippe; Li, Baoguo

2011-01-01

Background and Aims Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal species used for windbreak and sand stabilization in arid and semi-arid areas in northern China. A model-assisted analysis of its canopy architectural development and functions is valuable for better understanding its behaviour and roles in fragile ecosystems. However, due to the intrinsic complexity and variability of trees, the parametric identification of such models is currently a major obstacle to their evaluation and their validation with respect to real data. The aim of this paper was to present the mathematical framework of a stochastic functional–structural model (GL2) and its parameterization for Mongolian Scots pines, taking into account inter-plant variability in terms of topological development and biomass partitioning. Methods In GL2, plant organogenesis is determined by the realization of random variables representing the behaviour of axillary or apical buds. The associated probabilities are calibrated for Mongolian Scots pines using experimental data including means and variances of the numbers of organs per plant in each order-based class. The functional part of the model relies on the principles of source–sink regulation and is parameterized by direct observations of living trees and the inversion method using measured data for organ mass and dimensions. Key Results The final calibration accuracy satisfies both organogenetic and morphogenetic processes. Our hypothesis for the number of organs following a binomial distribution is found to be consistent with the real data. Based on the calibrated parameters, stochastic simulations of the growth of Mongolian Scots pines in plantations are generated by the Monte Carlo method, allowing analysis of the inter-individual variability of the number of organs and biomass partitioning. Three-dimensional (3D) architectures of young Mongolian Scots pines were simulated for 4-, 6- and 8-year-old trees. Conclusions This work provides a new method for characterizing tree structures and biomass allocation that can be used to build a 3D virtual Mongolian Scots pine forest. The work paves the way for bridging the gap between a single-plant model and a stand model. PMID:21062760

Computational Prediction of Kinetic Rate Constants

DTIC Science & Technology

2006-11-30

without requiring additional data. Zero-point energy ( ZPE ) anharmonicity has a large effect on the accuracy of approximate partition function estimates. If...the accurate ZPE is taken into account, separable approximation partition functions using the most accurate torsion treatment and harmonic treatments...for the remaining degrees of freedom agree with accurate QM partition functions to within a mean accuracy of 9%. If no ZPE anharmonicity correction

Reactive molecular dynamics of network polymers: Generation, characterization and mechanical properties

NASA Astrophysics Data System (ADS)

Shankar, Chandrashekar

The goal of this research was to gain a fundamental understanding of the properties of networks created by the ring opening metathesis polymerization (ROMP) of dicyclopentadiene (DCPD) used in self-healing materials. To this end we used molecular simulation methods to generate realistic structures of DCPD networks, characterize their structures, and determine their mechanical properties. Density functional theory (DFT) calculations, complemented by structural information derived from molecular dynamics simulations were used to reconstruct experimental Raman spectra and differential scanning calorimetry (DSC) data. We performed coarse-grained simulations comparing networks generated via the ROMP reaction process and compared them to those generated via a RANDOM process, which led to the fundamental realization that the polymer topology has a unique influence on the network properties. We carried out fully atomistic simulations of DCPD using a novel algorithm for recreating ROMP reactions of DCPD molecules. Mechanical properties derived from these atomistic networks are in excellent agreement with those obtained from coarse-grained simulations in which interactions between nodes are subject to angular constraints. This comparison provides self-consistent validation of our simulation results and helps to identify the level of detail necessary for the coarse-grained interaction model. Simulations suggest networks can classified into three stages: fluid-like, rubber-like or glass-like delineated by two thresholds in degree of reaction alpha: The onset of finite magnitudes for the Young's modulus, alphaY, and the departure of the Poisson ration from 0.5, alphaP. In each stage the polymer exhibits a different predominant mechanical response to deformation. At low alpha < alphaY it flows. At alpha Y < alpha < alphaP the response is entropic with no change in internal energy. At alpha > alphaP the response is enthalpic change in internal energy. We developed graph theory-based network characterizations to correlate between network topology and the simulated mechanical properties. (1) Eigenvector centrality (2) Graph fractal dimension, (3) Fiedler partitioning, and (4) Cross-link fraction (Q3+Q4). Of these quantities, the Fiedler partition is the best characteristic for the prediction of Young's Modulus. The new computational tools developed in this research are of great fundamental and practical interest.

Partitioning of Nb, Mo, Ba, Ce, Pb, Th and U between immiscible carbonate and silicate liquids: Evaluating the effects of P2O5,F, and carbonate composition

NASA Technical Reports Server (NTRS)

Jones, J. H.; Walker, D.

1993-01-01

Previously we have reported carbonate liq./silicate liq. partition coefficients (D) for a standard suite of trace elements (Nb, Mo, Ba, Ce, Pb, Th, and U) and Ra and Pa as well. In brief, we have found that immiscible liquid partitioning is a strong function of temperature. As the critical temperature of the carbonate-silicate solvus is approached, all partition coefficients approach unity. Additionally, for the overwhelming majority of the partitioning elements, InD is a linear function of 'ionic field strength,' z/r, where z is the charge of the partitioned cation and r is its ionic radius.

Crystal Melting and Wall Crossing Phenomena

NASA Astrophysics Data System (ADS)

Yamazaki, Masahito

This paper summarizes recent developments in the theory of Bogomol'nyi-Prasad-Sommerfield (BPS) state counting and the wall crossing phenomena, emphasizing in particular the role of the statistical mechanical model of crystal melting. This paper is divided into two parts, which are closely related to each other. In the first part, we discuss the statistical mechanical model of crystal melting counting BPS states. Each of the BPS states contributing to the BPS index is in one-to-one correspondence with a configuration of a molten crystal, and the statistical partition function of the melting crystal gives the BPS partition function. We also show that smooth geometry of the Calabi-Yau manifold emerges in the thermodynamic limit of the crystal. This suggests a remarkable interpretation that an atom in the crystal is a discretization of the classical geometry, giving an important clue as such to the geometry at the Planck scale. In the second part, we discuss the wall crossing phenomena. Wall crossing phenomena states that the BPS index depends on the value of the moduli of the Calabi-Yau manifold, and jumps along real codimension one subspaces in the moduli space. We show that by using type IIA/M-theory duality, we can provide a simple and an intuitive derivation of the wall crossing phenomena, furthermore clarifying the connection with the topological string theory. This derivation is consistent with another derivation from the wall crossing formula, motivated by multicentered BPS extremal black holes. We also explain the representation of the wall crossing phenomena in terms of crystal melting, and the generalization of the counting problem and the wall crossing to the open BPS invariants.

G-sequentially connectedness for topological groups with operations

NASA Astrophysics Data System (ADS)

Mucuk, Osman; Cakalli, Huseyin

2016-08-01

It is a well-known fact that for a Hausdorff topological group X, the limits of convergent sequences in X define a function denoted by lim from the set of all convergent sequences in X to X. This notion has been modified by Connor and Grosse-Erdmann for real functions by replacing lim with an arbitrary linear functional G defined on a linear subspace of the vector space of all real sequences. Recently some authors have extended the concept to the topological group setting and introduced the concepts of G-sequential continuity, G-sequential compactness and G-sequential connectedness. In this work, we present some results about G-sequentially closures, G-sequentially connectedness and fundamental system of G-sequentially open neighbourhoods for topological group with operations which include topological groups, topological rings without identity, R-modules, Lie algebras, Jordan algebras, and many others.

SCOUT: simultaneous time segmentation and community detection in dynamic networks

PubMed Central

Hulovatyy, Yuriy; Milenković, Tijana

2016-01-01

Many evolving complex real-world systems can be modeled via dynamic networks. An important problem in dynamic network research is community detection, which finds groups of topologically related nodes. Typically, this problem is approached by assuming either that each time point has a distinct community organization or that all time points share a single community organization. The reality likely lies between these two extremes. To find the compromise, we consider community detection in the context of the problem of segment detection, which identifies contiguous time periods with consistent network structure. Consequently, we formulate a combined problem of segment community detection (SCD), which simultaneously partitions the network into contiguous time segments with consistent community organization and finds this community organization for each segment. To solve SCD, we introduce SCOUT, an optimization framework that explicitly considers both segmentation quality and partition quality. SCOUT addresses limitations of existing methods that can be adapted to solve SCD, which consider only one of segmentation quality or partition quality. In a thorough evaluation, SCOUT outperforms the existing methods in terms of both accuracy and computational complexity. We apply SCOUT to biological network data to study human aging. PMID:27881879

3d expansions of 5d instanton partition functions

NASA Astrophysics Data System (ADS)

Nieri, Fabrizio; Pan, Yiwen; Zabzine, Maxim

2018-04-01

We propose a set of novel expansions of Nekrasov's instanton partition functions. Focusing on 5d supersymmetric pure Yang-Mills theory with unitary gauge group on C_{q,{t}^{-1}}^2× S^1 , we show that the instanton partition function admits expansions in terms of partition functions of unitary gauge theories living on the 3d subspaces C_q× S^1 , C_{t^{-1}}× S^1 and their intersection along S^1 . These new expansions are natural from the BPS/CFT viewpoint, as they can be matched with W q,t correlators involving an arbitrary number of screening charges of two kinds. Our constructions generalize and interpolate existing results in the literature.

Equivalence of several descriptions for 6d SCFT

NASA Astrophysics Data System (ADS)

Hayashi, Hirotaka; Kim, Sung-Soo; Lee, Kimyeong; Yagi, Futoshi

2017-01-01

We show that the three different looking BPS partition functions, namely the elliptic genus of the 6d N=(1, 0) Sp(1) gauge theory with 10 flavors and a tensor multiplet, the Nekrasov partition function of the 5d N=1 Sp(2) gauge theory with 10 flavors, and the Nekrasov partition function of the 5d N=1 SU(3) gauge theory with 10 flavors, are all equal to each other under specific maps among gauge theory parameters. This result strongly suggests that the three gauge theories have an identical UV fixed point. Type IIB 5-brane web diagrams play an essential role to compute the SU(3) Nekrasov partition function as well as establishing the maps.

Aperiodic topological order in the domain configurations of functional materials

NASA Astrophysics Data System (ADS)

Huang, Fei-Ting; Cheong, Sang-Wook

2017-03-01

In numerous functional materials, such as steels, ferroelectrics and magnets, new functionalities can be achieved through the engineering of the domain structures, which are associated with the ordering of certain parameters within the material. The recent progress in technologies that enable imaging at atomic-scale spatial resolution has transformed our understanding of domain topology, revealing that, along with simple stripe-like or irregularly shaped domains, intriguing vortex-type topological domain configurations also exist. In this Review, we present a new classification scheme of 'Zm Zn domains with Zl vortices' for 2D macroscopic domain structures with m directional variants and n translational antiphases. This classification, together with the concepts of topological protection and topological charge conservation, can be applied to a wide range of materials, such as multiferroics, improper ferroelectrics, layered transition metal dichalcogenides and magnetic superconductors, as we discuss using selected examples. The resulting topological considerations provide a new basis for the understanding of the formation, kinetics, manipulation and property optimization of domains and domain boundaries in functional materials.

Novel Approaches for Phylogenetic Inference from Morphological Data and Total-Evidence Dating in Squamate Reptiles (Lizards, Snakes, and Amphisbaenians).

PubMed

Pyron, R Alexander

2017-01-01

Here, I combine previously underutilized models and priors to perform more biologically realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backward transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for “asymmetric.” The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical data sets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend toward recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across data sets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological data sets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.

Scale-space measures for graph topology link protein network architecture to function.

PubMed

Hulsman, Marc; Dimitrakopoulos, Christos; de Ridder, Jeroen

2014-06-15

The network architecture of physical protein interactions is an important determinant for the molecular functions that are carried out within each cell. To study this relation, the network architecture can be characterized by graph topological characteristics such as shortest paths and network hubs. These characteristics have an important shortcoming: they do not take into account that interactions occur across different scales. This is important because some cellular functions may involve a single direct protein interaction (small scale), whereas others require more and/or indirect interactions, such as protein complexes (medium scale) and interactions between large modules of proteins (large scale). In this work, we derive generalized scale-aware versions of known graph topological measures based on diffusion kernels. We apply these to characterize the topology of networks across all scales simultaneously, generating a so-called graph topological scale-space. The comprehensive physical interaction network in yeast is used to show that scale-space based measures consistently give superior performance when distinguishing protein functional categories and three major types of functional interactions-genetic interaction, co-expression and perturbation interactions. Moreover, we demonstrate that graph topological scale spaces capture biologically meaningful features that provide new insights into the link between function and protein network architecture. Matlab(TM) code to calculate the scale-aware topological measures (STMs) is available at http://bioinformatics.tudelft.nl/TSSA © The Author 2014. Published by Oxford University Press.

On N = 1 partition functions without R-symmetry

DOE PAGES

Knodel, Gino; Liu, James T.; Zayas, Leopoldo A. Pando

2015-03-25

Here, we examine the dependence of four-dimensional Euclidean N = 1 partition functions on coupling constants. In particular, we focus on backgrounds without R-symmetry, which arise in the rigid limit of old minimal supergravity. Backgrounds preserving a single supercharge may be classified as having either trivial or SU(2) structure, with the former including S 4. We show that, in the absence of additional symmetries, the partition function depends non-trivially on all couplings in the trivial structure case, and (anti)-holomorphically on couplings in the SU(2) structure case. In both cases, this allows for ambiguities in the form of finite counterterms, whichmore » in principle render the partition function unphysical. However, we argue that on dimensional grounds, ambiguities are restricted to finite powers in relevant couplings, and can therefore be kept under control. On the other hand, for backgrounds preserving supercharges of opposite chiralities, the partition function is completely independent of all couplings. In this case, the background admits an R-symmetry, and the partition function is physical, in agreement with the results obtained in the rigid limit of new minimal supergravity. Based on a systematic analysis of supersymmetric invariants, we also demonstrate that N = 1 localization is not possible for backgrounds without R-symmetry.« less

Lagrangian transport near perturbed periodic lines in three-dimensional unsteady flows

NASA Astrophysics Data System (ADS)

Speetjens, Michel

2015-11-01

Periodic lines formed by continuous strings of periodic points are key organizing entities in the Lagrangian flow topology of certain three-dimensional (3D) time-periodic flows. Such lines generically consist of elliptic and/or hyperbolic points and thus give rise to 3D flow topologies made up of families of concentric closed trajectories embedded in chaotic regions. Weak perturbation destroys the periodic lines and causes said trajectories to coalesce into families of concentric tubes. However, emergence of isolated periodic points near the disintegrating periodic lines and/or partitioning of the original lines into elliptic and hyperbolic segments interrupt the tube formation. This yields incomplete tubes that interact with the (chaotic) environment through their open ends, resulting in intricate and essentially 3D flow topologies These phenomena have been observed in various realistic flows yet the underlying mechanisms are to date only partially understood. This study deepens insight into the (perturbed) Lagrangian dynamics of these flows by way of a linearized representation of the equations of motion near the periodic lines. Predictions on the basis of this investigation are in full (qualitative) agreement with observed behavior in the actual flows

Constraint Embedding Technique for Multibody System Dynamics

NASA Technical Reports Server (NTRS)

Woo, Simon S.; Cheng, Michael K.

2011-01-01

Multibody dynamics play a critical role in simulation testbeds for space missions. There has been a considerable interest in the development of efficient computational algorithms for solving the dynamics of multibody systems. Mass matrix factorization and inversion techniques and the O(N) class of forward dynamics algorithms developed using a spatial operator algebra stand out as important breakthrough on this front. Techniques such as these provide the efficient algorithms and methods for the application and implementation of such multibody dynamics models. However, these methods are limited only to tree-topology multibody systems. Closed-chain topology systems require different techniques that are not as efficient or as broad as those for tree-topology systems. The closed-chain forward dynamics approach consists of treating the closed-chain topology as a tree-topology system subject to additional closure constraints. The resulting forward dynamics solution consists of: (a) ignoring the closure constraints and using the O(N) algorithm to solve for the free unconstrained accelerations for the system; (b) using the tree-topology solution to compute a correction force to enforce the closure constraints; and (c) correcting the unconstrained accelerations with correction accelerations resulting from the correction forces. This constraint-embedding technique shows how to use direct embedding to eliminate local closure-loops in the system and effectively convert the system back to a tree-topology system. At this point, standard tree-topology techniques can be brought to bear on the problem. The approach uses a spatial operator algebra approach to formulating the equations of motion. The operators are block-partitioned around the local body subgroups to convert them into aggregate bodies. Mass matrix operator factorization and inversion techniques are applied to the reformulated tree-topology system. Thus in essence, the new technique allows conversion of a system with closure-constraints into an equivalent tree-topology system, and thus allows one to take advantage of the host of techniques available to the latter class of systems. This technology is highly suitable for the class of multibody systems where the closure-constraints are local, i.e., where they are confined to small groupings of bodies within the system. Important examples of such local closure-constraints are constraints associated with four-bar linkages, geared motors, differential suspensions, etc. One can eliminate these closure-constraints and convert the system into a tree-topology system by embedding the constraints directly into the system dynamics and effectively replacing the body groupings with virtual aggregate bodies. Once eliminated, one can apply the well-known results and algorithms for tree-topology systems to solve the dynamics of such closed-chain system.

Boundary perimeter Bethe ansatz

NASA Astrophysics Data System (ADS)

Frassek, Rouven

2017-06-01

We study the partition function of the six-vertex model in the rational limit on arbitrary Baxter lattices with reflecting boundary. Every such lattice is interpreted as an invariant of the twisted Yangian. This identification allows us to relate the partition function of the vertex model to the Bethe wave function of an open spin chain. We obtain the partition function in terms of creation operators on a reference state from the algebraic Bethe ansatz and as a sum of permutations and reflections from the coordinate Bethe ansatz.

Elliptic supersymmetric integrable model and multivariable elliptic functions

NASA Astrophysics Data System (ADS)

Motegi, Kohei

2017-12-01

We investigate the elliptic integrable model introduced by Deguchi and Martin [Int. J. Mod. Phys. A 7, Suppl. 1A, 165 (1992)], which is an elliptic extension of the Perk-Schultz model. We introduce and study a class of partition functions of the elliptic model by using the Izergin-Korepin analysis. We show that the partition functions are expressed as a product of elliptic factors and elliptic Schur-type symmetric functions. This result resembles recent work by number theorists in which the correspondence between the partition functions of trigonometric models and the product of the deformed Vandermonde determinant and Schur functions were established.

Wilson loops in supersymmetric gauge theories

NASA Astrophysics Data System (ADS)

Pestun, Vasily

This thesis is devoted to several exact computations in four-dimensional supersymmetric gauge field theories. In the first part of the thesis we prove conjecture due to Erickson-Semenoff-Zarembo and Drukker-Gross which relates supersymmetric circular Wilson loop operators in the N = 4 supersymmetric Yang-Mills theory with a Gaussian matrix model. We also compute the partition function and give a new matrix model formula for the expectation value of a supersymmetric circular Wilson loop operator for the pure N = 2 and the N* = 2 supersymmetric Yang-Mills theory on a four-sphere. Circular supersymmetric Wilson loops in four-dimensional N = 2 superconformal gauge theory are treated similarly. In the second part we consider supersymmetric Wilson loops of arbitrary shape restricted to a two-dimensional sphere in the four-dimensional N = 4 supersymmetric Yang-Mills theory. We show that expectation value for these Wilson loops can be exactly computed using a two-dimensional theory closely related to the topological two-dimensional Higgs-Yang-Mills theory, or two-dimensional Yang-Mills theory for the complexified gauge group.

Spatiotemporal motion boundary detection and motion boundary velocity estimation for tracking moving objects with a moving camera: a level sets PDEs approach with concurrent camera motion compensation.

PubMed

Feghali, Rosario; Mitiche, Amar

2004-11-01

The purpose of this study is to investigate a method of tracking moving objects with a moving camera. This method estimates simultaneously the motion induced by camera movement. The problem is formulated as a Bayesian motion-based partitioning problem in the spatiotemporal domain of the image quence. An energy functional is derived from the Bayesian formulation. The Euler-Lagrange descent equations determine imultaneously an estimate of the image motion field induced by camera motion and an estimate of the spatiotemporal motion undary surface. The Euler-Lagrange equation corresponding to the surface is expressed as a level-set partial differential equation for topology independence and numerically stable implementation. The method can be initialized simply and can track multiple objects with nonsimultaneous motions. Velocities on motion boundaries can be estimated from geometrical properties of the motion boundary. Several examples of experimental verification are given using synthetic and real-image sequences.

A Lie based 4-dimensional higher Chern-Simons theory

NASA Astrophysics Data System (ADS)

Zucchini, Roberto

2016-05-01

We present and study a model of 4-dimensional higher Chern-Simons theory, special Chern-Simons (SCS) theory, instances of which have appeared in the string literature, whose symmetry is encoded in a skeletal semistrict Lie 2-algebra constructed from a compact Lie group with non discrete center. The field content of SCS theory consists of a Lie valued 2-connection coupled to a background closed 3-form. SCS theory enjoys a large gauge and gauge for gauge symmetry organized in an infinite dimensional strict Lie 2-group. The partition function of SCS theory is simply related to that of a topological gauge theory localizing on flat connections with degree 3 second characteristic class determined by the background 3-form. Finally, SCS theory is related to a 3-dimensional special gauge theory whose 2-connection space has a natural symplectic structure with respect to which the 1-gauge transformation action is Hamiltonian, the 2-curvature map acting as moment map.

Effective field theories for topological insulators by functional bosonization

NASA Astrophysics Data System (ADS)

Chan, AtMa; Hughes, Taylor L.; Ryu, Shinsei; Fradkin, Eduardo

2013-02-01

Effective field theories that describe the dynamics of a conserved U(1) current in terms of “hydrodynamic” degrees of freedom of topological phases in condensed matter are discussed in general dimension D=d+1 using the functional bosonization technique. For noninteracting topological insulators (superconductors) with a conserved U(1) charge and characterized by an integer topological invariant [more specifically, they are topological insulators in the complex symmetry classes (class A and AIII), and in the “primary series” of topological insulators, in the eight real symmetry classes], we derive the BF-type topological field theories supplemented with the Chern-Simons (when D is odd) or the θ (when D is even) terms. For topological insulators characterized by a Z2 topological invariant (the first and second descendants of the primary series), their topological field theories are obtained by dimensional reduction. Building on this effective field theory description for noninteracting topological phases, we also discuss, following the spirit of the parton construction of the fractional quantum Hall effect by Block and Wen, the putative “fractional” topological insulators and their possible effective field theories, and use them to determine the physical properties of these nontrivial quantum phases.

Recurrence relations in one-dimensional Ising models.

PubMed

da Conceição, C M Silva; Maia, R N P

2017-09-01

The exact finite-size partition function for the nonhomogeneous one-dimensional (1D) Ising model is found through an approach using algebra operators. Specifically, in this paper we show that the partition function can be computed through a trace from a linear second-order recurrence relation with nonconstant coefficients in matrix form. A relation between the finite-size partition function and the generalized Lucas polynomials is found for the simple homogeneous model, thus establishing a recursive formula for the partition function. This is an important property and it might indicate the possible existence of recurrence relations in higher-dimensional Ising models. Moreover, assuming quenched disorder for the interactions within the model, the quenched averaged magnetic susceptibility displays a nontrivial behavior due to changes in the ferromagnetic concentration probability.

Compressible fluids with Maxwell-type equations, the minimal coupling with electromagnetic field and the Stefan–Boltzmann law

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mendes, Albert C.R., E-mail: albert@fisica.ufjf.br; Takakura, Flavio I., E-mail: takakura@fisica.ufjf.br; Abreu, Everton M.C., E-mail: evertonabreu@ufrrj.br

In this work we have obtained a higher-derivative Lagrangian for a charged fluid coupled with the electromagnetic fluid and the Dirac’s constraints analysis was discussed. A set of first-class constraints fixed by noncovariant gauge condition were obtained. The path integral formalism was used to obtain the partition function for the corresponding higher-derivative Hamiltonian and the Faddeev–Popov ansatz was used to construct an effective Lagrangian. Through the partition function, a Stefan–Boltzmann type law was obtained. - Highlights: • Higher-derivative Lagrangian for a charged fluid. • Electromagnetic coupling and Dirac’s constraint analysis. • Partition function through path integral formalism. • Stefan–Boltzmann-kind lawmore » through the partition function.« less

Characterization of topological phases of dimerized Kitaev chain via edge correlation functions

NASA Astrophysics Data System (ADS)

Wang, Yucheng; Miao, Jian-Jian; Jin, Hui-Ke; Chen, Shu

2017-11-01

We study analytically topological properties of a noninteracting modified dimerized Kitaev chain and an exactly solvable interacting dimerized Kitaev chain under open boundary conditions by analyzing two introduced edge correlation functions. The interacting dimerized Kitaev chain at the symmetry point Δ =t and the chemical potential μ =0 can be exactly solved by applying two Jordan-Wigner transformations and a spin rotation, which permits us to calculate the edge correlation functions analytically. We demonstrate that the two edge correlation functions can be used to characterize the trivial, Su-Schrieffer-Heeger-like topological and topological superconductor phases of both the noninteracting and interacting systems and give their phase diagrams.

Scaling theory of topological phase transitions

NASA Astrophysics Data System (ADS)

Chen, Wei

2016-02-01

Topologically ordered systems are characterized by topological invariants that are often calculated from the momentum space integration of a certain function that represents the curvature of the many-body state. The curvature function may be Berry curvature, Berry connection, or other quantities depending on the system. Akin to stretching a messy string to reveal the number of knots it contains, a scaling procedure is proposed for the curvature function in inversion symmetric systems, from which the topological phase transition can be identified from the flow of the driving energy parameters that control the topology (hopping, chemical potential, etc) under scaling. At an infinitesimal operation, one obtains the renormalization group (RG) equations for the driving energy parameters. A length scale defined from the curvature function near the gap-closing momentum is suggested to characterize the scale invariance at critical points and fixed points, and displays a universal critical behavior in a variety of systems examined.

Is the Internet gaming-addicted brain close to be in a pathological state?

PubMed

Park, Chang-Hyun; Chun, Ji-Won; Cho, Huyn; Jung, Young-Chul; Choi, Jihye; Kim, Dai Jin

2017-01-01

Internet gaming addiction (IGA) is becoming a common and widespread mental health concern. Although IGA induces a variety of negative psychosocial consequences, it is yet ambiguous whether the brain addicted to Internet gaming is considered to be in a pathological state. We investigated IGA-induced abnormalities of the brain specifically from the network perspective and qualitatively assessed whether the Internet gaming-addicted brain is in a state similar to the pathological brain. Topological properties of brain functional networks were examined by applying a graph-theoretical approach to analyzing functional magnetic resonance imaging data acquired during a resting state in 19 IGA adolescents and 20 age-matched healthy controls. We compared functional distance-based measures, global and local efficiency of resting state brain functional networks between the two groups to assess how the IGA subjects' brain was topologically altered from the controls' brain. The IGA subjects had severer impulsiveness and their brain functional networks showed higher global efficiency and lower local efficiency relative to the controls. These topological differences suggest that IGA induced brain functional networks to shift toward the random topological architecture, as exhibited in other pathological states. Furthermore, for the IGA subjects, the topological alterations were specifically attributable to interregional connections incident on the frontal region, and the degree of impulsiveness was associated with the topological alterations over the frontolimbic connections. The current findings lend support to the proposition that the Internet gaming-addicted brain could be in the state similar to pathological states in terms of topological characteristics of brain functional networks. © 2015 Society for the Study of Addiction.

Polytopol computing for multi-core and distributed systems

NASA Astrophysics Data System (ADS)

Spaanenburg, Henk; Spaanenburg, Lambert; Ranefors, Johan

2009-05-01

Multi-core computing provides new challenges to software engineering. The paper addresses such issues in the general setting of polytopol computing, that takes multi-core problems in such widely differing areas as ambient intelligence sensor networks and cloud computing into account. It argues that the essence lies in a suitable allocation of free moving tasks. Where hardware is ubiquitous and pervasive, the network is virtualized into a connection of software snippets judiciously injected to such hardware that a system function looks as one again. The concept of polytopol computing provides a further formalization in terms of the partitioning of labor between collector and sensor nodes. Collectors provide functions such as a knowledge integrator, awareness collector, situation displayer/reporter, communicator of clues and an inquiry-interface provider. Sensors provide functions such as anomaly detection (only communicating singularities, not continuous observation), they are generally powered or self-powered, amorphous (not on a grid) with generation-and-attrition, field re-programmable, and sensor plug-and-play-able. Together the collector and the sensor are part of the skeleton injector mechanism, added to every node, and give the network the ability to organize itself into some of many topologies. Finally we will discuss a number of applications and indicate how a multi-core architecture supports the security aspects of the skeleton injector.

Optimal network alignment with graphlet degree vectors.

PubMed

Milenković, Tijana; Ng, Weng Leong; Hayes, Wayne; Przulj, Natasa

2010-06-30

Important biological information is encoded in the topology of biological networks. Comparative analyses of biological networks are proving to be valuable, as they can lead to transfer of knowledge between species and give deeper insights into biological function, disease, and evolution. We introduce a new method that uses the Hungarian algorithm to produce optimal global alignment between two networks using any cost function. We design a cost function based solely on network topology and use it in our network alignment. Our method can be applied to any two networks, not just biological ones, since it is based only on network topology. We use our new method to align protein-protein interaction networks of two eukaryotic species and demonstrate that our alignment exposes large and topologically complex regions of network similarity. At the same time, our alignment is biologically valid, since many of the aligned protein pairs perform the same biological function. From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature. Also, we apply our method to find topological similarities between metabolic networks of different species and build phylogenetic trees based on our network alignment score. The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments. Our method detects topologically similar regions in large networks that are statistically significant. It does this independent of protein sequence or any other information external to network topology.

Wigner expansions for partition functions of nonrelativistic and relativistic oscillator systems

NASA Technical Reports Server (NTRS)

Zylka, Christian; Vojta, Guenter

1993-01-01

The equilibrium quantum statistics of various anharmonic oscillator systems including relativistic systems is considered within the Wigner phase space formalism. For this purpose the Wigner series expansion for the partition function is generalized to include relativistic corrections. The new series for partition functions and all thermodynamic potentials yield quantum corrections in terms of powers of h(sup 2) and relativistic corrections given by Kelvin functions (modified Hankel functions) K(sub nu)(mc(sup 2)/kT). As applications, the symmetric Toda oscillator, isotonic and singular anharmonic oscillators, and hindered rotators, i.e. oscillators with cosine potential, are addressed.

The Anatomical Distance of Functional Connections Predicts Brain Network Topology in Health and Schizophrenia

PubMed Central

Vértes, Petra E.; Stidd, Reva; Lalonde, François; Clasen, Liv; Rapoport, Judith; Giedd, Jay; Bullmore, Edward T.; Gogtay, Nitin

2013-01-01

The human brain is a topologically complex network embedded in anatomical space. Here, we systematically explored relationships between functional connectivity, complex network topology, and anatomical (Euclidean) distance between connected brain regions, in the resting-state functional magnetic resonance imaging brain networks of 20 healthy volunteers and 19 patients with childhood-onset schizophrenia (COS). Normal between-subject differences in average distance of connected edges in brain graphs were strongly associated with variation in topological properties of functional networks. In addition, a club or subset of connector hubs was identified, in lateral temporal, parietal, dorsal prefrontal, and medial prefrontal/cingulate cortical regions. In COS, there was reduced strength of functional connectivity over short distances especially, and therefore, global mean connection distance of thresholded graphs was significantly greater than normal. As predicted from relationships between spatial and topological properties of normal networks, this disorder-related proportional increase in connection distance was associated with reduced clustering and modularity and increased global efficiency of COS networks. Between-group differences in connection distance were localized specifically to connector hubs of multimodal association cortex. In relation to the neurodevelopmental pathogenesis of schizophrenia, we argue that the data are consistent with the interpretation that spatial and topological disturbances of functional network organization could arise from excessive “pruning” of short-distance functional connections in schizophrenia. PMID:22275481

Analysis of the structure of complex networks at different resolution levels

NASA Astrophysics Data System (ADS)

Arenas, A.; Fernández, A.; Gómez, S.

2008-05-01

Modular structure is ubiquitous in real-world complex networks, and its detection is important because it gives insights into the structure-functionality relationship. The standard approach is based on the optimization of a quality function, modularity, which is a relative quality measure for the partition of a network into modules. Recently, some authors (Fortunato and Barthélemy 2007 Proc. Natl Acad. Sci. USA 104 36 and Kumpula et al 2007 Eur. Phys. J. B 56 41) have pointed out that the optimization of modularity has a fundamental drawback: the existence of a resolution limit beyond which no modular structure can be detected even though these modules might have their own entity. The reason is that several topological descriptions of the network coexist at different scales, which is, in general, a fingerprint of complex systems. Here, we propose a method that allows for multiple resolution screening of the modular structure. The method has been validated using synthetic networks, discovering the predefined structures at all scales. Its application to two real social networks allows us to find the exact splits reported in the literature, as well as the substructure beyond the actual split.

TADs are 3D structural units of higher-order chromosome organization in Drosophila

PubMed Central

Szabo, Quentin; Jost, Daniel; Chang, Jia-Ming; Cattoni, Diego I.; Papadopoulos, Giorgio L.; Bonev, Boyan; Sexton, Tom; Gurgo, Julian; Jacquier, Caroline; Nollmann, Marcelo; Bantignies, Frédéric; Cavalli, Giacomo

2018-01-01

Deciphering the rules of genome folding in the cell nucleus is essential to understand its functions. Recent chromosome conformation capture (Hi-C) studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. Using a combination of Hi-C, three-dimensional (3D) fluorescent in situ hybridization, super-resolution microscopy, and polymer modeling, we provide an integrative view of chromatin folding in Drosophila. We observed that repressed TADs form a succession of discrete nanocompartments, interspersed by less condensed active regions. Single-cell analysis revealed a consistent TAD-based physical compartmentalization of the chromatin fiber, with some degree of heterogeneity in intra-TAD conformations and in cis and trans inter-TAD contact events. These results indicate that TADs are fundamental 3D genome units that engage in dynamic higher-order inter-TAD connections. This domain-based architecture is likely to play a major role in regulatory transactions during DNA-dependent processes. PMID:29503869

Aberrant brain functional connectome in patients with obstructive sleep apnea.

PubMed

Chen, Li-Ting; Fan, Xiao-Le; Li, Hai-Jun; Ye, Cheng-Long; Yu, Hong-Hui; Xin, Hui-Zhen; Gong, Hong-Han; Peng, De-Chang; Yan, Li-Ping

2018-01-01

Obstructive sleep apnea (OSA) is accompanied by widespread abnormal spontaneous regional activity related to cognitive deficits. However, little is known about the topological properties of the functional brain connectome of patients with OSA. This study aimed to use the graph theory approaches to investigate the topological properties and functional connectivity (FC) of the functional connectome in patients with OSA, based on resting-state functional magnetic resonance imaging (rs-fMRI). Forty-five male patients with newly diagnosed untreated severe OSA and 45 male good sleepers (GSs) underwent a polysomnography (PSG), clinical evaluations, and rs-fMRI scans. The automated anatomical labeling (AAL) atlas was used to construct the functional brain connectome. The topological organization and FC of brain functional networks in patients with OSA were characterized using graph theory methods and investigated the relationship between functional network topology and clinical variables. Both the patients with OSA and the GSs exhibited high-efficiency "small-world" network attributes. However, the patients with OSA exhibited decreased σ, γ, E glob ; increased Lp, λ; and abnormal nodal centralities in several default-mode network (DMN), salience network (SN), and central executive network (CEN) regions. However, the patients with OSA exhibited abnormal functional connections between the DMN, SN, and CEN. The disrupted FC was significantly positive correlations with the global network metrics γ and σ. The global network metrics were significantly correlated with the Epworth Sleepiness Scale (ESS) score, Montreal Cognitive Assessment (MoCA) score, and oxygen desaturation index. The findings suggest that the functional connectome of patients with OSA exhibited disrupted functional integration and segregation, and functional disconnections of the DMN, SN, and CEN. The aberrant topological attributes may be associated with disrupted FC and cognitive functions. These topological abnormalities and disconnections might be potential biomarkers of cognitive impairments in patients with OSA.

Asymptotics of quantum weighted Hurwitz numbers

NASA Astrophysics Data System (ADS)

Harnad, J.; Ortmann, Janosch

2018-06-01

This work concerns both the semiclassical and zero temperature asymptotics of quantum weighted double Hurwitz numbers. The partition function for quantum weighted double Hurwitz numbers can be interpreted in terms of the energy distribution of a quantum Bose gas with vanishing fugacity. We compute the leading semiclassical term of the partition function for three versions of the quantum weighted Hurwitz numbers, as well as lower order semiclassical corrections. The classical limit is shown to reproduce the simple single and double Hurwitz numbers studied by Okounkov and Pandharipande (2000 Math. Res. Lett. 7 447–53, 2000 Lett. Math. Phys. 53 59–74). The KP-Toda τ-function that serves as generating function for the quantum Hurwitz numbers is shown to have the τ-function of Okounkov and Pandharipande (2000 Math. Res. Lett. 7 447–53, 2000 Lett. Math. Phys. 53 59–74) as its leading term in the classical limit, and, with suitable scaling, the same holds for the partition function, the weights and expectations of Hurwitz numbers. We also compute the zero temperature limit of the partition function and quantum weighted Hurwitz numbers. The KP or Toda τ-function serving as generating function for the quantum Hurwitz numbers are shown to give the one for Belyi curves in the zero temperature limit and, with suitable scaling, the same holds true for the partition function, the weights and the expectations of Hurwitz numbers.

Multilevel Green's function interpolation method for scattering from composite metallic and dielectric objects.

PubMed

Shi, Yan; Wang, Hao Gang; Li, Long; Chan, Chi Hou

2008-10-01

A multilevel Green's function interpolation method based on two kinds of multilevel partitioning schemes--the quasi-2D and the hybrid partitioning scheme--is proposed for analyzing electromagnetic scattering from objects comprising both conducting and dielectric parts. The problem is formulated using the surface integral equation for homogeneous dielectric and conducting bodies. A quasi-2D multilevel partitioning scheme is devised to improve the efficiency of the Green's function interpolation. In contrast to previous multilevel partitioning schemes, noncubic groups are introduced to discretize the whole EM structure in this quasi-2D multilevel partitioning scheme. Based on the detailed analysis of the dimension of the group in this partitioning scheme, a hybrid quasi-2D/3D multilevel partitioning scheme is proposed to effectively handle objects with fine local structures. Selection criteria for some key parameters relating to the interpolation technique are given. The proposed algorithm is ideal for the solution of problems involving objects such as missiles, microstrip antenna arrays, photonic bandgap structures, etc. Numerical examples are presented to show that CPU time is between O(N) and O(N log N) while the computer memory requirement is O(N).

Disrupted topology of hippocampal connectivity is associated with short-term antidepressant response in major depressive disorder.

PubMed

Gong, Liang; Hou, Zhenghua; Wang, Zan; He, Cancan; Yin, Yingying; Yuan, Yonggui; Zhang, Haisan; Lv, Luxian; Zhang, Hongxing; Xie, Chunming; Zhang, Zhijun

2018-01-01

Graph theoretical analyses have identified disrupted functional topological organization across the brain in patients with major depressive disorder (MDD). However, the relationship between brain topology and short-term treatment responses in patients with MDD remains unknown. Sixty-eight patients with MDD and 63 cognitively normal (CN) subjects were recruited at baseline and underwent resting-state functional magnetic resonance imaging scans. Graph theory analysis was used to examine group differences in the whole-brain functional topological properties. The association between altered brain topology and the early antidepressant response was examined. Patients with MDD showed lower normalized clustering coefficients, lower small-worldness scalars and increased nodal efficiencies in the default mode network and decreased nodal efficiencies in basal ganglia and hippocampal networks. In addition, the decreased nodal efficiency in left hippocampus was negatively correlated with depressive severity at baseline and positively correlated with changes in the depressive scores after two weeks of antidepressant treatment. The patients in the present study received different medications. These findings indicated that the altered brain functional topological organization in patients with MDD is associated with the treatment response in the early phase of medication. Therefore, brain topology assessments might be considered a useful and convenient predictor of short-term antidepressant responses. Copyright © 2017 Elsevier B.V. All rights reserved.

Simulation of a pulsatile total artificial heart: Development of a partitioned Fluid Structure Interaction model

NASA Astrophysics Data System (ADS)

Sonntag, Simon J.; Kaufmann, Tim A. S.; Büsen, Martin R.; Laumen, Marco; Linde, Torsten; Schmitz-Rode, Thomas; Steinseifer, Ulrich

2013-04-01

Heart disease is one of the leading causes of death in the world. Due to a shortage in donor organs artificial hearts can be a bridge to transplantation or even serve as a destination therapy for patients with terminal heart insufficiency. A pusher plate driven pulsatile membrane pump, the Total Artificial Heart (TAH) ReinHeart, is currently under development at the Institute of Applied Medical Engineering of RWTH Aachen University.This paper presents the methodology of a fully coupled three-dimensional time-dependent Fluid Structure Interaction (FSI) simulation of the TAH using a commercial partitioned block-Gauss-Seidel coupling package. Partitioned coupling of the incompressible fluid with the slender flexible membrane as well as a high fluid/structure density ratio of about unity led inherently to a deterioration of the stability (‘artificial added mass instability’). The objective was to conduct a stable simulation with high accuracy of the pumping process. In order to achieve stability, a combined resistance and pressure outlet boundary condition as well as the interface artificial compressibility method was applied. An analysis of the contact algorithm and turbulence condition is presented. Independence tests are performed for the structural and the fluid mesh, the time step size and the number of pulse cycles. Because of the large deformation of the fluid domain, a variable mesh stiffness depending on certain mesh properties was specified for the fluid elements. Adaptive remeshing was avoided. Different approaches for the mesh stiffness function are compared with respect to convergence, preservation of mesh topology and mesh quality. The resulting mesh aspect ratios, mesh expansion factors and mesh orthogonalities are evaluated in detail. The membrane motion and flow distribution of the coupled simulations are compared with a top-view recording and stereo Particle Image Velocimetry (PIV) measurements, respectively, of the actual pump.

Network module detection: Affinity search technique with the multi-node topological overlap measure

PubMed Central

Li, Ai; Horvath, Steve

2009-01-01

Background Many clustering procedures only allow the user to input a pairwise dissimilarity or distance measure between objects. We propose a clustering method that can input a multi-point dissimilarity measure d(i1, i2, ..., iP) where the number of points P can be larger than 2. The work is motivated by gene network analysis where clusters correspond to modules of highly interconnected nodes. Here, we define modules as clusters of network nodes with high multi-node topological overlap. The topological overlap measure is a robust measure of interconnectedness which is based on shared network neighbors. In previous work, we have shown that the multi-node topological overlap measure yields biologically meaningful results when used as input of network neighborhood analysis. Findings We adapt network neighborhood analysis for the use of module detection. We propose the Module Affinity Search Technique (MAST), which is a generalized version of the Cluster Affinity Search Technique (CAST). MAST can accommodate a multi-node dissimilarity measure. Clusters grow around user-defined or automatically chosen seeds (e.g. hub nodes). We propose both local and global cluster growth stopping rules. We use several simulations and a gene co-expression network application to argue that the MAST approach leads to biologically meaningful results. We compare MAST with hierarchical clustering and partitioning around medoid clustering. Conclusion Our flexible module detection method is implemented in the MTOM software which can be downloaded from the following webpage: PMID:19619323

Network module detection: Affinity search technique with the multi-node topological overlap measure.

PubMed

Li, Ai; Horvath, Steve

2009-07-20

Many clustering procedures only allow the user to input a pairwise dissimilarity or distance measure between objects. We propose a clustering method that can input a multi-point dissimilarity measure d(i1, i2, ..., iP) where the number of points P can be larger than 2. The work is motivated by gene network analysis where clusters correspond to modules of highly interconnected nodes. Here, we define modules as clusters of network nodes with high multi-node topological overlap. The topological overlap measure is a robust measure of interconnectedness which is based on shared network neighbors. In previous work, we have shown that the multi-node topological overlap measure yields biologically meaningful results when used as input of network neighborhood analysis. We adapt network neighborhood analysis for the use of module detection. We propose the Module Affinity Search Technique (MAST), which is a generalized version of the Cluster Affinity Search Technique (CAST). MAST can accommodate a multi-node dissimilarity measure. Clusters grow around user-defined or automatically chosen seeds (e.g. hub nodes). We propose both local and global cluster growth stopping rules. We use several simulations and a gene co-expression network application to argue that the MAST approach leads to biologically meaningful results. We compare MAST with hierarchical clustering and partitioning around medoid clustering. Our flexible module detection method is implemented in the MTOM software which can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/MTOM/

Quark-parton model from dual topological unitarization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cohen-Tannoudji, G.; El Hassouni, A.; Kalinowski, J.

1979-06-01

Topology, which occurs in the topological expansion of quantum chromodynamics (QCD) and in the dual topological unitarization (DTU) schemes, allows us to establish a quantitative correspondence between QCD and the dual S-matrix approaches. This topological correspondence, proposed by Veneziano and made more explicit in a recent paper for current-induced reactions, provides a clarifying and unifying quark-parton interpretation of soft inclusive processes. Precise predictions for inclusive cross sections in hadron-hadron collisions, structure functions of hadrons, and quark fragmentation functions including absolute normalizations are shown to agree with data. On a more theoretical ground the proposed scheme suggests a new approach tomore » the confinement problem.« less

Topological entanglement Rényi entropy and reduced density matrix structure.

PubMed

Flammia, Steven T; Hamma, Alioscia; Hughes, Taylor L; Wen, Xiao-Gang

2009-12-31

We generalize the topological entanglement entropy to a family of topological Rényi entropies parametrized by a parameter alpha, in an attempt to find new invariants for distinguishing topologically ordered phases. We show that, surprisingly, all topological Rényi entropies are the same, independent of alpha for all nonchiral topological phases. This independence shows that topologically ordered ground-state wave functions have reduced density matrices with a certain simple structure, and no additional universal information can be extracted from the entanglement spectrum.

Topological Entanglement Rényi Entropy and Reduced Density Matrix Structure

NASA Astrophysics Data System (ADS)

Flammia, Steven T.; Hamma, Alioscia; Hughes, Taylor L.; Wen, Xiao-Gang

2009-12-01

We generalize the topological entanglement entropy to a family of topological Rényi entropies parametrized by a parameter α, in an attempt to find new invariants for distinguishing topologically ordered phases. We show that, surprisingly, all topological Rényi entropies are the same, independent of α for all nonchiral topological phases. This independence shows that topologically ordered ground-state wave functions have reduced density matrices with a certain simple structure, and no additional universal information can be extracted from the entanglement spectrum.

Uncertain Henry's law constants compromise equilibrium partitioning calculations of atmospheric oxidation products

NASA Astrophysics Data System (ADS)

Wang, Chen; Yuan, Tiange; Wood, Stephen A.; Goss, Kai-Uwe; Li, Jingyi; Ying, Qi; Wania, Frank

2017-06-01

Gas-particle partitioning governs the distribution, removal, and transport of organic compounds in the atmosphere and the formation of secondary organic aerosol (SOA). The large variety of atmospheric species and their wide range of properties make predicting this partitioning equilibrium challenging. Here we expand on earlier work and predict gas-organic and gas-aqueous phase partitioning coefficients for 3414 atmospherically relevant molecules using COSMOtherm, SPARC Performs Automated Reasoning in Chemistry (SPARC), and poly-parameter linear free-energy relationships. The Master Chemical Mechanism generated the structures by oxidizing primary emitted volatile organic compounds. Predictions for gas-organic phase partitioning coefficients (KWIOM/G) by different methods are on average within 1 order of magnitude of each other, irrespective of the numbers of functional groups, except for predictions by COSMOtherm and SPARC for compounds with more than three functional groups, which have a slightly higher discrepancy. Discrepancies between predictions of gas-aqueous partitioning (KW/G) are much larger and increase with the number of functional groups in the molecule. In particular, COSMOtherm often predicts much lower KW/G for highly functionalized compounds than the other methods. While the quantum-chemistry-based COSMOtherm accounts for the influence of intra-molecular interactions on conformation, highly functionalized molecules likely fall outside of the applicability domain of the other techniques, which at least in part rely on empirical data for calibration. Further analysis suggests that atmospheric phase distribution calculations are sensitive to the partitioning coefficient estimation method, in particular to the estimated value of KW/G. The large uncertainty in KW/G predictions for highly functionalized organic compounds needs to be resolved to improve the quantitative treatment of SOA formation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Flammia, Steven T.; Hamma, Alioscia; Hughes, Taylor L.

We generalize the topological entanglement entropy to a family of topological Renyi entropies parametrized by a parameter alpha, in an attempt to find new invariants for distinguishing topologically ordered phases. We show that, surprisingly, all topological Renyi entropies are the same, independent of alpha for all nonchiral topological phases. This independence shows that topologically ordered ground-state wave functions have reduced density matrices with a certain simple structure, and no additional universal information can be extracted from the entanglement spectrum.

Thermodynamics and statistical mechanics. [thermodynamic properties of gases

NASA Technical Reports Server (NTRS)

1976-01-01

The basic thermodynamic properties of gases are reviewed and the relations between them are derived from the first and second laws. The elements of statistical mechanics are then formulated and the partition function is derived. The classical form of the partition function is used to obtain the Maxwell-Boltzmann distribution of kinetic energies in the gas phase and the equipartition of energy theorem is given in its most general form. The thermodynamic properties are all derived as functions of the partition function. Quantum statistics are reviewed briefly and the differences between the Boltzmann distribution function for classical particles and the Fermi-Dirac and Bose-Einstein distributions for quantum particles are discussed.

Random Partition Distribution Indexed by Pairwise Information

PubMed Central

Dahl, David B.; Day, Ryan; Tsai, Jerry W.

2017-01-01

We propose a random partition distribution indexed by pairwise similarity information such that partitions compatible with the similarities are given more probability. The use of pairwise similarities, in the form of distances, is common in some clustering algorithms (e.g., hierarchical clustering), but we show how to use this type of information to define a prior partition distribution for flexible Bayesian modeling. A defining feature of the distribution is that it allocates probability among partitions within a given number of subsets, but it does not shift probability among sets of partitions with different numbers of subsets. Our distribution places more probability on partitions that group similar items yet keeps the total probability of partitions with a given number of subsets constant. The distribution of the number of subsets (and its moments) is available in closed-form and is not a function of the similarities. Our formulation has an explicit probability mass function (with a tractable normalizing constant) so the full suite of MCMC methods may be used for posterior inference. We compare our distribution with several existing partition distributions, showing that our formulation has attractive properties. We provide three demonstrations to highlight the features and relative performance of our distribution. PMID:29276318

Plate/shell structure topology optimization of orthotropic material for buckling problem based on independent continuous topological variables

NASA Astrophysics Data System (ADS)

Ye, Hong-Ling; Wang, Wei-Wei; Chen, Ning; Sui, Yun-Kang

2017-10-01

The purpose of the present work is to study the buckling problem with plate/shell topology optimization of orthotropic material. A model of buckling topology optimization is established based on the independent, continuous, and mapping method, which considers structural mass as objective and buckling critical loads as constraints. Firstly, composite exponential function (CEF) and power function (PF) as filter functions are introduced to recognize the element mass, the element stiffness matrix, and the element geometric stiffness matrix. The filter functions of the orthotropic material stiffness are deduced. Then these filter functions are put into buckling topology optimization of a differential equation to analyze the design sensitivity. Furthermore, the buckling constraints are approximately expressed as explicit functions with respect to the design variables based on the first-order Taylor expansion. The objective function is standardized based on the second-order Taylor expansion. Therefore, the optimization model is translated into a quadratic program. Finally, the dual sequence quadratic programming (DSQP) algorithm and the global convergence method of moving asymptotes algorithm with two different filter functions (CEF and PF) are applied to solve the optimal model. Three numerical results show that DSQP&CEF has the best performance in the view of structural mass and discretion.

Positron Emission Tomography Reveals Abnormal Topological Organization in Functional Brain Network in Diabetic Patients.

PubMed

Qiu, Xiangzhe; Zhang, Yanjun; Feng, Hongbo; Jiang, Donglang

2016-01-01

Recent studies have demonstrated alterations in the topological organization of structural brain networks in diabetes mellitus (DM). However, the DM-related changes in the topological properties in functional brain networks are unexplored so far. We therefore used fluoro-D-glucose positron emission tomography (FDG-PET) data to construct functional brain networks of 73 DM patients and 91 sex- and age-matched normal controls (NCs), followed by a graph theoretical analysis. We found that both DM patients and NCs had a small-world topology in functional brain network. In comparison to the NC group, the DM group was found to have significantly lower small-world index, lower normalized clustering coefficients and higher normalized characteristic path length. Moreover, for diabetic patients, the nodal centrality was significantly reduced in the right rectus, the right cuneus, the left middle occipital gyrus, and the left postcentral gyrus, and it was significantly increased in the orbitofrontal region of the left middle frontal gyrus, the left olfactory region, and the right paracentral lobule. Our results demonstrated that the diabetic brain was associated with disrupted topological organization in the functional PET network, thus providing functional evidence for the abnormalities of brain networks in DM.

Intelligent automated surface grid generation

NASA Technical Reports Server (NTRS)

Yao, Ke-Thia; Gelsey, Andrew

1995-01-01

The goal of our research is to produce a flexible, general grid generator for automated use by other programs, such as numerical optimizers. The current trend in the gridding field is toward interactive gridding. Interactive gridding more readily taps into the spatial reasoning abilities of the human user through the use of a graphical interface with a mouse. However, a sometimes fruitful approach to generating new designs is to apply an optimizer with shape modification operators to improve an initial design. In order for this approach to be useful, the optimizer must be able to automatically grid and evaluate the candidate designs. This paper describes and intelligent gridder that is capable of analyzing the topology of the spatial domain and predicting approximate physical behaviors based on the geometry of the spatial domain to automatically generate grids for computational fluid dynamics simulators. Typically gridding programs are given a partitioning of the spatial domain to assist the gridder. Our gridder is capable of performing this partitioning. This enables the gridder to automatically grid spatial domains of wide range of configurations.

Marginal Consistency: Upper-Bounding Partition Functions over Commutative Semirings.

PubMed

Werner, Tomás

2015-07-01

Many inference tasks in pattern recognition and artificial intelligence lead to partition functions in which addition and multiplication are abstract binary operations forming a commutative semiring. By generalizing max-sum diffusion (one of convergent message passing algorithms for approximate MAP inference in graphical models), we propose an iterative algorithm to upper bound such partition functions over commutative semirings. The iteration of the algorithm is remarkably simple: change any two factors of the partition function such that their product remains the same and their overlapping marginals become equal. In many commutative semirings, repeating this iteration for different pairs of factors converges to a fixed point when the overlapping marginals of every pair of factors coincide. We call this state marginal consistency. During that, an upper bound on the partition function monotonically decreases. This abstract algorithm unifies several existing algorithms, including max-sum diffusion and basic constraint propagation (or local consistency) algorithms in constraint programming. We further construct a hierarchy of marginal consistencies of increasingly higher levels and show than any such level can be enforced by adding identity factors of higher arity (order). Finally, we discuss instances of the framework for several semirings, including the distributive lattice and the max-sum and sum-product semirings.

High-efficient Extraction of Drainage Networks from Digital Elevation Model Data Constrained by Enhanced Flow Enforcement from Known River Map

NASA Astrophysics Data System (ADS)

Wu, T.; Li, T.; Li, J.; Wang, G.

2017-12-01

Improved drainage network extraction can be achieved by flow enforcement whereby information of known river maps is imposed to the flow-path modeling process. However, the common elevation-based stream burning method can sometimes cause unintended topological errors and misinterpret the overall drainage pattern. We presented an enhanced flow enforcement method to facilitate accurate and efficient process of drainage network extraction. Both the topology of the mapped hydrography and the initial landscape of the DEM are well preserved and fully utilized in the proposed method. An improved stream rasterization is achieved here, yielding continuous, unambiguous and stream-collision-free raster equivalent of stream vectors for flow enforcement. By imposing priority-based enforcement with a complementary flow direction enhancement procedure, the drainage patterns of the mapped hydrography are fully represented in the derived results. The proposed method was tested over the Rogue River Basin, using DEMs with various resolutions. As indicated by the visual and statistical analyses, the proposed method has three major advantages: (1) it significantly reduces the occurrences of topological errors, yielding very accurate watershed partition and channel delineation, (2) it ensures scale-consistent performance at DEMs of various resolutions, and (3) the entire extraction process is well-designed to achieve great computational efficiency.

The impact of network characteristics on the diffusion of innovations

NASA Astrophysics Data System (ADS)

Peres, Renana

2014-05-01

This paper studies the influence of network topology on the speed and reach of new product diffusion. While previous research has focused on comparing network types, this paper explores explicitly the relationship between topology and measurements of diffusion effectiveness. We study simultaneously the effect of three network metrics: the average degree, the relative degree of social hubs (i.e., the ratio of the average degree of highly-connected individuals to the average degree of the entire population), and the clustering coefficient. A novel network-generation procedure based on random graphs with a planted partition is used to generate 160 networks with a wide range of values for these topological metrics. Using an agent-based model, we simulate diffusion on these networks and check the dependence of the net present value (NPV) of the number of adopters over time on the network metrics. We find that the average degree and the relative degree of social hubs have a positive influence on diffusion. This result emphasizes the importance of high network connectivity and strong hubs. The clustering coefficient has a negative impact on diffusion, a finding that contributes to the ongoing controversy on the benefits and disadvantages of transitivity. These results hold for both monopolistic and duopolistic markets, and were also tested on a sample of 12 real networks.

A dynamic re-partitioning strategy based on the distribution of key in Spark

NASA Astrophysics Data System (ADS)

Zhang, Tianyu; Lian, Xin

2018-05-01

Spark is a memory-based distributed data processing framework, has the ability of processing massive data and becomes a focus in Big Data. But the performance of Spark Shuffle depends on the distribution of data. The naive Hash partition function of Spark can not guarantee load balancing when data is skewed. The time of job is affected by the node which has more data to process. In order to handle this problem, dynamic sampling is used. In the process of task execution, histogram is used to count the key frequency distribution of each node, and then generate the global key frequency distribution. After analyzing the distribution of key, load balance of data partition is achieved. Results show that the Dynamic Re-Partitioning function is better than the default Hash partition, Fine Partition and the Balanced-Schedule strategy, it can reduce the execution time of the task and improve the efficiency of the whole cluster.

Invariance of Topological Indices Under Hilbert Space Truncation

DOE PAGES

Huang, Zhoushen; Zhu, Wei; Arovas, Daniel P.; ...

2018-01-05

Here, we show that the topological index of a wave function, computed in the space of twisted boundary phases, is preserved under Hilbert space truncation, provided the truncated state remains normalizable. If truncation affects the boundary condition of the resulting state, the invariant index may acquire a different physical interpretation. If the index is symmetry protected, the truncation should preserve the protecting symmetry. We discuss implications of this invariance using paradigmatic integer and fractional Chern insulators, Z 2 topological insulators, and spin-1 Affleck-Kennedy-Lieb-Tasaki and Heisenberg chains, as well as its relation with the notion of bulk entanglement. As a possiblemore » application, we propose a partial quantum tomography scheme from which the topological index of a generic multicomponent wave function can be extracted by measuring only a small subset of wave function components, equivalent to the measurement of a bulk entanglement topological index.« less

Invariance of Topological Indices Under Hilbert Space Truncation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Zhoushen; Zhu, Wei; Arovas, Daniel P.

Here, we show that the topological index of a wave function, computed in the space of twisted boundary phases, is preserved under Hilbert space truncation, provided the truncated state remains normalizable. If truncation affects the boundary condition of the resulting state, the invariant index may acquire a different physical interpretation. If the index is symmetry protected, the truncation should preserve the protecting symmetry. We discuss implications of this invariance using paradigmatic integer and fractional Chern insulators, Z 2 topological insulators, and spin-1 Affleck-Kennedy-Lieb-Tasaki and Heisenberg chains, as well as its relation with the notion of bulk entanglement. As a possiblemore » application, we propose a partial quantum tomography scheme from which the topological index of a generic multicomponent wave function can be extracted by measuring only a small subset of wave function components, equivalent to the measurement of a bulk entanglement topological index.« less

Refined counting of necklaces in one-loop N=4 SYM

NASA Astrophysics Data System (ADS)

Suzuki, Ryo

2017-06-01

We compute the grand partition function of N=4 SYM at one-loop in the SU(2) sector with general chemical potentials, extending the results of Pólya's theorem. We make use of finite group theory, applicable to all orders of perturbative 1 /N c expansion. We show that only the planar terms contribute to the grand partition function, which is therefore equal to the grand partition function of an ensemble of {XXX}_{1/2} spin chains. We discuss how Hagedorn temperature changes on the complex plane of chemical potentials.

Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacCarthy, Brian; Carr, Hamish; Weber, Gunther H.

2011-06-30

Existing topological interfaces to volume rendering are limited by their reliance on sophisticated knowledge of topology by the user. We extend previous work by describing topological galleries, an interface for novice users that is based on the design galleries approach. We report three contributions: an interface based on hierarchical thumbnail galleries to display the containment relationships between topologically identifiable features, the use of the pruning hierarchy instead of branch decomposition for contour tree simplification, and drag-and-drop transfer function assignment for individual components. Initial results suggest that this approach suffers from limitations due to rapid drop-off of feature size in themore » pruning hierarchy. We explore these limitations by providing statistics of feature size as function of depth in the pruning hierarchy of the contour tree.« less

Partition functions for heterotic WZW conformal field theories

NASA Astrophysics Data System (ADS)

Gannon, Terry

1993-08-01

Thus far in the search for, and classification of, "physical" modular invariant partition functions ΣN LRχ Lχ R∗ the attention has been focused on the symmetric case where the holomorphic and anti-holomorphic sectors, and hence the characters χLand χR, are associated with the same Kac-Moody algebras ĝL = ĝR and levels κ L = κ R. In this paper we consider the more general possibility where ( ĝL, κ L) may not equal ( ĝR, κ R). We discuss which choices of algebras and levels may correspond to well-defined conformal field theories, we find the "smallest" such heterotic (i.e. asymmetric) partition functions, and we give a method, generalizing the Roberts-Terao-Warner lattice method, for explicitly constructing many other modular invariants. We conclude the paper by proving that this new lattice method will succeed in generating all the heterotic partition functions, for all choices of algebras and levels.

Topology guided demons registration with local rigidity preservation.

PubMed

Chaojie Zheng; Xiuying Wang; Dagan Feng

2016-08-01

Demons has been well recognized for its deformable registration capability. However, it might lead to misregistration due to the large spatial distance between the expected corresponding contents or erroneous diffusion tendency. In this paper, we propose a new energy function with topology energy, distance function and demons energy for deformable registration. The new energy function incorporates topological relationships to guide the correct diffusion and deformation, and contributes to local rigidity preservation. The distance function contributes to pulling the corresponding regions into accurate alignment despite of a possible large distance gap. The method was validated on synthetic, phantom and real medical image data.

Distributed and localized horizontal tectonic deformation as inferred from drainage network geometry and topology: A case study from Lebanon

NASA Astrophysics Data System (ADS)

Goren, Liran; Castelltort, Sébastien; Klinger, Yann

2016-04-01

Partitioning of horizontal deformation between localized and distributed modes in regions of oblique tectonic convergence is, in many cases, hard to quantify. As a case study, we consider the Dead Sea Fault System that changes its orientation across Lebanon and forms a restraining bend. The oblique deformation along the Lebanese restraining bend is characterized by a complex suite of tectonic structures, among which, the Yammouneh fault, is believed to be the main strand that relays deformation from the southern section to the northern section of the Dead Sea Fault System. However, uncertainties regarding slip rates along the Yammouneh fault and strain partitioning in Lebanon still prevail. In the current work we use the geometry and topology of river basins together with numerical modeling to evaluate modes and rates of the horizontal deformation in Mount Lebanon that is associated with the Arabia-Sinai relative plate motion. We focus on river basins that drain Mount Lebanon to the Mediterranean and originate close to the Yammouneh fault. We quantify a systematic counterclockwise rotation of these basins and evaluate drainage area disequilibrium using an application of the χ mapping technique, which aims at estimating the degree of geometrical and topological disequilibrium in river networks. The analysis indicates a systematic spatial pattern whereby tributaries of the rotated basins appear to experience drainage area loss or gain with respect to channel length. A kinematic model that is informed by river basin geometry reveals that since the late Miocene, about a quarter of the relative plate motion parallel to the plate boundary has been distributed along a wide band of deformation to the west of the Yammouneh fault. Taken together with previous, shorter-term estimates, the model indicates little variation of slip rate along the Yammouneh fault since the late Miocene. Kinematic model results are compatible with late Miocene paleomagnetic rotations in western Mount Lebanon. A numerical landscape evolution experiment demonstrates the emergence of a similar χ pattern of drainage area disequilibrium in response to progressive distributed shear deformation of river basins with relatively minor drainage network reorganization.

Continuity and Separation in Symmetric Topologies

ERIC Educational Resources Information Center

Harris, J.; Lynch, M.

2007-01-01

In this note, it is shown that in a symmetric topological space, the pairs of sets separated by the topology determine the topology itself. It is then shown that when the codomain is symmetric, functions which separate only those pairs of sets that are already separated are continuous, generalizing a result found by M. Lynch.

Algebraic Topology of Multi-Brain Connectivity Networks Reveals Dissimilarity in Functional Patterns during Spoken Communications

PubMed Central

Tadić, Bosiljka; Andjelković, Miroslav; Boshkoska, Biljana Mileva; Levnajić, Zoran

2016-01-01

Human behaviour in various circumstances mirrors the corresponding brain connectivity patterns, which are suitably represented by functional brain networks. While the objective analysis of these networks by graph theory tools deepened our understanding of brain functions, the multi-brain structures and connections underlying human social behaviour remain largely unexplored. In this study, we analyse the aggregate graph that maps coordination of EEG signals previously recorded during spoken communications in two groups of six listeners and two speakers. Applying an innovative approach based on the algebraic topology of graphs, we analyse higher-order topological complexes consisting of mutually interwoven cliques of a high order to which the identified functional connections organise. Our results reveal that the topological quantifiers provide new suitable measures for differences in the brain activity patterns and inter-brain synchronisation between speakers and listeners. Moreover, the higher topological complexity correlates with the listener’s concentration to the story, confirmed by self-rating, and closeness to the speaker’s brain activity pattern, which is measured by network-to-network distance. The connectivity structures of the frontal and parietal lobe consistently constitute distinct clusters, which extend across the listener’s group. Formally, the topology quantifiers of the multi-brain communities exceed the sum of those of the participating individuals and also reflect the listener’s rated attributes of the speaker and the narrated subject. In the broader context, the presented study exposes the relevance of higher topological structures (besides standard graph measures) for characterising functional brain networks under different stimuli. PMID:27880802

Beta-diversity of ectoparasites at two spatial scales: nested hierarchy, geography and habitat type.

PubMed

Warburton, Elizabeth M; van der Mescht, Luther; Stanko, Michal; Vinarski, Maxim V; Korallo-Vinarskaya, Natalia P; Khokhlova, Irina S; Krasnov, Boris R

2017-06-01

Beta-diversity of biological communities can be decomposed into (a) dissimilarity of communities among units of finer scale within units of broader scale and (b) dissimilarity of communities among units of broader scale. We investigated compositional, phylogenetic/taxonomic and functional beta-diversity of compound communities of fleas and gamasid mites parasitic on small Palearctic mammals in a nested hierarchy at two spatial scales: (a) continental scale (across the Palearctic) and (b) regional scale (across sites within Slovakia). At each scale, we analyzed beta-diversity among smaller units within larger units and among larger units with partitioning based on either geography or ecology. We asked (a) whether compositional, phylogenetic/taxonomic and functional dissimilarities of flea and mite assemblages are scale dependent; (b) how geographical (partitioning of sites according to geographic position) or ecological (partitioning of sites according to habitat type) characteristics affect phylogenetic/taxonomic and functional components of dissimilarity of ectoparasite assemblages and (c) whether assemblages of fleas and gamasid mites differ in their degree of dissimilarity, all else being equal. We found that compositional, phylogenetic/taxonomic, or functional beta-diversity was greater on a continental rather than a regional scale. Compositional and phylogenetic/taxonomic components of beta-diversity were greater among larger units than among smaller units within larger units, whereas functional beta-diversity did not exhibit any consistent trend regarding site partitioning. Geographic partitioning resulted in higher values of beta-diversity of ectoparasites than ecological partitioning. Compositional and phylogenetic components of beta-diversity were higher in fleas than mites but the opposite was true for functional beta-diversity in some, but not all, traits.

Warfarin: history, tautomerism and activity

NASA Astrophysics Data System (ADS)

Porter, William R.

2010-06-01

The anticoagulant drug warfarin, normally administered as the racemate, can exist in solution in potentially as many as 40 topologically distinct tautomeric forms. Only 11 of these forms for each enantiomer can be distinguished by selected computational software commonly used to estimate octanol-water partition coefficients and/or ionization constants. The history of studies on warfarin tautomerism is reviewed, along with the implications of tautomerism to its biological properties (activity, protein binding and metabolism) and chemical properties (log P, log D, p K a). Experimental approaches to assessing warfarin tautomerism and computational results for different tautomeric forms are presented.

Unique topological characterization of braided magnetic fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yeates, A. R.; Hornig, G.

We introduce a topological flux function to quantify the topology of magnetic braids: non-zero, line-tied magnetic fields whose field lines all connect between two boundaries. This scalar function is an ideal invariant defined on a cross-section of the magnetic field, and measures the average poloidal magnetic flux around any given field line, or the average pairwise crossing number between a given field line and all others. Moreover, its integral over the cross-section yields the relative magnetic helicity. Using the fact that the flux function is also an action in the Hamiltonian formulation of the field line equations, we prove thatmore » it uniquely characterizes the field line mapping and hence the magnetic topology.« less

Plasmid partition system of the P1par family from the pWR100 virulence plasmid of Shigella flexneri.

PubMed

Sergueev, Kirill; Dabrazhynetskaya, Alena; Austin, Stuart

2005-05-01

P1par family members promote the active segregation of a variety of plasmids and plasmid prophages in gram-negative bacteria. Each has genes for ParA and ParB proteins, followed by a parS partition site. The large virulence plasmid pWR100 of Shigella flexneri contains a new P1par family member: pWR100par. Although typical parA and parB genes are present, the putative pWR100parS site is atypical in sequence and organization. However, pWR100parS promoted accurate plasmid partition in Escherichia coli when the pWR100 Par proteins were supplied. Unique BoxB hexamer motifs within parS define species specificities among previously described family members. Although substantially different from P1parS from the P1 plasmid prophage of E. coli, pWR100parS has the same BoxB sequence. As predicted, the species specificity of the two types proved identical. They also shared partition-mediated incompatibility, consistent with the proposed mechanistic link between incompatibility and species specificity. Among several informative sequence differences between pWR100parS and P1parS is the presence of a 21-bp insert at the center of the pWR100parS site. Deletion of this insert left much of the parS activity intact. Tolerance of central inserts with integral numbers of helical DNA turns reflects the critical topology of these sites, which are bent by binding the host IHF protein.

A New Spinel-Olivine Oxybarometer: Near-Liquidus Partitioning of V between Olivine-Melt, Spinel-Melt, and Spinel-Olivine in Martian Basalt Composition Y980459 as a Function of Oxygen Fugacity

NASA Technical Reports Server (NTRS)

Papike, J. J.; Le, L.; Burger, P. V.; Shearer, C. K.; Bell, A. S.; Jones, J.

2013-01-01

Our research on valence state partitioning began in 2005 with a review of Cr, Fe, Ti, and V partitioning among crystallographic sites in olivine, pyroxene, and spinel [1]. That paper was followed by several on QUE94201 melt composition and specifically on Cr, V, and Eu partitioning between pyroxene and melt [2-5]. This paper represents the continuation of our examination of the partitioning of multivalent V between olivine, spinel, and melt in martian olivine-phyric basalts of Y980459 composition [6, 7]. Here we introduce a new, potentially powerful oxybarometer, V partitioning between spinel and olivine, which can be used when no melt is preserved in the meteorite. The bulk composition of QUE94201 was ideal for our study of martian pyroxene-phyric basalts and specifically the partitioning between pyroxene-melt for Cr, V, and Eu. Likewise, bulk composition Y980459 is ideal for the study of martian olivine-phyric basalts and specifically for olivine-melt, spinel-melt, and spinel-olivine partitioning of V as a function of oxygen fugacity.

Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction.

PubMed

Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

2015-04-30

The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.

A Recursive Method for Calculating Certain Partition Functions.

ERIC Educational Resources Information Center

Woodrum, Luther; And Others

1978-01-01

Describes a simple recursive method for calculating the partition function and average energy of a system consisting of N electrons and L energy levels. Also, presents an efficient APL computer program to utilize the recursion relation. (Author/GA)

Liquid computing on and off the edge of chaos with a striatal microcircuit

PubMed Central

Toledo-Suárez, Carlos; Duarte, Renato; Morrison, Abigail

2014-01-01

In reinforcement learning theories of the basal ganglia, there is a need for the expected rewards corresponding to relevant environmental states to be maintained and modified during the learning process. However, the representation of these states that allows them to be associated with reward expectations remains unclear. Previous studies have tended to rely on pre-defined partitioning of states encoded by disjunct neuronal groups or sparse topological drives. A more likely scenario is that striatal neurons are involved in the encoding of multiple different states through their spike patterns, and that an appropriate partitioning of an environment is learned on the basis of task constraints, thus minimizing the number of states involved in solving a particular task. Here we show that striatal activity is sufficient to implement a liquid state, an important prerequisite for such a computation, whereby transient patterns of striatal activity are mapped onto the relevant states. We develop a simple small scale model of the striatum which can reproduce key features of the experimentally observed activity of the major cell types of the striatum. We then use the activity of this network as input for the supervised training of four simple linear readouts to learn three different functions on a plane, where the network is stimulated with the spike coded position of the agent. We discover that the network configuration that best reproduces striatal activity statistics lies on the edge of chaos and has good performance on all three tasks, but that in general, the edge of chaos is a poor predictor of network performance. PMID:25484864

Revealing topological organization of human brain functional networks with resting-state functional near infrared spectroscopy.

PubMed

Niu, Haijing; Wang, Jinhui; Zhao, Tengda; Shu, Ni; He, Yong

2012-01-01

The human brain is a highly complex system that can be represented as a structurally interconnected and functionally synchronized network, which assures both the segregation and integration of information processing. Recent studies have demonstrated that a variety of neuroimaging and neurophysiological techniques such as functional magnetic resonance imaging (MRI), diffusion MRI and electroencephalography/magnetoencephalography can be employed to explore the topological organization of human brain networks. However, little is known about whether functional near infrared spectroscopy (fNIRS), a relatively new optical imaging technology, can be used to map functional connectome of the human brain and reveal meaningful and reproducible topological characteristics. We utilized resting-state fNIRS (R-fNIRS) to investigate the topological organization of human brain functional networks in 15 healthy adults. Brain networks were constructed by thresholding the temporal correlation matrices of 46 channels and analyzed using graph-theory approaches. We found that the functional brain network derived from R-fNIRS data had efficient small-world properties, significant hierarchical modular structure and highly connected hubs. These results were highly reproducible both across participants and over time and were consistent with previous findings based on other functional imaging techniques. Our results confirmed the feasibility and validity of using graph-theory approaches in conjunction with optical imaging techniques to explore the topological organization of human brain networks. These results may expand a methodological framework for utilizing fNIRS to study functional network changes that occur in association with development, aging and neurological and psychiatric disorders.

Partitioning of functional gene expression data using principal points.

PubMed

Kim, Jaehee; Kim, Haseong

2017-10-12

DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data since they are considered as independent realizations of a stochastic process. This process requires appropriate models to identify patterns of gene functions. The partitioning of the functional data can find homogeneous subgroups of entities for the massive genes within the inherent biological networks. Therefor it can be a useful technique for the analysis of time-course gene expression data. We propose a new self-consistent partitioning method of functional coefficients for individual expression profiles based on the orthonormal basis system. A principal points based functional partitioning method is proposed for time-course gene expression data. The method explores the relationship between genes using Legendre coefficients as principal points to extract the features of gene functions. Our proposed method provides high connectivity in connectedness after clustering for simulated data and finds a significant subsets of genes with the increased connectivity. Our approach has comparative advantages that fewer coefficients are used from the functional data and self-consistency of principal points for partitioning. As real data applications, we are able to find partitioned genes through the gene expressions found in budding yeast data and Escherichia coli data. The proposed method benefitted from the use of principal points, dimension reduction, and choice of orthogonal basis system as well as provides appropriately connected genes in the resulting subsets. We illustrate our method by applying with each set of cell-cycle-regulated time-course yeast genes and E. coli genes. The proposed method is able to identify highly connected genes and to explore the complex dynamics of biological systems in functional genomics.

Painlevé equations, topological type property and reconstruction by the topological recursion

NASA Astrophysics Data System (ADS)

Iwaki, K.; Marchal, O.; Saenz, A.

2018-01-01

In this article we prove that Lax pairs associated with ħ-dependent six Painlevé equations satisfy the topological type property proposed by Bergère, Borot and Eynard for any generic choice of the monodromy parameters. Consequently we show that one can reconstruct the formal ħ-expansion of the isomonodromic τ-function and of the determinantal formulas by applying the so-called topological recursion to the spectral curve attached to the Lax pair in all six Painlevé cases. Finally we illustrate the former results with the explicit computations of the first orders of the six τ-functions.

Hydraulic geometry of the Platte River in south-central Nebraska

USGS Publications Warehouse

Eschner, T.R.

1982-01-01

At-a-station hydraulic-geometry of the Platte River in south-central Nebraska is complex. The range of exponents of simple power-function relations is large, both between different reaches of the river, and among different sections within a given reach. The at-a-station exponents plot in several fields of the b-f-m diagram, suggesting that morphologic and hydraulic changes with increasing discharge vary considerably. Systematic changes in the plotting positions of the exponents with time indicate that in general, the width exponent has decreased, although trends are not readily apparent in the other exponents. Plots of the hydraulic-geometry relations indicate that simple power functions are not the proper model in all instances. For these sections, breaks in the slopes of the hydraulic geometry relations serve to partition the data sets. Power functions fit separately to the partitioned data described the width-, depth-, and velocity-discharge relations more accurately than did a single power function. Plotting positions of the exponents from hydraulic geometry relations of partitioned data sets on b-f-m diagrams indicate that much of the apparent variations of plotting positions of single power functions results because the single power functions compromise both subsets of partitioned data. For several sections, the shape of the channel primarily accounts for the better fit of two-power functions to partitioned data than a single power function over the entire range of data. These non-log linear relations may have significance for channel maintenance. (USGS)

Topological electronic liquids: Electronic physics of one dimension beyond the one spatial dimension

NASA Astrophysics Data System (ADS)

Wiegmann, P. B.

1999-06-01

There is a class of electronic liquids in dimensions greater than 1 that shows all essential properties of one-dimensional electronic physics. These are topological liquids-correlated electronic systems with a spectral flow. Compressible topological electronic liquids are superfluids. In this paper we present a study of a conventional model of a topological superfluid in two spatial dimensions. This model is thought to be relevant to a doped Mott insulator. We show how the spectral flow leads to the superfluid hydrodynamics and how the orthogonality catastrophe affects off-diagonal matrix elements. We also compute the major electronic correlation functions. Among them are the spectral function, the pair wave function, and various tunneling amplitudes. To compute correlation functions we develop a method of current algebra-an extension of the bosonization technique of one spatial dimension. In order to emphasize a similarity between electronic liquids in one dimension and topological liquids in dimensions greater than 1, we first review the Fröhlich-Peierls mechanism of ideal conductivity in one dimension and then extend the physics and the methods into two spatial dimensions.

A strategy to load balancing for non-connectivity MapReduce job

NASA Astrophysics Data System (ADS)

Zhou, Huaping; Liu, Guangzong; Gui, Haixia

2017-09-01

MapReduce has been widely used in large scale and complex datasets as a kind of distributed programming model. Original Hash partitioning function in MapReduce often results the problem of data skew when data distribution is uneven. To solve the imbalance of data partitioning, we proposes a strategy to change the remaining partitioning index when data is skewed. In Map phase, we count the amount of data which will be distributed to each reducer, then Job Tracker monitor the global partitioning information and dynamically modify the original partitioning function according to the data skew model, so the Partitioner can change the index of these partitioning which will cause data skew to the other reducer that has less load in the next partitioning process, and can eventually balance the load of each node. Finally, we experimentally compare our method with existing methods on both synthetic and real datasets, the experimental results show our strategy can solve the problem of data skew with better stability and efficiency than Hash method and Sampling method for non-connectivity MapReduce task.

ATDM LANL FleCSI: Topology and Execution Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bergen, Benjamin Karl

FleCSI is a compile-time configurable C++ framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. This means that FleCSI is potentially useful to many different ECP projects. Current support includes multidimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures (to identify data dependencies between distributed-memory address spaces). FleCSI introduces a functional programming model with control, execution, and data abstractionsmore » that are consistent with state-of-the-art task-based runtimes such as Legion and Charm++. The model also provides support for fine-grained, data-parallel execution with backend support for runtimes such as OpenMP and C++17. The FleCSI abstraction layer provides the developer with insulation from the underlying runtimes, while allowing support for multiple runtime systems, including conventional models like asynchronous MPI. The intent is to give developers a concrete set of user-friendly programming tools that can be used now, while allowing flexibility in choosing runtime implementations and optimizations that can be applied to architectures and runtimes that arise in the future. This project is essential to the ECP Ristra Next-Generation Code project, part of ASC ATDM, because it provides a hierarchically parallel programming model that is consistent with the design of modern system architectures, but which allows for the straightforward expression of algorithmic parallelism in a portably performant manner.« less

Aspects géométriques et intégrables des modèles de matrices aléatoires

NASA Astrophysics Data System (ADS)

Marchal, Olivier

2010-12-01

This thesis deals with the geometric and integrable aspects associated with random matrix models. Its purpose is to provide various applications of random matrix theory, from algebraic geometry to partial differential equations of integrable systems. The variety of these applications shows why matrix models are important from a mathematical point of view. First, the thesis will focus on the study of the merging of two intervals of the eigenvalues density near a singular point. Specifically, we will show why this special limit gives universal equations from the Painlevé II hierarchy of integrable systems theory. Then, following the approach of (bi) orthogonal polynomials introduced by Mehta to compute partition functions, we will find Riemann-Hilbert and isomonodromic problems connected to matrix models, making the link with the theory of Jimbo, Miwa and Ueno. In particular, we will describe how the hermitian two-matrix models provide a degenerate case of Jimbo-Miwa-Ueno's theory that we will generalize in this context. Furthermore, the loop equations method, with its central notions of spectral curve and topological expansion, will lead to the symplectic invariants of algebraic geometry recently proposed by Eynard and Orantin. This last point will be generalized to the case of non-hermitian matrix models (arbitrary beta) paving the way to "quantum algebraic geometry" and to the generalization of symplectic invariants to "quantum curves". Finally, this set up will be applied to combinatorics in the context of topological string theory, with the explicit computation of an hermitian random matrix model enumerating the Gromov-Witten invariants of a toric Calabi-Yau threefold.

Altered brain functional networks in people with Internet gaming disorder: Evidence from resting-state fMRI.

PubMed

Wang, Lingxiao; Wu, Lingdan; Lin, Xiao; Zhang, Yifen; Zhou, Hongli; Du, Xiaoxia; Dong, Guangheng

2016-08-30

Although numerous neuroimaging studies have detected structural and functional abnormality in specific brain regions and connections in subjects with Internet gaming disorder (IGD), the topological organization of the whole-brain network in IGD remain unclear. In this study, we applied graph theoretical analysis to explore the intrinsic topological properties of brain networks in Internet gaming disorder (IGD). 37 IGD subjects and 35 matched healthy control (HC) subjects underwent a resting-state functional magnetic resonance imaging scan. The functional networks were constructed by thresholding partial correlation matrices of 90 brain regions. Then we applied graph-based approaches to analysis their topological attributes, including small-worldness, nodal metrics, and efficiency. Both IGD and HC subjects show efficient and economic brain network, and small-world topology. Although there was no significant group difference in global topology metrics, the IGD subjects showed reduced regional centralities in the prefrontal cortex, left posterior cingulate cortex, right amygdala, and bilateral lingual gyrus, and increased functional connectivity in sensory-motor-related brain networks compared to the HC subjects. These results imply that people with IGD may be associated with functional network dysfunction, including impaired executive control and emotional management, but enhanced coordination among visual, sensorimotor, auditory and visuospatial systems. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Dominant partition method. [based on a wave function formalism

NASA Technical Reports Server (NTRS)

Dixon, R. M.; Redish, E. F.

1979-01-01

By use of the L'Huillier, Redish, and Tandy (LRT) wave function formalism, a partially connected method, the dominant partition method (DPM) is developed for obtaining few body reductions of the many body problem in the LRT and Bencze, Redish, and Sloan (BRS) formalisms. The DPM maps the many body problem to a fewer body one by using the criterion that the truncated formalism must be such that consistency with the full Schroedinger equation is preserved. The DPM is based on a class of new forms for the irreducible cluster potential, which is introduced in the LRT formalism. Connectivity is maintained with respect to all partitions containing a given partition, which is referred to as the dominant partition. Degrees of freedom corresponding to the breakup of one or more of the clusters of the dominant partition are treated in a disconnected manner. This approach for simplifying the complicated BRS equations is appropriate for physical problems where a few body reaction mechanism prevails.

Structural Insights into Triglyceride Storage Mediated by Fat Storage-Inducing Transmembrane (FIT) Protein 2

PubMed Central

Gross, David A.; Snapp, Erik L.; Silver, David L.

2010-01-01

Fat storage-Inducing Transmembrane proteins 1 & 2 (FIT1/FITM1 and FIT2/FITM2) belong to a unique family of evolutionarily conserved proteins localized to the endoplasmic reticulum that are involved in triglyceride lipid droplet formation. FIT proteins have been shown to mediate the partitioning of cellular triglyceride into lipid droplets, but not triglyceride biosynthesis. FIT proteins do not share primary sequence homology with known proteins and no structural information is available to inform on the mechanism by which FIT proteins function. Here, we present the experimentally-solved topological models for FIT1 and FIT2 using N-glycosylation site mapping and indirect immunofluorescence techniques. These methods indicate that both proteins have six-transmembrane-domains with both N- and C-termini localized to the cytosol. Utilizing this model for structure-function analysis, we identified and characterized a gain-of-function mutant of FIT2 (FLL(157-9)AAA) in transmembrane domain 4 that markedly augmented the total number and mean size of lipid droplets. Using limited-trypsin proteolysis we determined that the FLL(157-9)AAA mutant has enhanced trypsin cleavage at K86 relative to wild-type FIT2, indicating a conformational change. Taken together, these studies indicate that FIT2 is a 6 transmembrane domain-containing protein whose conformation likely regulates its activity in mediating lipid droplet formation. PMID:20520733

Equivariant Verlinde Formula from Fivebranes and Vortices

NASA Astrophysics Data System (ADS)

Gukov, Sergei; Pei, Du

2017-10-01

We study complex Chern-Simons theory on a Seifert manifold M 3 by embedding it into string theory. We show that complex Chern-Simons theory on M 3 is equivalent to a topologically twisted supersymmetric theory and its partition function can be naturally regularized by turning on a mass parameter. We find that the dimensional reduction of this theory to 2d gives the low energy dynamics of vortices in four-dimensional gauge theory, the fact apparently overlooked in the vortex literature. We also generalize the relations between (1) the Verlinde algebra, (2) quantum cohomology of the Grassmannian, (3) Chern-Simons theory on {Σ× S^1} and (4) index of a spin c Dirac operator on the moduli space of flat connections to a new set of relations between (1) the "equivariant Verlinde algebra" for a complex group, (2) the equivariant quantum K-theory of the vortex moduli space, (3) complex Chern-Simons theory on {Σ × S^1} and (4) the equivariant index of a spin c Dirac operator on the moduli space of Higgs bundles.

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model.

PubMed

Tsai, Min-Yeh; Yuan, Jian-Min; Teranishi, Yoshiaki; Lin, Sheng Hsien

2012-09-01

Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.

Determination of octanol-air partition coefficients and supercooled liquid vapor pressures of PAHs as a function of temperature: Application to gas-particle partitioning in an urban atmosphere

NASA Astrophysics Data System (ADS)

Odabasi, Mustafa; Cetin, Eylem; Sofuoglu, Aysun

Octanol-air partition coefficients ( KOA) for 14 polycyclic aromatic hydrocarbons (PAHs) were determined as a function of temperature using the gas chromatographic retention time method. log KOA values at 25° ranged over six orders of magnitude, between 6.34 (acenaphthylene) and 12.59 (dibenz[ a,h]anthracene). The determined KOA values were within factor of 0.7 (dibenz[ a,h]anthracene) to 15.1 (benz[ a]anthracene) of values calculated as the ratio of octanol-water partition coefficient to dimensionless Henry's law constant. Supercooled liquid vapor pressures ( PL) of 13 PAHs were also determined using the gas chromatographic retention time technique. Activity coefficients in octanol calculated using KOA and PL ranged between 3.2 and 6.2 indicating near-ideal solution behavior. Atmospheric concentrations measured in this study in Izmir, Turkey were used to investigate the partitioning of PAHs between particle and gas-phases. Experimental gas-particle partition coefficients ( Kp) were compared to the predictions of KOA absorption and KSA (soot-air partition coefficient) models. Octanol-based absorptive partitioning model predicted lower partition coefficients especially for relatively volatile PAHs. Ratios of measured/modeled partition coefficients ranged between 1.1 and 15.5 (4.5±6.0, average±SD) for KOA model. KSA model predictions were relatively better and measured to modeled ratios ranged between 0.6 and 5.6 (2.3±2.7, average±SD).

Computer code for controller partitioning with IFPC application: A user's manual

NASA Technical Reports Server (NTRS)

Schmidt, Phillip H.; Yarkhan, Asim

1994-01-01

A user's manual for the computer code for partitioning a centralized controller into decentralized subcontrollers with applicability to Integrated Flight/Propulsion Control (IFPC) is presented. Partitioning of a centralized controller into two subcontrollers is described and the algorithm on which the code is based is discussed. The algorithm uses parameter optimization of a cost function which is described. The major data structures and functions are described. Specific instructions are given. The user is led through an example of an IFCP application.

Real-space mapping of topological invariants using artificial neural networks

NASA Astrophysics Data System (ADS)

Carvalho, D.; García-Martínez, N. A.; Lado, J. L.; Fernández-Rossier, J.

2018-03-01

Topological invariants allow one to characterize Hamiltonians, predicting the existence of topologically protected in-gap modes. Those invariants can be computed by tracing the evolution of the occupied wave functions under twisted boundary conditions. However, those procedures do not allow one to calculate a topological invariant by evaluating the system locally, and thus require information about the wave functions in the whole system. Here we show that artificial neural networks can be trained to identify the topological order by evaluating a local projection of the density matrix. We demonstrate this for two different models, a one-dimensional topological superconductor and a two-dimensional quantum anomalous Hall state, both with spatially modulated parameters. Our neural network correctly identifies the different topological domains in real space, predicting the location of in-gap states. By combining a neural network with a calculation of the electronic states that uses the kernel polynomial method, we show that the local evaluation of the invariant can be carried out by evaluating a local quantity, in particular for systems without translational symmetry consisting of tens of thousands of atoms. Our results show that supervised learning is an efficient methodology to characterize the local topology of a system.

An Investigation of Document Partitions.

ERIC Educational Resources Information Center

Shaw, W. M., Jr.

1986-01-01

Empirical significance of document partitions is investigated as a function of index term-weight and similarity thresholds. Results show the same empirically preferred partitions can be detected by two independent strategies: an analysis of cluster-based retrieval analysis and an analysis of regularities in the underlying structure of the document…

ESTIMATING DISSOLVED ORGANIC CARBON PARTITION COEFFICIENTS FOR NONIONIC ORGANIC CHEMICALS

EPA Science Inventory

A literature search was performed for dissolved organic carbon/water partition coefficients for nonionic chemicals (Kdoc) and Kdoc data was taken from more than sixty references. The Kdoc data were evaluated as a function of the n-octanol/water partition coefficients (Kow). A pre...

M-theoretic derivations of 4d-2d dualities: from a geometric Langlands duality for surfaces, to the AGT correspondence, to integrable systems

NASA Astrophysics Data System (ADS)

Tan, Meng-Chwan

2013-07-01

In part I, we extend our analysis in [arXiv:0807.1107], and show that a mathematically conjectured geometric Langlands duality for complex surfaces in [1], and its generalizations — which relate some cohomology of the moduli space of certain ("ramified") G-instantons to the integrable representations of the Langlands dual of certain affine (sub) G-algebras, where G is any compact Lie group — can be derived, purely physically, from the principle that the spacetime BPS spectra of string-dual M-theory compactifications ought to be equivalent. In part II, to the setup in part I, we introduce Omega-deformation via fluxbranes and add half-BPS boundary defects via M9-branes, and show that the celebrated AGT correspondence in [2, 3], and its generalizations — which essentially relate, among other things, some equivariant cohomology of the moduli space of certain ("ramified") G-instantons to the integrable representations of the Langlands dual of certain affine -algebras — can likewise be derived from the principle that the spacetime BPS spectra of string-dual M-theory compactifications ought to be equivalent. In part III, we consider various limits of our setup in part II, and connect our story to chiral fermions and integrable systems. Among other things, we derive the NekrasovOkounkov conjecture in [4] — which relates the topological string limit of the dual Nekrasov partition function for pure G to the integrable representations of the Langlands dual of an affine G-algebra — and also demonstrate that the Nekrasov-Shatashvili limit of the "fullyramified" Nekrasov instanton partition function for pure G is a simultaneous eigenfunction of the quantum Toda Hamiltonians associated with the Langlands dual of an affine G-algebra. Via the case with matter, we also make contact with Hitchin systems and the "ramified" geometric Langlands correspondence for curves.

Complex Chern-Simons Theory at Level k via the 3d-3d Correspondence

NASA Astrophysics Data System (ADS)

Dimofte, Tudor

2015-10-01

We use the 3d-3d correspondence together with the DGG construction of theories T n [ M] labelled by 3-manifolds M to define a non-perturbative state-integral model for Chern-Simons theory at any level k, based on ideal triangulations. The resulting partition functions generalize a widely studied k = 1 state-integral, as well as the 3d index, which is k = 0. The Chern-Simons partition functions correspond to partition functions of T n [ M] on squashed lens spaces L( k, 1). At any k, they admit a holomorphic-antiholomorphic factorization, corresponding to the decomposition of L( k, 1) into two solid tori, and the associated holomorphic block decomposition of the partition functions of T n [ M]. A generalization to L( k, p) is also presented. Convergence of the state integrals, for any k, requires triangulations to admit a positive angle structure; we propose that this is also necessary for the DGG gauge theory T n [ M] to flow to a desired IR SCFT.

Prediction of passive blood-brain partitioning: straightforward and effective classification models based on in silico derived physicochemical descriptors

PubMed Central

Vilar, Santiago; Chakrabarti, Mayukh; Costanzi, Stefano

2010-01-01

The distribution of compounds between blood and brain is a very important consideration for new candidate drug molecules. In this paper, we describe the derivation of two linear discriminant analysis (LDA) models for the prediction of passive blood-brain partitioning, expressed in terms of log BB values. The models are based on computationally derived physicochemical descriptors, namely the octanol/water partition coefficient (log P), the topological polar surface area (TPSA) and the total number of acidic and basic atoms, and were obtained using a homogeneous training set of 307 compounds, for all of which the published experimental log BB data had been determined in vivo. In particular, since molecules with log BB > 0.3 cross the blood-brain barrier (BBB) readily while molecules with log BB < −1 are poorly distributed to the brain, on the basis of these thresholds we derived two distinct models, both of which show a percentage of good classification of about 80%. Notably, the predictive power of our models was confirmed by the analysis of a large external dataset of compounds with reported activity on the central nervous system (CNS) or lack thereof. The calculation of straightforward physicochemical descriptors is the only requirement for the prediction of the log BB of novel compounds through our models, which can be conveniently applied in conjunction with drug design and virtual screenings. PMID:20427217

Prediction of passive blood-brain partitioning: straightforward and effective classification models based on in silico derived physicochemical descriptors.

PubMed

Vilar, Santiago; Chakrabarti, Mayukh; Costanzi, Stefano

2010-06-01

The distribution of compounds between blood and brain is a very important consideration for new candidate drug molecules. In this paper, we describe the derivation of two linear discriminant analysis (LDA) models for the prediction of passive blood-brain partitioning, expressed in terms of logBB values. The models are based on computationally derived physicochemical descriptors, namely the octanol/water partition coefficient (logP), the topological polar surface area (TPSA) and the total number of acidic and basic atoms, and were obtained using a homogeneous training set of 307 compounds, for all of which the published experimental logBB data had been determined in vivo. In particular, since molecules with logBB>0.3 cross the blood-brain barrier (BBB) readily while molecules with logBB<-1 are poorly distributed to the brain, on the basis of these thresholds we derived two distinct models, both of which show a percentage of good classification of about 80%. Notably, the predictive power of our models was confirmed by the analysis of a large external dataset of compounds with reported activity on the central nervous system (CNS) or lack thereof. The calculation of straightforward physicochemical descriptors is the only requirement for the prediction of the logBB of novel compounds through our models, which can be conveniently applied in conjunction with drug design and virtual screenings. Published by Elsevier Inc.

Mesh Algorithms for PDE with Sieve I: Mesh Distribution

DOE PAGES

Knepley, Matthew G.; Karpeev, Dmitry A.

2009-01-01

We have developed a new programming framework, called Sieve, to support parallel numerical partial differential equation(s) (PDE) algorithms operating over distributed meshes. We have also developed a reference implementation of Sieve in C++ as a library of generic algorithms operating on distributed containers conforming to the Sieve interface. Sieve makes instances of the incidence relation, or arrows, the conceptual first-class objects represented in the containers. Further, generic algorithms acting on this arrow container are systematically used to provide natural geometric operations on the topology and also, through duality, on the data. Finally, coverings and duality are used to encode notmore » only individual meshes, but all types of hierarchies underlying PDE data structures, including multigrid and mesh partitions. In order to demonstrate the usefulness of the framework, we show how the mesh partition data can be represented and manipulated using the same fundamental mechanisms used to represent meshes. We present the complete description of an algorithm to encode a mesh partition and then distribute a mesh, which is independent of the mesh dimension, element shape, or embedding. Moreover, data associated with the mesh can be similarly distributed with exactly the same algorithm. The use of a high level of abstraction within the Sieve leads to several benefits in terms of code reuse, simplicity, and extensibility. We discuss these benefits and compare our approach to other existing mesh libraries.« less

Drug Distribution. Part 1. Models to Predict Membrane Partitioning.

PubMed

Nagar, Swati; Korzekwa, Ken

2017-03-01

Tissue partitioning is an important component of drug distribution and half-life. Protein binding and lipid partitioning together determine drug distribution. Two structure-based models to predict partitioning into microsomal membranes are presented. An orientation-based model was developed using a membrane template and atom-based relative free energy functions to select drug conformations and orientations for neutral and basic drugs. The resulting model predicts the correct membrane positions for nine compounds tested, and predicts the membrane partitioning for n = 67 drugs with an average fold-error of 2.4. Next, a more facile descriptor-based model was developed for acids, neutrals and bases. This model considers the partitioning of neutral and ionized species at equilibrium, and can predict membrane partitioning with an average fold-error of 2.0 (n = 92 drugs). Together these models suggest that drug orientation is important for membrane partitioning and that membrane partitioning can be well predicted from physicochemical properties.

Statistical mechanics of free particles on space with Lie-type noncommutativity

NASA Astrophysics Data System (ADS)

Shariati, Ahmad; Khorrami, Mohammad; Fatollahi, Amir H.

2010-07-01

Effects of Lie-type noncommutativity on thermodynamic properties of a system of free identical particles are investigated. A definition for finite volume of the configuration space is given, and the grandcanonical partition function in the thermodynamic limit is calculated. Two possible definitions for the pressure are discussed, which are equivalent when the noncommutativity vanishes. The thermodynamic observables are extracted from the partition function. Different limits are discussed where either the noncommutativity or the quantum effects are important. Finally, specific cases are discussed where the group is SU(2) or SO(3), and the partition function of a nondegenerate gas is calculated.

Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality

DOE PAGES

Song, Hyun-Seob; McClure, Ryan S.; Bernstein, Hans C.; ...

2015-03-27

Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as ‘topologically important.’ Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termedmore » as ‘functionally important’ genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.« less

Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Hyun-Seob; McClure, Ryan S.; Bernstein, Hans C.

Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as ‘topologically important.’ Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termedmore » as ‘functionally important’ genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.« less

Do motifs reflect evolved function?--No convergent evolution of genetic regulatory network subgraph topologies.

PubMed

Knabe, Johannes F; Nehaniv, Chrystopher L; Schilstra, Maria J

2008-01-01

Methods that analyse the topological structure of networks have recently become quite popular. Whether motifs (subgraph patterns that occur more often than in randomized networks) have specific functions as elementary computational circuits has been cause for debate. As the question is difficult to resolve with currently available biological data, we approach the issue using networks that abstractly model natural genetic regulatory networks (GRNs) which are evolved to show dynamical behaviors. Specifically one group of networks was evolved to be capable of exhibiting two different behaviors ("differentiation") in contrast to a group with a single target behavior. In both groups we find motif distribution differences within the groups to be larger than differences between them, indicating that evolutionary niches (target functions) do not necessarily mold network structure uniquely. These results show that variability operators can have a stronger influence on network topologies than selection pressures, especially when many topologies can create similar dynamics. Moreover, analysis of motif functional relevance by lesioning did not suggest that motifs were of greater importance to the functioning of the network than arbitrary subgraph patterns. Only when drastically restricting network size, so that one motif corresponds to a whole functionally evolved network, was preference for particular connection patterns found. This suggests that in non-restricted, bigger networks, entanglement with the rest of the network hinders topological subgraph analysis.

Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

EPA Science Inventory

Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feedin...

Emergent functions of quantum materials

NASA Astrophysics Data System (ADS)

Tokura, Yoshinori; Kawasaki, Masashi; Nagaosa, Naoto

2017-11-01

Materials can harbour quantum many-body systems, most typically in the form of strongly correlated electrons in solids, that lead to novel and remarkable functions thanks to emergence--collective behaviours that arise from strong interactions among the elements. These include the Mott transition, high-temperature superconductivity, topological superconductivity, colossal magnetoresistance, giant magnetoelectric effect, and topological insulators. These phenomena will probably be crucial for developing the next-generation quantum technologies that will meet the urgent technological demands for achieving a sustainable and safe society. Dissipationless electronics using topological currents and quantum spins, energy harvesting such as photovoltaics and thermoelectrics, and secure quantum computing and communication are the three major fields of applications working towards this goal. Here, we review the basic principles and the current status of the emergent phenomena and functions in materials from the viewpoint of strong correlation and topology.

An Approach to Develop 3d Geo-Dbms Topological Operators by Re-Using Existing 2d Operators

NASA Astrophysics Data System (ADS)

Xu, D.; Zlatanova, S.

2013-09-01

Database systems are continuously extending their capabilities to store, process and analyse 3D data. Topological relationships which describe the interaction of objects in space is one of the important spatial issues. However, spatial operators for 3D objects are still insufficient. In this paper we present the development of a new 3D topological function to distinguish intersections of 3D planar polygons. The development uses existing 2D functions in the DBMS and two geometric transformations (rotation and projection). This function is tested for a real dataset to detect overlapping 3D city objects. The paper presents the algorithms and analyses the challenges. Suggestions for improvements of the current algorithm as well as possible extensions to handle more 3D topological cases are discussed at the end.

Conformal field theory construction for non-Abelian hierarchy wave functions

NASA Astrophysics Data System (ADS)

Tournois, Yoran; Hermanns, Maria

2017-12-01

The fractional quantum Hall effect is the paradigmatic example of topologically ordered phases. One of its most fascinating aspects is the large variety of different topological orders that may be realized, in particular non-Abelian ones. Here we analyze a class of non-Abelian fractional quantum Hall model states which are generalizations of the Abelian Haldane-Halperin hierarchy. We derive their topological properties and show that the quasiparticles obey non-Abelian fusion rules of type su (q)k . For a subset of these states we are able to derive the conformal field theory description that makes the topological properties—in particular braiding—of the state manifest. The model states we study provide explicit wave functions for a large variety of interesting topological orders, which may be relevant for certain fractional quantum Hall states observed in the first excited Landau level.

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

NASA Astrophysics Data System (ADS)

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.

Phase transition and field effect topological quantum transistor made of monolayer MoS2

NASA Astrophysics Data System (ADS)

Simchi, H.; Simchi, M.; Fardmanesh, M.; Peeters, F. M.

2018-06-01

We study topological phase transitions and topological quantum field effect transistor in monolayer molybdenum disulfide (MoS2) using a two-band Hamiltonian model. Without considering the quadratic (q 2) diagonal term in the Hamiltonian, we show that the phase diagram includes quantum anomalous Hall effect, quantum spin Hall effect, and spin quantum anomalous Hall effect regions such that the topological Kirchhoff law is satisfied in the plane. By considering the q 2 diagonal term and including one valley, it is shown that MoS2 has a non-trivial topology, and the valley Chern number is non-zero for each spin. We show that the wave function is (is not) localized at the edges when the q 2 diagonal term is added (deleted) to (from) the spin-valley Dirac mass equation. We calculate the quantum conductance of zigzag MoS2 nanoribbons by using the nonequilibrium Green function method and show how this device works as a field effect topological quantum transistor.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

PubMed

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-09-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

PubMed Central

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-01-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648

Trivial topological phase of CaAgP and the topological nodal-line transition in CaAg (P1 -xA sx)

NASA Astrophysics Data System (ADS)

Xu, N.; Qian, Y. T.; Wu, Q. S.; Autès, G.; Matt, C. E.; Lv, B. Q.; Yao, M. Y.; Strocov, V. N.; Pomjakushina, E.; Conder, K.; Plumb, N. C.; Radovic, M.; Yazyev, O. V.; Qian, T.; Ding, H.; Mesot, J.; Shi, M.

2018-04-01

By performing angle-resolved photoemission spectroscopy and first-principles calculations, we address the topological phase of CaAgP and investigate the topological phase transition in CaAg (P1 -xA sx) . We reveal that in CaAgP, the bulk band gap and surface states with a large bandwidth are topologically trivial, in agreement with hybrid density functional theory calculations. The calculations also indicate that application of "negative" hydrostatic pressure can transform trivial semiconducting CaAgP into an ideal topological nodal-line semimetal phase. The topological transition can be realized by partial isovalent P/As substitution at x =0.38 .

Surface smoothing and template partitioning for cranial implant CAD

NASA Astrophysics Data System (ADS)

Min, Kyoung-june; Dean, David

2005-04-01

Employing patient-specific prefabricated implants can be an effective treatment for large cranial defects (i.e., > 25 cm2). We have previously demonstrated the use of Computer Aided Design (CAD) software that starts with the patient"s 3D head CT-scan. A template is accurately matched to the pre-detected skull defect margin. For unilateral cranial defects the template is derived from a left-to-right mirrored skull image. However, two problems arise: (1) slice edge artifacts generated during isosurface polygonalization are inherited by the final implant; and (2) partitioning (i.e., cookie-cutting) the implant surface from the mirrored skull image usually results in curvature discontinuities across the interface between the patient"s defect and the implant. To solve these problems, we introduce a novel space curve-to-surface partitioning algorithm following a ray-casting surface re-sampling and smoothing procedure. Specifically, the ray-cast re-sampling is followed by bilinear interpolation and low-pass filtering. The resulting surface has a highly regular grid-like topological structure of quadrilaterally arranged triangles. Then, we replace the regions to be partitioned with predefined sets of triangular elements thereby cutting the template surface to accurately fit the defect margin at high resolution and without surface curvature discontinuities. Comparisons of the CAD implants for five patients against the manually generated implant that the patient actually received show an average implant-patient gap of 0.45mm for the former and 2.96mm for the latter. Also, average maximum normalized curvature of interfacing surfaces was found to be smoother, 0.043, for the former than the latter, 0.097. This indicates that the CAD implants would provide a significantly better fit.

A brief history of partitions of numbers, partition functions and their modern applications

NASA Astrophysics Data System (ADS)

Debnath, Lokenath

2016-04-01

'Number rules the universe.' The Pythagoras 'If you wish to forsee the future of mathematics our course is to study the history and present conditions of the science.' Henri Poincaré 'The primary source (Urqell) of all mathematics are integers.' Hermann Minkowski This paper is written to commemorate the centennial anniversary of the Mathematical Association of America. It deals with a short history of different kinds of natural numbers including triangular, square, pentagonal, hexagonal and k-gonal numbers, and their simple properties and their geometrical representations. Included are Euclid's and Pythagorean's main contributions to elementary number theory with the main contents of the Euclid Elements of the 13-volume masterpiece of mathematical work. This is followed by Euler's new discovery of the additive number theory based on partitions of numbers. Special attention is given to many examples, Euler's theorems on partitions of numbers with geometrical representations of Ferrers' graphs, Young's diagrams, Lagrange's four-square theorem and the celebrated Waring problem. Included are Euler's generating functions for the partitions of numbers, Euler's pentagonal number theorem, Gauss' triangular and square number theorems and the Jacobi triple product identity. Applications of the theory of partitions of numbers to different statistics such as the Bose- Einstein, Fermi- Dirac, Gentile, and Maxwell- Boltzmann statistics are briefly discussed. Special attention is given to pedagogical information through historical approach to number theory so that students and teachers at the school, college and university levels can become familiar with the basic concepts of partitions of numbers, partition functions and their modern applications, and can pursue advanced study and research in analytical and computational number theory.

Topological properties and functionalities in oxide thin films and interfaces

NASA Astrophysics Data System (ADS)

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.

Statistics of contractive cracking patterns. [frozen soil-water rheology

NASA Technical Reports Server (NTRS)

Noever, David A.

1991-01-01

The statistics of convective soil patterns are analyzed using statistical crystallography. An underlying hierarchy of order is found to span four orders of magnitude in characteristic pattern length. Strict mathematical requirements determine the two-dimensional (2D) topology, such that random partitioning of space yields a predictable statistical geometry for polygons. For all lengths, Aboav's and Lewis's laws are verified; this result is consistent both with the need to fill 2D space and most significantly with energy carried not by the patterns' interior, but by the boundaries. Together, this suggests a common mechanism of formation for both micro- and macro-freezing patterns.

NaSi⇌CaAl exchange equilibrium between plagioclase and amphibole

NASA Astrophysics Data System (ADS)

Spear, Frank S.

1980-03-01

The exchange equilibrium between plagioclase and amphibole, 2 albite+tschermakite=2 anorthite+glaucophane, has been calibrated empirically using data from natural amphibolites. The partition coefficient, K D, for the exchange reaction is ( X an/ X ab)plag ·(Na, M4/Ca, M4)amph.. Partitioning is systematic between plagioclase and amphibole in suites collected from single exposures, but the solid solutions are highly non-ideal: values of In K D range from -3.0 at X an=0.30 to -1.0 at X an=0.90 in samples from a single roadcut. Changes in both K D and the topology of the ternary reciprocal exchange diagram occur with increasing metamorphic grade. Temperature dependence of In K D is moderate with Δ ¯H≃35 to 47 kcal at X an=0.25; pressure dependence is small with Δ ¯V≃ -0.24 cal/bar. Usefulness of this exchange equilibrium as a geothermometer is restricted by uncertainties in the calculation of the amphibole formula from a microprobe analysis, especially with regard to Na, M4 in amphibole, to approximately ±50 ° C.

Estimating the Octanol/Water Partition Coefficient for Aliphatic Organic Compounds Using Semi-Empirical Electrotopological Index

PubMed Central

Souza, Erica Silva; Zaramello, Laize; Kuhnen, Carlos Alberto; Junkes, Berenice da Silva; Yunes, Rosendo Augusto; Heinzen, Vilma Edite Fonseca

2011-01-01

A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (ISET). The predictability of four octanol/water partition coefficient (log P) calculation models was compared using a set of 131 aliphatic organic compounds from five different classes. Log P values were calculated employing atomic-contribution methods, as in the Ghose/Crippen approach and its later refinement, AlogP; using fragmental methods through the ClogP method; and employing an approach considering the whole molecule using topological indices with the MlogP method. The efficiency and the applicability of the ISET in terms of calculating log P were demonstrated through good statistical quality (r > 0.99; s < 0.18), high internal stability and good predictive ability for an external group of compounds in the same order as the widely used models based on the fragmental method, ClogP, and the atomic contribution method, AlogP, which are among the most used methods of predicting log P. PMID:22072945

Estimating the octanol/water partition coefficient for aliphatic organic compounds using semi-empirical electrotopological index.

PubMed

Souza, Erica Silva; Zaramello, Laize; Kuhnen, Carlos Alberto; Junkes, Berenice da Silva; Yunes, Rosendo Augusto; Heinzen, Vilma Edite Fonseca

2011-01-01

A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (I(SET)). The predictability of four octanol/water partition coefficient (log P) calculation models was compared using a set of 131 aliphatic organic compounds from five different classes. Log P values were calculated employing atomic-contribution methods, as in the Ghose/Crippen approach and its later refinement, AlogP; using fragmental methods through the ClogP method; and employing an approach considering the whole molecule using topological indices with the MlogP method. The efficiency and the applicability of the I(SET) in terms of calculating log P were demonstrated through good statistical quality (r > 0.99; s < 0.18), high internal stability and good predictive ability for an external group of compounds in the same order as the widely used models based on the fragmental method, ClogP, and the atomic contribution method, AlogP, which are among the most used methods of predicting log P.

Identifying Turbulent Structures through Topological Segmentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bremer, Peer-Timo; Gruber, Andrea; Bennett, Janine C.

2016-01-01

A new method of extracting vortical structures from a turbulent flow is proposed whereby topological segmentation of an indicator function scalar field is used to identify the regions of influence of the individual vortices. This addresses a long-standing challenge in vector field topological analysis: indicator functions commonly used produce a scalar field based on the local velocity vector field; reconstructing regions of influence for a particular structure requires selecting a threshold to define vortex extent. In practice, the same threshold is rarely meaningful throughout a given flow. By also considering the topology of the indicator field function, the characteristics ofmore » vortex strength and extent can be separated and the ambiguity in the choice of the threshold reduced. The proposed approach is able to identify several types of vortices observed in a jet in cross-flow configuration simultaneously where no single threshold value for a selection of common indicator functions appears able to identify all of these vortex types.« less

Linking Resting-State Networks in the Prefrontal Cortex to Executive Function: A Functional Near Infrared Spectroscopy Study.

PubMed

Zhao, Jia; Liu, Jiangang; Jiang, Xin; Zhou, Guifei; Chen, Guowei; Ding, Xiao P; Fu, Genyue; Lee, Kang

2016-01-01

Executive function (EF) plays vital roles in our everyday adaptation to the ever-changing environment. However, limited existing studies have linked EF to the resting-state brain activity. The functional connectivity in the resting state between the sub-regions of the brain can reveal the intrinsic neural mechanisms involved in cognitive processing of EF without disturbance from external stimuli. The present study investigated the relations between the behavioral executive function (EF) scores and the resting-state functional network topological properties in the Prefrontal Cortex (PFC). We constructed complex brain functional networks in the PFC from 90 healthy young adults using functional near infrared spectroscopy (fNIRS). We calculated the correlations between the typical network topological properties (regional topological properties and global topological properties) and the scores of both the Total EF and components of EF measured by computer-based Cambridge Neuropsychological Test Automated Battery (CANTAB). We found that the Total EF scores were positively correlated with regional properties in the right dorsal superior frontal gyrus (SFG), whereas the opposite pattern was found in the right triangular inferior frontal gyrus (IFG). Different EF components were related to different regional properties in various PFC areas, such as planning in the right middle frontal gyrus (MFG), working memory mainly in the right MFG and triangular IFG, short-term memory in the left dorsal SFG, and task switch in the right MFG. In contrast, there were no significant findings for global topological properties. Our findings suggested that the PFC plays an important role in individuals' behavioral performance in the executive function tasks. Further, the resting-state functional network can reveal the intrinsic neural mechanisms involved in behavioral EF abilities.

Age Related Changes in Topological Properties of Brain Functional Network and Structural Connectivity.

PubMed

Shah, Chandan; Liu, Jia; Lv, Peilin; Sun, Huaiqiang; Xiao, Yuan; Liu, Jieke; Zhao, Youjin; Zhang, Wenjing; Yao, Li; Gong, Qiyong; Lui, Su

2018-01-01

Introduction: There are still uncertainties about the true nature of age related changes in topological properties of the brain functional network and its structural connectivity during various developmental stages. In this cross- sectional study, we investigated the effects of age and its relationship with regional nodal properties of the functional brain network and white matter integrity. Method: DTI and fMRI data were acquired from 458 healthy Chinese participants ranging from age 8 to 81 years. Tractography was conducted on the DTI data using FSL. Graph Theory analyses were conducted on the functional data yielding topological properties of the functional network using SPM and GRETNA toolbox. Two multiple regressions were performed to investigate the effects of age on nodal topological properties of the functional brain network and white matter integrity. Result: For the functional studies, we observed that regional nodal characteristics such as node betweenness were decreased while node degree and node efficiency was increased in relation to increasing age. Perversely, we observed that the relationship between nodal topological properties and fasciculus structures were primarily positive for nodal betweenness but negative for nodal degree and nodal efficiency. Decrease in functional nodal betweenness was primarily located in superior frontal lobe, right occipital lobe and the global hubs. These brain regions also had both direct and indirect anatomical relationships with the 14 fiber bundles. A linear age related decreases in the Fractional anisotropy (FA) value was found in the callosum forceps minor. Conclusion: These results suggests that age related differences were more pronounced in the functional than in structural measure indicating these measures do not have direct one-to-one mapping. Our study also indicates that the fiber bundles with longer fibers exhibited a more pronounced effect on the properties of functional network.

Topological Nodal Cooper Pairing in Doped Weyl Metals

NASA Astrophysics Data System (ADS)

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.

Hierarchical functional modularity in the resting-state human brain.

PubMed

Ferrarini, Luca; Veer, Ilya M; Baerends, Evelinda; van Tol, Marie-José; Renken, Remco J; van der Wee, Nic J A; Veltman, Dirk J; Aleman, André; Zitman, Frans G; Penninx, Brenda W J H; van Buchem, Mark A; Reiber, Johan H C; Rombouts, Serge A R B; Milles, Julien

2009-07-01

Functional magnetic resonance imaging (fMRI) studies have shown that anatomically distinct brain regions are functionally connected during the resting state. Basic topological properties in the brain functional connectivity (BFC) map have highlighted the BFC's small-world topology. Modularity, a more advanced topological property, has been hypothesized to be evolutionary advantageous, contributing to adaptive aspects of anatomical and functional brain connectivity. However, current definitions of modularity for complex networks focus on nonoverlapping clusters, and are seriously limited by disregarding inclusive relationships. Therefore, BFC's modularity has been mainly qualitatively investigated. Here, we introduce a new definition of modularity, based on a recently improved clustering measurement, which overcomes limitations of previous definitions, and apply it to the study of BFC in resting state fMRI of 53 healthy subjects. Results show hierarchical functional modularity in the brain. Copyright 2009 Wiley-Liss, Inc

A large-grain mapping approach for multiprocessor systems through data flow model. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Kim, Hwa-Soo

1991-01-01

A large-grain level mapping method is presented of numerical oriented applications onto multiprocessor systems. The method is based on the large-grain data flow representation of the input application and it assumes a general interconnection topology of the multiprocessor system. The large-grain data flow model was used because such representation best exhibits inherited parallelism in many important applications, e.g., CFD models based on partial differential equations can be presented in large-grain data flow format, very effectively. A generalized interconnection topology of the multiprocessor architecture is considered, including such architectural issues as interprocessor communication cost, with the aim to identify the 'best matching' between the application and the multiprocessor structure. The objective is to minimize the total execution time of the input algorithm running on the target system. The mapping strategy consists of the following: (1) large-grain data flow graph generation from the input application using compilation techniques; (2) data flow graph partitioning into basic computation blocks; and (3) physical mapping onto the target multiprocessor using a priority allocation scheme for the computation blocks.

Foam morphology, frustration and topological defects in a Negatively curved Hele-Shaw geometry

NASA Astrophysics Data System (ADS)

Mughal, Adil; Schroeder-Turk, Gerd; Evans, Myfanwy

2014-03-01

We present preliminary simulations of foams and single bubbles confined in a narrow gap between parallel surfaces. Unlike previous work, in which the bounding surfaces are flat (the so called Hele-Shaw geometry), we consider surfaces with non-vanishing Gaussian curvature. We demonstrate that the curvature of the bounding surfaces induce a geometric frustration in the preferred order of the foam. This frustration can be relieved by the introduction of topological defects (disclinations, dislocations and complex scar arrangements). We give a detailed analysis of these defects for foams confined in curved Hele-Shaw cells and compare our results with exotic honeycombs, built by bees on surfaces of varying Gaussian curvature. Our simulations, while encompassing surfaces of constant Gaussian curvature (such as the sphere and the cylinder), focus on surfaces with negative Gaussian curvature and in particular triply periodic minimal surfaces (such as the Schwarz P-surface and the Schoen's Gyroid surface). We use the results from a sphere-packing algorithm to generate a Voronoi partition that forms the basis of a Surface Evolver simulation, which yields a realistic foam morphology.

Topology-guided deformable registration with local importance preservation for biomedical images

NASA Astrophysics Data System (ADS)

Zheng, Chaojie; Wang, Xiuying; Zeng, Shan; Zhou, Jianlong; Yin, Yong; Feng, Dagan; Fulham, Michael

2018-01-01

The demons registration (DR) model is well recognized for its deformation capability. However, it might lead to misregistration due to erroneous diffusion direction when there are no overlaps between corresponding regions. We propose a novel registration energy function, introducing topology energy, and incorporating a local energy function into the DR in a progressive registration scheme, to address these shortcomings. The topology energy that is derived from the topological information of the images serves as a direction inference to guide diffusion transformation to retain the merits of DR. The local energy constrains the deformation disparity of neighbouring pixels to maintain important local texture and density features. The energy function is minimized in a progressive scheme steered by a topology tree graph and we refer to it as topology-guided deformable registration (TDR). We validated our TDR on 20 pairs of synthetic images with Gaussian noise, 20 phantom PET images with artificial deformations and 12 pairs of clinical PET-CT studies. We compared it to three methods: (1) free-form deformation registration method, (2) energy-based DR and (3) multi-resolution DR. The experimental results show that our TDR outperformed the other three methods in regard to structural correspondence and preservation of the local important information including texture and density, while retaining global correspondence.

Finite-time braiding exponents

NASA Astrophysics Data System (ADS)

Budišić, Marko; Thiffeault, Jean-Luc

2015-08-01

Topological entropy of a dynamical system is an upper bound for the sum of positive Lyapunov exponents; in practice, it is strongly indicative of the presence of mixing in a subset of the domain. Topological entropy can be computed by partition methods, by estimating the maximal growth rate of material lines or other material elements, or by counting the unstable periodic orbits of the flow. All these methods require detailed knowledge of the velocity field that is not always available, for example, when ocean flows are measured using a small number of floating sensors. We propose an alternative calculation, applicable to two-dimensional flows, that uses only a sparse set of flow trajectories as its input. To represent the sparse set of trajectories, we use braids, algebraic objects that record how trajectories exchange positions with respect to a projection axis. Material curves advected by the flow are represented as simplified loop coordinates. The exponential rate at which a braid stretches loops over a finite time interval is the Finite-Time Braiding Exponent (FTBE). We study FTBEs through numerical simulations of the Aref Blinking Vortex flow, as a representative of a general class of flows having a single invariant component with positive topological entropy. The FTBEs approach the value of the topological entropy from below as the length and number of trajectories is increased; we conjecture that this result holds for a general class of ergodic, mixing systems. Furthermore, FTBEs are computed robustly with respect to the numerical time step, details of braid representation, and choice of initial conditions. We find that, in the class of systems we describe, trajectories can be re-used to form different braids, which greatly reduces the amount of data needed to assess the complexity of the flow.

Finite-time braiding exponents.

PubMed

Budišić, Marko; Thiffeault, Jean-Luc

2015-08-01

Topological entropy of a dynamical system is an upper bound for the sum of positive Lyapunov exponents; in practice, it is strongly indicative of the presence of mixing in a subset of the domain. Topological entropy can be computed by partition methods, by estimating the maximal growth rate of material lines or other material elements, or by counting the unstable periodic orbits of the flow. All these methods require detailed knowledge of the velocity field that is not always available, for example, when ocean flows are measured using a small number of floating sensors. We propose an alternative calculation, applicable to two-dimensional flows, that uses only a sparse set of flow trajectories as its input. To represent the sparse set of trajectories, we use braids, algebraic objects that record how trajectories exchange positions with respect to a projection axis. Material curves advected by the flow are represented as simplified loop coordinates. The exponential rate at which a braid stretches loops over a finite time interval is the Finite-Time Braiding Exponent (FTBE). We study FTBEs through numerical simulations of the Aref Blinking Vortex flow, as a representative of a general class of flows having a single invariant component with positive topological entropy. The FTBEs approach the value of the topological entropy from below as the length and number of trajectories is increased; we conjecture that this result holds for a general class of ergodic, mixing systems. Furthermore, FTBEs are computed robustly with respect to the numerical time step, details of braid representation, and choice of initial conditions. We find that, in the class of systems we describe, trajectories can be re-used to form different braids, which greatly reduces the amount of data needed to assess the complexity of the flow.

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation

PubMed Central

Hoggard, Timothy; Liachko, Ivan; Burt, Cassaundra; Meikle, Troy; Jiang, Katherine; Craciun, Gheorghe; Dunham, Maitreya J.; Fox, Catherine A.

2016-01-01

The ability of plasmids to propagate in Saccharomyces cerevisiae has been instrumental in defining eukaryotic chromosomal control elements. Stable propagation demands both plasmid replication, which requires a chromosomal replication origin (i.e., an ARS), and plasmid distribution to dividing cells, which requires either a chromosomal centromere for segregation or a plasmid-partitioning element. While our knowledge of yeast ARSs and centromeres is relatively advanced, we know less about chromosomal regions that can function as plasmid partitioning elements. The Rap1 protein-binding site (RAP1) present in transcriptional silencers and telomeres of budding yeast is a known plasmid-partitioning element that functions to anchor a plasmid to the inner nuclear membrane (INM), which in turn facilitates plasmid distribution to daughter cells. This Rap1-dependent INM-anchoring also has an important chromosomal role in higher-order chromosomal structures that enhance transcriptional silencing and telomere stability. Thus, plasmid partitioning can reflect fundamental features of chromosome structure and biology, yet a systematic screen for plasmid partitioning elements has not been reported. Here, we couple deep sequencing with competitive growth experiments of a plasmid library containing thousands of short ARS fragments to identify new plasmid partitioning elements. Competitive growth experiments were performed with libraries that differed only in terms of the presence or absence of a centromere. Comparisons of the behavior of ARS fragments in the two experiments allowed us to identify sequences that were likely to drive plasmid partitioning. In addition to the silencer RAP1 site, we identified 74 new putative plasmid-partitioning motifs predicted to act as binding sites for DNA binding proteins enriched for roles in negative regulation of gene expression and G2/M-phase associated biology. These data expand our knowledge of chromosomal elements that may function in plasmid partitioning and suggest underlying biological roles shared by such elements. PMID:26865697

Influence of electronic band topology on phonon properties in Dirac materials

NASA Astrophysics Data System (ADS)

Garate, Ion; Saha, Kush; Légaré, Katherine

2015-03-01

In Dirac materials, the interaction between electrons and long-wavelength phonons has been shown to induce and stabilize topological insulation [1-2]. Here report on a theoretical study of the converse effect, namely the influence of band topology on phonon properties. We calculate how electron-phonon interactions change the bulk phonon dispersion as a function of pressure and temperature, in both trivial and topological phases. We find that (i) topological insulators are more prone to lattice instabilities than trivial insulators, and (ii) Raman and neutron scattering measurements can be used to determine the electronic band topology. Research funded by Canada's NSERC and Québec's RQMP.

Investigation of another approach in topology optimization

NASA Astrophysics Data System (ADS)

Krotkikh, A. A.; Maximov, P. V.

2018-05-01

The paper presents investigation of another approach in topology optimization. The authors realized the method of topology optimization with using ideas of the SIMP method which was created by Martin P. Bends0e. There are many ways in objective function formulation of topology optimization methods. In terms of elasticity theory, the objective function of the SIMP method is a compliance of an object which should be minimized. The main idea of this paper was avoiding the filtering procedure in the SIMP method. Reformulation of the statement of the problem in terms of function minimization allows us to solve this by big variety of methods. The authors decided to use the interior point method which was realized in Wolfram Mathematica. This way can generate side effects which should be investigated for preventing their appearing in future. Results comparison of the SIMP method and the suggested method are presented in paper and analyzed.

Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins.

PubMed

Langó, Tamás; Róna, Gergely; Hunyadi-Gulyás, Éva; Turiák, Lilla; Varga, Julia; Dobson, László; Várady, György; Drahos, László; Vértessy, Beáta G; Medzihradszky, Katalin F; Szakács, Gergely; Tusnády, Gábor E

2017-02-13

Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins.

Localization in abelian Chern-Simons theory

NASA Astrophysics Data System (ADS)

McLellan, B. D. K.

2013-02-01

Chern-Simons theory on a closed contact three-manifold is studied when the Lie group for gauge transformations is compact, connected, and abelian. The abelian Chern-Simons partition function is derived using the Faddeev-Popov gauge fixing method. The partition function is then formally computed using the technique of non-abelian localization. This study leads to a natural identification of the abelian Reidemeister-Ray-Singer torsion as a specific multiple of the natural unit symplectic volume form on the moduli space of flat abelian connections for the class of Sasakian three-manifolds. The torsion part of the abelian Chern-Simons partition function is computed explicitly in terms of Seifert data for a given Sasakian three-manifold.

Correction: Conceptual design of tetraazaporphyrin- and subtetraazaporphyrin-based functional nanocarbon materials: electronic structures, topologies, optical properties, and methane storage capacities.

PubMed

Belosludov, Rodion V; Rhoda, Hannah M; Zhdanov, Ravil K; Belosludov, Vladimir R; Kawazoe, Yoshiyuki; Nemykin, Victor N

2017-08-02

Correction for 'Conceptual design of tetraazaporphyrin- and subtetraazaporphyrin-based functional nanocarbon materials: electronic structures, topologies, optical properties, and methane storage capacities' by Rodion V. Belosludov et al., Phys. Chem. Chem. Phys., 2016, 18, 13503-13518.

Aberrant functional brain connectome in people with antisocial personality disorder

PubMed Central

Tang, Yan; Long, Jun; Wang, Wei; Liao, Jian; Xie, Hua; Zhao, Guihu; Zhang, Hao

2016-01-01

Antisocial personality disorder (ASPD) is characterised by a disregard for social obligations and callous unconcern for the feelings of others. Studies have demonstrated that ASPD is associated with abnormalities in brain regions and aberrant functional connectivity. In this paper, topological organisation was examined in resting-state fMRI data obtained from 32 ASPD patients and 32 non-ASPD controls. The frequency-dependent functional networks were constructed using wavelet-based correlations over 90 brain regions. The topology of the functional networks of ASPD subjects was analysed via graph theoretical analysis. Furthermore, the abnormal functional connectivity was determined with a network-based statistic (NBS) approach. Our results revealed that, compared with the controls, the ASPD patients exhibited altered topological configuration of the functional connectome in the frequency interval of 0.016–0.031 Hz, as indicated by the increased clustering coefficient and decreased betweenness centrality in the medial superior frontal gyrus, precentral gyrus, Rolandic operculum, superior parietal gyrus, angular gyrus, and middle temporal pole. In addition, the ASPD patients showed increased functional connectivity mainly located in the default-mode network. The present study reveals an aberrant topological organisation of the functional brain network in individuals with ASPD. Our findings provide novel insight into the neuropathological mechanisms of ASPD. PMID:27257047

Aberrant functional brain connectome in people with antisocial personality disorder.

PubMed

Tang, Yan; Long, Jun; Wang, Wei; Liao, Jian; Xie, Hua; Zhao, Guihu; Zhang, Hao

2016-06-03

Antisocial personality disorder (ASPD) is characterised by a disregard for social obligations and callous unconcern for the feelings of others. Studies have demonstrated that ASPD is associated with abnormalities in brain regions and aberrant functional connectivity. In this paper, topological organisation was examined in resting-state fMRI data obtained from 32 ASPD patients and 32 non-ASPD controls. The frequency-dependent functional networks were constructed using wavelet-based correlations over 90 brain regions. The topology of the functional networks of ASPD subjects was analysed via graph theoretical analysis. Furthermore, the abnormal functional connectivity was determined with a network-based statistic (NBS) approach. Our results revealed that, compared with the controls, the ASPD patients exhibited altered topological configuration of the functional connectome in the frequency interval of 0.016-0.031 Hz, as indicated by the increased clustering coefficient and decreased betweenness centrality in the medial superior frontal gyrus, precentral gyrus, Rolandic operculum, superior parietal gyrus, angular gyrus, and middle temporal pole. In addition, the ASPD patients showed increased functional connectivity mainly located in the default-mode network. The present study reveals an aberrant topological organisation of the functional brain network in individuals with ASPD. Our findings provide novel insight into the neuropathological mechanisms of ASPD.

[Aberrant topological properties of whole-brain functional network in chronic right-sided sensorineural hearing loss: a resting-state functional MRI study].

PubMed

Zhang, Lingling; Liu, Bin; Xu, Yangwen; Yang, Ming; Feng, Yuan; Huang, Yaqing; Huan, Zhichun; Hou, Zhaorui

2015-02-03

To investigate the topological properties of the functional brain network in unilateral sensorineural hearing loss patients. In this study, we acquired resting-state BOLD- fMRI data from 19 right-sided SNHL patients and 31 healthy controls with normal hearing and constructed their whole brain functional networks. Two-sample two-tailed t-tests were performed to investigate group differences in topological parameters between the USNHL patients and the controls. Partial correlation analysis was conducted to determine the relationships between the network metrics and USNHL-related variables. Both USNHL patients and controls exhibited small-word architecture in their brain functional networks within the range 0. 1 - 0. 2 of sparsity. Compared to the controls, USNHL patients showed significant increase in characteristic path length and normalized characteristic path length, but significant decrease in global efficiency. Clustering coefficient, local efficiency and normalized clustering coefficient demonstrated no significant difference. Furthermore, USNHL patients exhibited no significant association between the altered network metrics and the duration of USNHL or the severity of hearing loss. Our results indicated the altered topological properties of whole brain functional networks in USNHL patients, which may help us to understand pathophysiologic mechanism of USNHL patients.

Morse oscillator propagator in the high temperature limit I: Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toutounji, Mohamad, E-mail: Mtoutounji@uaeu.ac.ae

2017-02-15

In an earlier work of the author the time evolution of Morse oscillator was studied analytically and exactly at low temperatures whereupon optical correlation functions were calculated using Morse oscillator coherent states were employed. Morse oscillator propagator in the high temperature limit is derived and a closed form of its corresponding canonical partition function is obtained. Both diagonal and off-diagonal forms of Morse oscillator propagator are derived in the high temperature limit. Partition functions of diatomic molecules are calculated. - Highlights: • Derives the quantum propagator of Morse oscillator in the high temperature limit. • Uses the resulting diagonal propagatormore » to derive a closed form of Morse oscillator partition function. • Provides a more sophisticated formula of the quantum propagator to test the accuracy of the herein results.« less

Using periodic orbits to compute chaotic transport rates between resonance zones.

PubMed

Sattari, Sulimon; Mitchell, Kevin A

2017-11-01

Transport properties of chaotic systems are computable from data extracted from periodic orbits. Given a sufficient number of periodic orbits, the escape rate can be computed using the spectral determinant, a function that incorporates the eigenvalues and periods of periodic orbits. The escape rate computed from periodic orbits converges to the true value as more and more periodic orbits are included. Escape from a given region of phase space can be computed by considering only periodic orbits that lie within the region. An accurate symbolic dynamics along with a corresponding partitioning of phase space is useful for systematically obtaining all periodic orbits up to a given period, to ensure that no important periodic orbits are missing in the computation. Homotopic lobe dynamics (HLD) is an automated technique for computing accurate partitions and symbolic dynamics for maps using the topological forcing of intersections of stable and unstable manifolds of a few periodic anchor orbits. In this study, we apply the HLD technique to compute symbolic dynamics and periodic orbits, which are then used to find escape rates from different regions of phase space for the Hénon map. We focus on computing escape rates in parameter ranges spanning hyperbolic plateaus, which are parameter intervals where the dynamics is hyperbolic and the symbolic dynamics does not change. After the periodic orbits are computed for a single parameter value within a hyperbolic plateau, periodic orbit continuation is used to compute periodic orbits over an interval that spans the hyperbolic plateau. The escape rates computed from a few thousand periodic orbits agree with escape rates computed from Monte Carlo simulations requiring hundreds of billions of orbits.

How Incorrect Is the Classical Partition Function for the Ideal Gas?

ERIC Educational Resources Information Center

Kroemer, Herbert

1980-01-01

Discussed is the classical partition function for the ideal gas and how it differs from the exact value for bosons or fermions in the classical regime. The differences in the two values are negligible hence the classical treatment leads in the end to correct answers for all observables. (Author/DS)

Discrete wavelet approach to multifractality

NASA Astrophysics Data System (ADS)

Isaacson, Susana I.; Gabbanelli, Susana C.; Busch, Jorge R.

2000-12-01

The use of wavelet techniques for the multifractal analysis generalizes the box counting approach, and in addition provides information on eventual deviations of multifractal behavior. By the introduction of a wavelet partition function Wq and its corresponding free energy (beta) (q), the discrepancies between (beta) (q) and the multifractal free energy r(q) are shown to be indicative of these deviations. We study with Daubechies wavelets (D4) some 1D examples previously treated with Haar wavelets, and we apply the same ideas to some 2D Monte Carlo configurations, that simulate a solution under the action of an attractive potential. In this last case, we study the influence in the multifractal spectra and partition functions of four physical parameters: the intensity of the pairwise potential, the temperature, the range of the model potential, and the concentration of the solution. The wavelet partition function Wq carries more information about the cluster statistics than the multifractal partition function Zq, and the location of its peaks contributes to the determination of characteristic sales of the measure. In our experiences, the information provided by Daubechies wavelet sis slightly more accurate than the one obtained by Haar wavelets.

Topological nearly entropy

NASA Astrophysics Data System (ADS)

Gulamsarwar, Syazwani; Salleh, Zabidin

2017-08-01

The purpose of this paper is to generalize the notions of Adler's topological entropy along with their several fundamental properties. A function f : X → Y is said to be R-map if f-1 (V) is regular open in X for every regular open set V in Y. Thus, we initiated a notion of topological nearly entropy for topological R-dynamical systems which is based on nearly compact relative to the space by using R-map.

Finite temperature behavior of the CPT-even and parity-even electrodynamics of the standard model extension

DOE Office of Scientific and Technical Information (OSTI.GOV)

Casana, Rodolfo; Ferreira, Manoel M. Jr; Rodrigues, Josberg S.

2009-10-15

In this work, we examine the finite temperature properties of the CPT-even and Lorentz-invariance-violating (LIV) electrodynamics of the standard model extension, represented by the term W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}F{sup {alpha}}{sup {nu}}F{sup {rho}}{sup {phi}}. We begin analyzing the Hamiltonian structure following the Dirac's procedure for constrained systems and construct a well-defined and gauge invariant partition function in the functional integral formalism. Next, we specialize for the nonbirefringent coefficients of the tensor W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}. In the sequel, the partition function is explicitly carried out for the parity-even sector of the tensor W{sub {alpha}}{sub {nu}}{sub {rho}}{sub {phi}}. The modifiedmore » partition function is a power of the Maxwell's partition function. It is observed that the LIV coefficients induce an anisotropy in the black body angular energy density distribution. The Planck's radiation law, however, retains its frequency dependence and the Stefan-Boltzmann law keeps the usual form, except for a change in the Stefan-Boltzmann constant by a factor containing the LIV contributions.« less

An iterative network partition algorithm for accurate identification of dense network modules

PubMed Central

Sun, Siqi; Dong, Xinran; Fu, Yao; Tian, Weidong

2012-01-01

A key step in network analysis is to partition a complex network into dense modules. Currently, modularity is one of the most popular benefit functions used to partition network modules. However, recent studies suggested that it has an inherent limitation in detecting dense network modules. In this study, we observed that despite the limitation, modularity has the advantage of preserving the primary network structure of the undetected modules. Thus, we have developed a simple iterative Network Partition (iNP) algorithm to partition a network. The iNP algorithm provides a general framework in which any modularity-based algorithm can be implemented in the network partition step. Here, we tested iNP with three modularity-based algorithms: multi-step greedy (MSG), spectral clustering and Qcut. Compared with the original three methods, iNP achieved a significant improvement in the quality of network partition in a benchmark study with simulated networks, identified more modules with significantly better enrichment of functionally related genes in both yeast protein complex network and breast cancer gene co-expression network, and discovered more cancer-specific modules in the cancer gene co-expression network. As such, iNP should have a broad application as a general method to assist in the analysis of biological networks. PMID:22121225

Structure, Function, and Propagation of Information across Living Two, Four, and Eight Node Degree Topologies.

PubMed

Alagapan, Sankaraleengam; Franca, Eric; Pan, Liangbin; Leondopulos, Stathis; Wheeler, Bruce C; DeMarse, Thomas B

2016-01-01

In this study, we created four network topologies composed of living cortical neurons and compared resultant structural-functional dynamics including the nature and quality of information transmission. Each living network was composed of living cortical neurons and were created using microstamping of adhesion promoting molecules and each was "designed" with different levels of convergence embedded within each structure. Networks were cultured over a grid of electrodes that permitted detailed measurements of neural activity at each node in the network. Of the topologies we tested, the "Random" networks in which neurons connect based on their own intrinsic properties transmitted information embedded within their spike trains with higher fidelity relative to any other topology we tested. Within our patterned topologies in which we explicitly manipulated structure, the effect of convergence on fidelity was dependent on both topology and time-scale (rate vs. temporal coding). A more detailed examination using tools from network analysis revealed that these changes in fidelity were also associated with a number of other structural properties including a node's degree, degree-degree correlations, path length, and clustering coefficients. Whereas information transmission was apparent among nodes with few connections, the greatest transmission fidelity was achieved among the few nodes possessing the highest number of connections (high degree nodes or putative hubs). These results provide a unique view into the relationship between structure and its affect on transmission fidelity, at least within these small neural populations with defined network topology. They also highlight the potential role of tools such as microstamp printing and microelectrode array recordings to construct and record from arbitrary network topologies to provide a new direction in which to advance the study of structure-function relationships.

Partition functions. I. Improved partition functions and thermodynamic quantities for normal, equilibrium, and ortho and para molecular hydrogen

NASA Astrophysics Data System (ADS)

Popovas, A.; Jørgensen, U. G.

2016-11-01

Context. Hydrogen is the most abundant molecule in the Universe. Its thermodynamic quantities dominate the physical conditions in molecular clouds, protoplanetary disks, etc. It is also of high interest in plasma physics. Therefore thermodynamic data for molecular hydrogen have to be as accurate as possible in a wide temperature range. Aims: We here rigorously show the shortcomings of various simplifications that are used to calculate the total internal partition function. These shortcomings can lead to errors of up to 40 percent or more in the estimated partition function. These errors carry on to calculations of thermodynamic quantities. Therefore a more complicated approach has to be taken. Methods: Seven possible simplifications of various complexity are described, together with advantages and disadvantages of direct summation of experimental values. These were compared to what we consider the most accurate and most complete treatment (case 8). Dunham coefficients were determined from experimental and theoretical energy levels of a number of electronically excited states of H2. Both equilibrium and normal hydrogen was taken into consideration. Results: Various shortcomings in existing calculations are demonstrated, and the reasons for them are explained. New partition functions for equilibrium, normal, and ortho and para hydrogen are calculated and thermodynamic quantities are reported for the temperature range 1-20 000 K. Our results are compared to previous estimates in the literature. The calculations are not limited to the ground electronic state, but include all bound and quasi-bound levels of excited electronic states. Dunham coefficients of these states of H2 are also reported. Conclusions: For most of the relevant astrophysical cases it is strongly advised to avoid using simplifications, such as a harmonic oscillator and rigid rotor or ad hoc summation limits of the eigenstates to estimate accurate partition functions and to be particularly careful when using polynomial fits to the computed values. Reported internal partition functions and thermodynamic quantities in the present work are shown to be more accurate than previously available data. The full datasets in 1 K temperature steps are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/595/A130

Jaccard Similarity Leads to the Marczewski-Steinhaus Topology for Information Retrieval.

ERIC Educational Resources Information Center

Rousseau, Ronald

1998-01-01

Demonstrates that if the similarity function of a retrieval system leads to a (pseudo-) metric, the retrieval, similarity and Everett-Cater metric topology coincide and are different from the discrete topology; this is the case if documents are represented by lists, using the Jaccard similarity measure. The corresponding metric is the…

A level set-based topology optimization method for simultaneous design of elastic structure and coupled acoustic cavity using a two-phase material model

NASA Astrophysics Data System (ADS)

Noguchi, Yuki; Yamamoto, Takashi; Yamada, Takayuki; Izui, Kazuhiro; Nishiwaki, Shinji

2017-09-01

This papers proposes a level set-based topology optimization method for the simultaneous design of acoustic and structural material distributions. In this study, we develop a two-phase material model that is a mixture of an elastic material and acoustic medium, to represent an elastic structure and an acoustic cavity by controlling a volume fraction parameter. In the proposed model, boundary conditions at the two-phase material boundaries are satisfied naturally, avoiding the need to express these boundaries explicitly. We formulate a topology optimization problem to minimize the sound pressure level using this two-phase material model and a level set-based method that obtains topologies free from grayscales. The topological derivative of the objective functional is approximately derived using a variational approach and the adjoint variable method and is utilized to update the level set function via a time evolutionary reaction-diffusion equation. Several numerical examples present optimal acoustic and structural topologies that minimize the sound pressure generated from a vibrating elastic structure.

Topological phase transitions of (BixSb1-x)2Se3 alloys by density functional theory.

PubMed

Abdalla, L B; Padilha José, E; Schmidt, T M; Miwa, R H; Fazzio, A

2015-07-01

We have performed an ab initio total energy investigation of the topological phase transition, and the electronic properties of topologically protected surface states of (BixSb1-x)2Se3 alloys. In order to provide an accurate alloy concentration for the phase transition, we have considered the special quasirandom structures to describe the alloy system. The trivial → topological transition concentration was obtained by (i) the calculation of the band gap closing as a function of Bi concentration (x), and (ii) the calculation of the Z2 topological invariant number. We show that there is a topological phase transition, for x around 0.4, verified for both procedures (i) and (ii). We also show that in the concentration range 0.4 < x < 0.7, the alloy does not present any other band at the Fermi level besides the Dirac cone, where the Dirac point is far from the bulk states. This indicates that a possible suppression of the scattering process due to bulk states will occur.

Kinetic energy partition method applied to ground state helium-like atoms.

PubMed

Chen, Yu-Hsin; Chao, Sheng D

2017-03-28

We have used the recently developed kinetic energy partition (KEP) method to solve the quantum eigenvalue problems for helium-like atoms and obtain precise ground state energies and wave-functions. The key to treating properly the electron-electron (repulsive) Coulomb potential energies for the KEP method to be applied is to introduce a "negative mass" term into the partitioned kinetic energy. A Hartree-like product wave-function from the subsystem wave-functions is used to form the initial trial function, and the variational search for the optimized adiabatic parameters leads to a precise ground state energy. This new approach sheds new light on the all-important problem of solving many-electron Schrödinger equations and hopefully opens a new way to predictive quantum chemistry. The results presented here give very promising evidence that an effective one-electron model can be used to represent a many-electron system, in the spirit of density functional theory.

Discovering Link Communities in Complex Networks by an Integer Programming Model and a Genetic Algorithm

PubMed Central

Li, Zhenping; Zhang, Xiang-Sun; Wang, Rui-Sheng; Liu, Hongwei; Zhang, Shihua

2013-01-01

Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks. PMID:24386268

Bridging the Gap between the Human and Macaque Connectome: A Quantitative Comparison of Global Interspecies Structure-Function Relationships and Network Topology

PubMed Central

Miranda-Dominguez, Oscar; Mills, Brian D.; Grayson, David; Woodall, Andrew; Grant, Kathleen A.; Kroenke, Christopher D.

2014-01-01

Resting state functional connectivity MRI (rs-fcMRI) may provide a powerful and noninvasive “bridge” for comparing brain function between patients and experimental animal models; however, the relationship between human and macaque rs-fcMRI remains poorly understood. Here, using a novel surface deformation process for species comparisons in the same anatomical space (Van Essen, 2004, 2005), we found high correspondence, but also unique hub topology, between human and macaque functional connectomes. The global functional connectivity match between species was moderate to strong (r = 0.41) and increased when considering the top 15% strongest connections (r = 0.54). Analysis of the match between functional connectivity and the underlying anatomical connectivity, derived from a previous retrograde tracer study done in macaques (Markov et al., 2012), showed impressive structure–function correspondence in both the macaque and human. When examining the strongest structural connections, we found a 70–80% match between structural and functional connectivity matrices in both species. Finally, we compare species on two widely used metrics for studying hub topology: degree and betweenness centrality. The data showed topological agreement across the species, with nodes of the posterior cingulate showing high degree and betweenness centrality. In contrast, nodes in medial frontal and parietal cortices were identified as having high degree and betweenness in the human as opposed to the macaque. Our results provide: (1) a thorough examination and validation for a surface-based interspecies deformation process, (2) a strong theoretical foundation for making interspecies comparisons of rs-fcMRI, and (3) a unique look at topological distinctions between the species. PMID:24741045

Diagrammatic analysis of correlations in polymer fluids: Cluster diagrams via Edwards' field theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morse, David C.

2006-10-15

Edwards' functional integral approach to the statistical mechanics of polymer liquids is amenable to a diagrammatic analysis in which free energies and correlation functions are expanded as infinite sums of Feynman diagrams. This analysis is shown to lead naturally to a perturbative cluster expansion that is closely related to the Mayer cluster expansion developed for molecular liquids by Chandler and co-workers. Expansion of the functional integral representation of the grand-canonical partition function yields a perturbation theory in which all quantities of interest are expressed as functionals of a monomer-monomer pair potential, as functionals of intramolecular correlation functions of non-interacting molecules,more » and as functions of molecular activities. In different variants of the theory, the pair potential may be either a bare or a screened potential. A series of topological reductions yields a renormalized diagrammatic expansion in which collective correlation functions are instead expressed diagrammatically as functionals of the true single-molecule correlation functions in the interacting fluid, and as functions of molecular number density. Similar renormalized expansions are also obtained for a collective Ornstein-Zernicke direct correlation function, and for intramolecular correlation functions. A concise discussion is given of the corresponding Mayer cluster expansion, and of the relationship between the Mayer and perturbative cluster expansions for liquids of flexible molecules. The application of the perturbative cluster expansion to coarse-grained models of dense multi-component polymer liquids is discussed, and a justification is given for the use of a loop expansion. As an example, the formalism is used to derive a new expression for the wave-number dependent direct correlation function and recover known expressions for the intramolecular two-point correlation function to first-order in a renormalized loop expansion for coarse-grained models of binary homopolymer blends and diblock copolymer melts.« less

A Geographic and Functional Network Flow Analysis Tool

DTIC Science & Technology

2014-06-01

a context for the games to be run. By definition, a dystopia is “a place where bad things happen”—a fitting name for a place where the scenarios are...design identified by Topology Zoo and the BRITE Topology generator (Byers et al. 2014; Bowden 2013). Both projects aim to accurately map the network...Knight, Simon, Nguyen, Hung, Falkner, Nickolas, and Matthew Roughan. 2014. “The Internet Topology Zoo .” The Internet Topology Zoo . Accessed March

High-Harmonic Generation in Solids with and without Topological Edge States

NASA Astrophysics Data System (ADS)

Bauer, Dieter; Hansen, Kenneth K.

2018-04-01

High-harmonic generation in the two topological phases of a finite, one-dimensional, periodic structure is investigated using a self-consistent time-dependent density functional theory approach. For harmonic photon energies smaller than the band gap, the harmonic yield is found to differ by up to 14 orders of magnitude for the two topological phases. This giant topological effect is explained by the degree of destructive interference in the harmonic emission of all valence-band (and edge-state) electrons, which strongly depends on whether or not topological edge states are present. The combination of strong-field laser physics with topological condensed matter opens up new possibilities to electronically control strong-field-based light or particle sources or—conversely—to steer by all optical means topological electronics.

One-loop tests of supersymmetric gauge theories on spheres

DOE PAGES

Minahan, Joseph A.; Naseer, Usman

2017-07-14

Here, we show that a recently conjectured form for perturbative supersymmetric partition functions on spheres of general dimension d is consistent with the at space limit of 6-dimensional N = 1 super Yang-Mills. We also show that the partition functions for N = 1 8- and 9-dimensional theories are consistent with their known at space limits.

Comments on "The multisynapse neural network and its application to fuzzy clustering".

PubMed

Yu, Jian; Hao, Pengwei

2005-05-01

In the above-mentioned paper, Wei and Fahn proposed a neural architecture, the multisynapse neural network, to solve constrained optimization problems including high-order, logarithmic, and sinusoidal forms, etc. As one of its main applications, a fuzzy bidirectional associative clustering network (FBACN) was proposed for fuzzy-partition clustering according to the objective-functional method. The connection between the objective-functional-based fuzzy c-partition algorithms and FBACN is the Lagrange multiplier approach. Unfortunately, the Lagrange multiplier approach was incorrectly applied so that FBACN does not equivalently minimize its corresponding constrained objective-function. Additionally, Wei and Fahn adopted traditional definition of fuzzy c-partition, which is not satisfied by FBACN. Therefore, FBACN can not solve constrained optimization problems, either.

Integer Partitions and Convexity

NASA Astrophysics Data System (ADS)

Bouroubi, Sadek

2007-06-01

Let n be an integer >=1, and let p(n,k) and P(n,k) count the number of partitions of n into k parts, and the number of partitions of n into parts less than or equal to k, respectively. In this paper, we show that these functions are convex. The result includes the actual value of the constant of Bateman and Erdos.

State-dependent metabolic partitioning and energy conservation: A theoretical framework for understanding the function of sleep.

PubMed

Schmidt, Markus H; Swang, Theodore W; Hamilton, Ian M; Best, Janet A

2017-01-01

Metabolic rate reduction has been considered the mechanism by which sleep conserves energy, similar to torpor or hibernation. This mechanism of energy savings is in conflict with the known upregulation (compared to wake) of diverse functions during sleep and neglects a potential role in energy conservation for partitioning of biological operations by behavioral state. Indeed, energy savings as derived from state-dependent resource allocations have yet to be examined. A mathematical model is presented based on relative rates of energy deployment for biological processes upregulated during either wake or sleep. Using this model, energy savings from sleep-wake cycling over constant wakefulness is computed by comparing stable limit cycles for systems of differential equations. A primary objective is to compare potential energy savings derived from state-dependent metabolic partitioning versus metabolic rate reduction. Additionally, energy conservation from sleep quota and the circadian system are also quantified in relation to a continuous wake condition. As a function of metabolic partitioning, our calculations show that coupling of metabolic operations with behavioral state may provide comparatively greater energy savings than the measured decrease in metabolic rate, suggesting that actual energy savings derived from sleep may be more than 4-fold greater than previous estimates. A combination of state-dependent metabolic partitioning and modest metabolic rate reduction during sleep may enhance energy savings beyond what is achievable through metabolic partitioning alone; however, the relative contribution from metabolic partitioning diminishes as metabolic rate is decreased during the rest phase. Sleep quota and the circadian system further augment energy savings in the model. Finally, we propose that state-dependent resource allocation underpins both sleep homeostasis and the optimization of daily energy conservation across species. This new paradigm identifies an evolutionary selective advantage for the upregulation of central and peripheral biological processes during sleep, presenting a unifying construct to understand sleep function.

The effect of cholesterol on the partitioning of 1-octanol into POPC vesicles

NASA Astrophysics Data System (ADS)

Zakariaee Kouchaksaraee, Roja

Microcalorimetry has become a method of choice for sensitive characterization of biomolecular interactions. In this study, isothermal titration calorimetry (ITC) was used to measure the partitioning of 1-octanol into lipid bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a semi-unsaturated lipid, and cholesterol, a steroid, as a function of cholesterol molar concentration. The ITC instrument measures the heat evolved or absorbed upon titration of a liposome dispersion, at concentrations ranging from 0 to 40% cholesterol, into a suspension of 1-octanol in water. A model function was fit to the data in order to determine the partition coefficient of octanol into POPC bilayers and the enthalpy of interaction. I found that the partition coefficient increases and the heat of interaction becomes less negative with increasing cholesterol content, in contrast to results found by other groups for partitioning of alcohols into lipid-cholesterol bilayers containing saturated lipids. The heat of dilution of vesicles was also measured. Keywords: Partition coefficient; POPC; 1-Octanol; Cholesterol; Isothermal titration calorimetry; Lipid-alcohol interactions. Subject Terms: Calorimetry; Membranes (Biology); Biophysics; Biology -- Technique; Bilayer lipid membranes -- Biotechnology; Lipid membranes -- Biotechnology.

Topological characters in Fe (Te1 -xSex ) thin films

NASA Astrophysics Data System (ADS)

Wu, Xianxin; Qin, Shengshan; Liang, Yi; Fan, Heng; Hu, Jiangping

2016-03-01

We investigate topological properties in the Fe(Te,Se) thin films. We find that the single layer FeTe1 -xSex has nontrivial Z2 topological invariance which originates from the parity exchange at the Γ point of the Brillouin zone. The nontrivial topology is mainly controlled by the Te(Se) height. Adjusting the anion height, which can be realized as the function of lattice constants and x in FeTe1 -xSex , can drive a topological phase transition. In a bulk material, the two-dimensional Z2 topology invariance is extended to a strong three-dimensional one. In a thin film, we predict that the topological invariance oscillates with the number of layers. The results can also be applied to iron pnictides. Our research establishes FeTe1 -xSex as a unique system to integrate high-Tc superconductivity and topological properties in a single electronic structure.

Thermodynamic holography.

PubMed

Wei, Bo-Bo; Jiang, Zhan-Feng; Liu, Ren-Bao

2015-10-19

The holographic principle states that the information about a volume of a system is encoded on the boundary surface of the volume. Holography appears in many branches of physics, such as optics, electromagnetism, many-body physics, quantum gravity, and string theory. Here we show that holography is also an underlying principle in thermodynamics, a most important foundation of physics. The thermodynamics of a system is fully determined by its partition function. We prove that the partition function of a finite but arbitrarily large system is an analytic function on the complex plane of physical parameters, and therefore the partition function in a region on the complex plane is uniquely determined by its values along the boundary. The thermodynamic holography has applications in studying thermodynamics of nano-scale systems (such as molecule engines, nano-generators and macromolecules) and provides a new approach to many-body physics.

Motifs in triadic random graphs based on Steiner triple systems

NASA Astrophysics Data System (ADS)

Winkler, Marco; Reichardt, Jörg

2013-08-01

Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade, the overabundance of certain subnetwork patterns, i.e., the so-called motifs, has attracted much attention. It has been hypothesized that these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information, is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graph models (ERGMs) to define models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obstacle, we use Steiner triple systems (STSs). These are partitions of sets of nodes into pair-disjoint triads, which thus can be specified independently. Combining the concepts of ERGMs and STSs, we suggest generative models capable of generating ensembles of networks with nontrivial triadic Z-score profiles. Further, we discover inevitable correlations between the abundance of triad patterns, which occur solely for statistical reasons and need to be taken into account when discussing the functional implications of motif statistics. Moreover, we calculate the degree distributions of our triadic random graphs analytically.

Constructing IGA-suitable planar parameterization from complex CAD boundary by domain partition and global/local optimization

NASA Astrophysics Data System (ADS)

Xu, Gang; Li, Ming; Mourrain, Bernard; Rabczuk, Timon; Xu, Jinlan; Bordas, Stéphane P. A.

2018-01-01

In this paper, we propose a general framework for constructing IGA-suitable planar B-spline parameterizations from given complex CAD boundaries consisting of a set of B-spline curves. Instead of forming the computational domain by a simple boundary, planar domains with high genus and more complex boundary curves are considered. Firstly, some pre-processing operations including B\\'ezier extraction and subdivision are performed on each boundary curve in order to generate a high-quality planar parameterization; then a robust planar domain partition framework is proposed to construct high-quality patch-meshing results with few singularities from the discrete boundary formed by connecting the end points of the resulting boundary segments. After the topology information generation of quadrilateral decomposition, the optimal placement of interior B\\'ezier curves corresponding to the interior edges of the quadrangulation is constructed by a global optimization method to achieve a patch-partition with high quality. Finally, after the imposition of C1=G1-continuity constraints on the interface of neighboring B\\'ezier patches with respect to each quad in the quadrangulation, the high-quality B\\'ezier patch parameterization is obtained by a C1-constrained local optimization method to achieve uniform and orthogonal iso-parametric structures while keeping the continuity conditions between patches. The efficiency and robustness of the proposed method are demonstrated by several examples which are compared to results obtained by the skeleton-based parameterization approach.

Complete theory of symmetry-based indicators of band topology.

PubMed

Po, Hoi Chun; Vishwanath, Ashvin; Watanabe, Haruki

2017-06-30

The interplay between symmetry and topology leads to a rich variety of electronic topological phases, protecting states such as the topological insulators and Dirac semimetals. Previous results, like the Fu-Kane parity criterion for inversion-symmetric topological insulators, demonstrate that symmetry labels can sometimes unambiguously indicate underlying band topology. Here we develop a systematic approach to expose all such symmetry-based indicators of band topology in all the 230 space groups. This is achieved by first developing an efficient way to represent band structures in terms of elementary basis states, and then isolating the topological ones by removing the subset of atomic insulators, defined by the existence of localized symmetric Wannier functions. Aside from encompassing all earlier results on such indicators, including in particular the notion of filling-enforced quantum band insulators, our theory identifies symmetry settings with previously hidden forms of band topology, and can be applied to the search for topological materials.Understanding the role of topology in determining electronic structure can lead to the discovery, or appreciation, of materials with exotic properties such as protected surface states. Here, the authors present a framework for identifying topologically distinct band-structures for all 3D space groups.

Quenched dynamics and spin-charge separation in an interacting topological lattice

NASA Astrophysics Data System (ADS)

Barbiero, L.; Santos, L.; Goldman, N.

2018-05-01

We analyze the static and dynamical properties of a one-dimensional topological lattice, the fermionic Su-Schrieffer-Heeger model, in the presence of on-site interactions. Based on a study of charge and spin correlation functions, we elucidate the nature of the topological edge modes, which, depending on the sign of the interactions, either display particles of opposite spin on opposite edges, or a pair and a holon. This study of correlation functions also highlights the strong entanglement that exists between the opposite edges of the system. This last feature has remarkable consequences upon subjecting the system to a quench, where an instantaneous edge-to-edge signal appears in the correlation functions characterizing the edge modes. Besides, other correlation functions are shown to propagate in the bulk according to the light cone imposed by the Lieb-Robinson bound. Our study reveals how one-dimensional lattices exhibiting entangled topological edge modes allow for a nontrivial correlation spreading, while providing an accessible platform to detect spin-charge separation using state-of-the-art experimental techniques.

Self-consistent adjoint analysis for topology optimization of electromagnetic waves

NASA Astrophysics Data System (ADS)

Deng, Yongbo; Korvink, Jan G.

2018-05-01

In topology optimization of electromagnetic waves, the Gâteaux differentiability of the conjugate operator to the complex field variable results in the complexity of the adjoint sensitivity, which evolves the original real-valued design variable to be complex during the iterative solution procedure. Therefore, the self-inconsistency of the adjoint sensitivity is presented. To enforce the self-consistency, the real part operator has been used to extract the real part of the sensitivity to keep the real-value property of the design variable. However, this enforced self-consistency can cause the problem that the derived structural topology has unreasonable dependence on the phase of the incident wave. To solve this problem, this article focuses on the self-consistent adjoint analysis of the topology optimization problems for electromagnetic waves. This self-consistent adjoint analysis is implemented by splitting the complex variables of the wave equations into the corresponding real parts and imaginary parts, sequentially substituting the split complex variables into the wave equations with deriving the coupled equations equivalent to the original wave equations, where the infinite free space is truncated by the perfectly matched layers. Then, the topology optimization problems of electromagnetic waves are transformed into the forms defined on real functional spaces instead of complex functional spaces; the adjoint analysis of the topology optimization problems is implemented on real functional spaces with removing the variational of the conjugate operator; the self-consistent adjoint sensitivity is derived, and the phase-dependence problem is avoided for the derived structural topology. Several numerical examples are implemented to demonstrate the robustness of the derived self-consistent adjoint analysis.

Assessment of the instantaneous unit hydrograph derived from the theory of topologically random networks

USGS Publications Warehouse

Karlinger, M.R.; Troutman, B.M.

1985-01-01

An instantaneous unit hydrograph (iuh) based on the theory of topologically random networks (topological iuh) is evaluated in terms of sets of basin characteristics and hydraulic parameters. Hydrographs were computed using two linear routing methods for each of two drainage basins in the southeastern United States and are the basis of comparison for the topological iuh's. Elements in the sets of basin characteristics for the topological iuh's are the number of first-order streams only, (N), or the nuber of sources together with the number of channel links in the topological diameter (N, D); the hydraulic parameters are values of the celerity and diffusivity constant. Sensitivity analyses indicate that the mean celerity of the internal links in the network is the critical hydraulic parameter for determining the shape of the topological iuh, while the diffusivity constant has minimal effect on the topological iuh. Asymptotic results (source-only) indicate the number of sources need not be large to approximate the topological iuh with the Weibull probability density function.

Graph theoretical analysis reveals disrupted topological properties of whole brain functional networks in temporal lobe epilepsy.

PubMed

Wang, Junjing; Qiu, Shijun; Xu, Yong; Liu, Zhenyin; Wen, Xue; Hu, Xiangshu; Zhang, Ruibin; Li, Meng; Wang, Wensheng; Huang, Ruiwang

2014-09-01

Temporal lobe epilepsy (TLE) is one of the most common forms of drug-resistant epilepsy. Previous studies have indicated that the TLE-related impairments existed in extensive local functional networks. However, little is known about the alterations in the topological properties of whole brain functional networks. In this study, we acquired resting-state BOLD-fMRI (rsfMRI) data from 26 TLE patients and 25 healthy controls, constructed their whole brain functional networks, compared the differences in topological parameters between the TLE patients and the controls, and analyzed the correlation between the altered topological properties and the epilepsy duration. The TLE patients showed significant increases in clustering coefficient and characteristic path length, but significant decrease in global efficiency compared to the controls. We also found altered nodal parameters in several regions in the TLE patients, such as the bilateral angular gyri, left middle temporal gyrus, right hippocampus, triangular part of left inferior frontal gyrus, left inferior parietal but supramarginal and angular gyri, and left parahippocampus gyrus. Further correlation analysis showed that the local efficiency of the TLE patients correlated positively with the epilepsy duration. Our results indicated the disrupted topological properties of whole brain functional networks in TLE patients. Our findings indicated the TLE-related impairments in the whole brain functional networks, which may help us to understand the clinical symptoms of TLE patients and offer a clue for the diagnosis and treatment of the TLE patients. Copyright © 2014 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Ocean surface partitioning strategies using ocean colour remote Sensing: A review

NASA Astrophysics Data System (ADS)

Krug, Lilian Anne; Platt, Trevor; Sathyendranath, Shubha; Barbosa, Ana B.

2017-06-01

The ocean surface is organized into regions with distinct properties reflecting the complexity of interactions between environmental forcing and biological responses. The delineation of these functional units, each with unique, homogeneous properties and underlying ecosystem structure and dynamics, can be defined as ocean surface partitioning. The main purposes and applications of ocean partitioning include the evaluation of particular marine environments; generation of more accurate satellite ocean colour products; assimilation of data into biogeochemical and climate models; and establishment of ecosystem-based management practices. This paper reviews the diverse approaches implemented for ocean surface partition into functional units, using ocean colour remote sensing (OCRS) data, including their purposes, criteria, methods and scales. OCRS offers a synoptic, high spatial-temporal resolution, multi-decadal coverage of bio-optical properties, relevant to the applications and value of ocean surface partitioning. In combination with other biotic and/or abiotic data, OCRS-derived data (e.g., chlorophyll-a, optical properties) provide a broad and varied source of information that can be analysed using different delineation methods derived from subjective, expert-based to unsupervised learning approaches (e.g., cluster, fuzzy and empirical orthogonal function analyses). Partition schemes are applied at global to mesoscale spatial coverage, with static (time-invariant) or dynamic (time-varying) representations. A case study, the highly heterogeneous area off SW Iberian Peninsula (NE Atlantic), illustrates how the selection of spatial coverage and temporal representation affects the discrimination of distinct environmental drivers of phytoplankton variability. Advances in operational oceanography and in the subject area of satellite ocean colour, including development of new sensors, algorithms and products, are among the potential benefits from extended use, scope and applications of ocean surface partitioning using OCRS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chinthavali, Madhu Sudhan; Onar, Omer C; Campbell, Steven L

Integrated charger topologies that have been researched so far with dc-dc converters and the charging functionality have no isolation in the system. Isolation is an important feature that is required for user interface systems that have grid connections and therefore is a major limitation that needs to be addressed along with the integrated functionality. The topology proposed in this paper is a unique and a first of its kind topology that integrates a wireless charging system and the boost converter for the traction drive system. The new topology is also compared with an on-board charger system from a commercial electricmore » vehicle (EV). The ac-dc efficiency of the proposed system is 85.05% and the specific power and power density of the onboard components is ~455 W/kg and ~302 W/ .« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chinthavali, Madhu Sudhan; Onar, Omer C; Campbell, Steven L

Integrated charger topologies that have been researched so far with dc-dc converters and the charging functionality have no isolation in the system. Isolation is an important feature that is required for user interface systems that have grid connections and therefore is a major limitation that needs to be addressed along with the integrated functionality. The topology proposed in this paper is a unique and a first of its kind topology that integrates a wireless charging system and the boost converter for the traction drive system. The new topology is also compared with an on-board charger system from a commercial electricmore » vehicle (EV). The ac-dc efficiency of the proposed system is 85.1% and the specific power and power density of the onboard components is ~455 W/kg and ~320 W/ .« less

The impact of aerosol composition on the particle to gas partitioning of reactive mercury.

PubMed

Rutter, Andrew P; Schauer, James J

2007-06-01

A laboratory system was developed to study the gas-particle partitioning of reactive mercury (RM) as a function of aerosol composition in synthetic atmospheric particulate matter. The collection of RM was achieved by filter- and sorbent-based methods. Analyses of the RM collected on the filters and sorbents were performed using thermal extraction combined with cold vapor atomic fluorescence spectroscopy (CVAFS), allowing direct measurement of the RM load on the substrates. Laboratory measurements of the gas-particle partitioning coefficients of RM to atmospheric aerosol particles revealed a strong dependence on aerosol composition, with partitioning coefficients that varied by orders of magnitude depending on the composition of the particles. Particles of sodium nitrate and the chlorides of potassium and sodium had high partitioning coefficients, shifting the RM partitioning toward the particle phase, while ammonium sulfate, levoglucosan, and adipic acid caused the RM to partition toward the gas phase and, therefore, had partitioning coefficients that were lower by orders of magnitude.

Food Web Topology in High Mountain Lakes

PubMed Central

Sánchez-Hernández, Javier; Cobo, Fernando; Amundsen, Per-Arne

2015-01-01

Although diversity and limnology of alpine lake systems are well studied, their food web structure and properties have rarely been addressed. Here, the topological food webs of three high mountain lakes in Central Spain were examined. We first addressed the pelagic networks of the lakes, and then we explored how food web topology changed when benthic biota was included to establish complete trophic networks. We conducted a literature search to compare our alpine lacustrine food webs and their structural metrics with those of 18 published lentic webs using a meta-analytic approach. The comparison revealed that the food webs in alpine lakes are relatively simple, in terms of structural network properties (linkage density and connectance), in comparison with lowland lakes, but no great differences were found among pelagic networks. The studied high mountain food webs were dominated by a high proportion of omnivores and species at intermediate trophic levels. Omnivores can exploit resources at multiple trophic levels, and this characteristic might reduce competition among interacting species. Accordingly, the trophic overlap, measured as trophic similarity, was very low in all three systems. Thus, these alpine networks are characterized by many omnivorous consumers with numerous prey species and few consumers with a single or few prey and with low competitive interactions among species. The present study emphasizes the ecological significance of omnivores in high mountain lakes as promoters of network stability and as central players in energy flow pathways via food partitioning and enabling energy mobility among trophic levels. PMID:26571235

QSAR modeling of flotation collectors using principal components extracted from topological indices.

PubMed

Natarajan, R; Nirdosh, Inderjit; Basak, Subhash C; Mills, Denise R

2002-01-01

Several topological indices were calculated for substituted-cupferrons that were tested as collectors for the froth flotation of uranium. The principal component analysis (PCA) was used for data reduction. Seven principal components (PC) were found to account for 98.6% of the variance among the computed indices. The principal components thus extracted were used in stepwise regression analyses to construct regression models for the prediction of separation efficiencies (Es) of the collectors. A two-parameter model with a correlation coefficient of 0.889 and a three-parameter model with a correlation coefficient of 0.913 were formed. PCs were found to be better than partition coefficient to form regression equations, and inclusion of an electronic parameter such as Hammett sigma or quantum mechanically derived electronic charges on the chelating atoms did not improve the correlation coefficient significantly. The method was extended to model the separation efficiencies of mercaptobenzothiazoles (MBT) and aminothiophenols (ATP) used in the flotation of lead and zinc ores, respectively. Five principal components were found to explain 99% of the data variability in each series. A three-parameter equation with correlation coefficient of 0.985 and a two-parameter equation with correlation coefficient of 0.926 were obtained for MBT and ATP, respectively. The amenability of separation efficiencies of chelating collectors to QSAR modeling using PCs based on topological indices might lead to the selection of collectors for synthesis and testing from a virtual database.

Food Web Topology in High Mountain Lakes.

PubMed

Sánchez-Hernández, Javier; Cobo, Fernando; Amundsen, Per-Arne

2015-01-01

Although diversity and limnology of alpine lake systems are well studied, their food web structure and properties have rarely been addressed. Here, the topological food webs of three high mountain lakes in Central Spain were examined. We first addressed the pelagic networks of the lakes, and then we explored how food web topology changed when benthic biota was included to establish complete trophic networks. We conducted a literature search to compare our alpine lacustrine food webs and their structural metrics with those of 18 published lentic webs using a meta-analytic approach. The comparison revealed that the food webs in alpine lakes are relatively simple, in terms of structural network properties (linkage density and connectance), in comparison with lowland lakes, but no great differences were found among pelagic networks. The studied high mountain food webs were dominated by a high proportion of omnivores and species at intermediate trophic levels. Omnivores can exploit resources at multiple trophic levels, and this characteristic might reduce competition among interacting species. Accordingly, the trophic overlap, measured as trophic similarity, was very low in all three systems. Thus, these alpine networks are characterized by many omnivorous consumers with numerous prey species and few consumers with a single or few prey and with low competitive interactions among species. The present study emphasizes the ecological significance of omnivores in high mountain lakes as promoters of network stability and as central players in energy flow pathways via food partitioning and enabling energy mobility among trophic levels.

Local performance optimization for a class of redundant eight-degree-of-freedom manipulators

NASA Technical Reports Server (NTRS)

Williams, Robert L., II

1994-01-01

Local performance optimization for joint limit avoidance and manipulability maximization (singularity avoidance) is obtained by using the Jacobian matrix pseudoinverse and by projecting the gradient of an objective function into the Jacobian null space. Real-time redundancy optimization control is achieved for an eight-joint redundant manipulator having a three-axis spherical shoulder, a single elbow joint, and a four-axis spherical wrist. Symbolic solutions are used for both full-Jacobian and wrist-partitioned pseudoinverses, partitioned null-space projection matrices, and all objective function gradients. A kinematic limitation of this class of manipulators and the limitation's effect on redundancy resolution are discussed. Results obtained with graphical simulation are presented to demonstrate the effectiveness of local redundant manipulator performance optimization. Actual hardware experiments performed to verify the simulated results are also discussed. A major result is that the partitioned solution is desirable because of low computation requirements. The partitioned solution is suboptimal compared with the full solution because translational and rotational terms are optimized separately; however, the results show that the difference is not significant. Singularity analysis reveals that no algorithmic singularities exist for the partitioned solution. The partitioned and full solutions share the same physical manipulator singular conditions. When compared with the full solution, the partitioned solution is shown to be ill-conditioned in smaller neighborhoods of the shared singularities.

Brain Network Regional Synchrony Analysis in Deafness

PubMed Central

Xu, Lei; Liang, Mao-Jin

2018-01-01

Deafness, the most common auditory disease, has greatly affected people for a long time. The major treatment for deafness is cochlear implantation (CI). However, till today, there is still a lack of objective and precise indicator serving as evaluation of the effectiveness of the cochlear implantation. The goal of this EEG-based study is to effectively distinguish CI children from those prelingual deafened children without cochlear implantation. The proposed method is based on the functional connectivity analysis, which focuses on the brain network regional synchrony. Specifically, we compute the functional connectivity between each channel pair first. Then, we quantify the brain network synchrony among regions of interests (ROIs), where both intraregional synchrony and interregional synchrony are computed. And finally the synchrony values are concatenated to form the feature vector for the SVM classifier. What is more, we develop a new ROI partition method of 128-channel EEG recording system. That is, both the existing ROI partition method and the proposed ROI partition method are used in the experiments. Compared with the existing EEG signal classification methods, our proposed method has achieved significant improvements as large as 87.20% and 86.30% when the existing ROI partition method and the proposed ROI partition method are used, respectively. It further demonstrates that the new ROI partition method is comparable to the existing ROI partition method. PMID:29854776

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

NASA Astrophysics Data System (ADS)

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.

Topologically-protected one-way leaky waves in nonreciprocal plasmonic structures

NASA Astrophysics Data System (ADS)

Hassani Gangaraj, S. Ali; Monticone, Francesco

2018-03-01

We investigate topologically-protected unidirectional leaky waves on magnetized plasmonic structures acting as homogeneous photonic topological insulators. Our theoretical analyses and numerical experiments aim at unveiling the general properties of these exotic surface waves, and their nonreciprocal and topological nature. In particular, we study the behavior of topological leaky modes in stratified structures composed of a magnetized plasma at the interface with isotropic conventional media, and we show how to engineer their propagation and radiation properties, leading to topologically-protected backscattering-immune wave propagation, and highly directive and tunable radiation. Taking advantage of the non-trivial topological properties of these leaky modes, we also theoretically demonstrate advanced functionalities, including arbitrary re-routing of leaky waves on the surface of bodies with complex shapes, as well as the realization of topological leaky-wave (nano)antennas with isolated channels of radiation that are completely independent and separately tunable. Our findings help shedding light on the behavior of topologically-protected modes in open wave-guiding structures, and may open intriguing directions for future antenna generations based on topological structures, at microwaves and optical frequencies.

Comparison of modeling approaches for carbon partitioning: Impact on estimates of global net primary production and equilibrium biomass of woody vegetation from MODIS GPP

Treesearch

Takeshi Ise; Creighton M. Litton; Christian P. Giardina; Akihiko Ito

2010-01-01

Partitioning of gross primary production (GPP) to aboveground versus belowground, to growth versus respiration, and to short versus long�]lived tissues exerts a strong influence on ecosystem structure and function, with potentially large implications for the global carbon budget. A recent meta-analysis of forest ecosystems suggests that carbon partitioning...

Witten index for noncompact dynamics

NASA Astrophysics Data System (ADS)

Lee, Seung-Joo; Yi, Piljin

2016-06-01

Among gauged dynamics motivated by string theory, we find many with gapless asymptotic directions. Although the natural boundary condition for ground states is L 2, one often turns on chemical potentials or supersymmetric mass terms to regulate the infrared issues, instead, and computes the twisted partition function. We point out how this procedure generically fails to capture physical L 2 Witten index with often misleading results. We also explore how, nevertheless, the Witten index is sometimes intricately embedded in such twisted partition functions. For d = 1 theories with gapless continuum sector from gauge multiplets, such as non-primitive quivers and pure Yang-Mills, a further subtlety exists, leading to fractional expressions. Quite unexpectedly, however, the integral L 2 Witten index can be extracted directly and easily from the twisted partition function of such theories. This phenomenon is tied to the notion of the rational invariant that appears naturally in the wall-crossing formulae, and offers a general mechanism of reading off Witten index directly from the twisted partition function. Along the way, we correct early numerical results for some of mathcal{N} = 4 , 8 , 16 pure Yang-Mills quantum mechanics, and count threshold bound states for general gauge groups beyond SU( N ).

Distinct Roles of Chromatin Insulator Proteins in Control of the Drosophila Bithorax Complex

PubMed Central

Savitsky, Mikhail; Kim, Maria; Kravchuk, Oksana; Schwartz, Yuri B.

2016-01-01

Chromatin insulators are remarkable regulatory elements that can bring distant genomic sites together and block unscheduled enhancer–promoter communications. Insulators act via associated insulator proteins of two classes: sequence-specific DNA binding factors and “bridging” proteins. The latter are required to mediate interactions between distant insulator elements. Chromatin insulators are critical for correct expression of complex loci; however, their mode of action is poorly understood. Here, we use the Drosophila bithorax complex as a model to investigate the roles of the bridging proteins Cp190 and Mod(mdg4). The bithorax complex consists of three evolutionarily conserved homeotic genes Ubx, abd-A, and Abd-B, which specify anterior–posterior identity of the last thoracic and all abdominal segments of the fly. Looking at effects of CTCF, mod(mdg4), and Cp190 mutations on expression of the bithorax complex genes, we provide the first functional evidence that Mod(mdg4) acts in concert with the DNA binding insulator protein CTCF. We find that Mod(mdg4) and Cp190 are not redundant and may have distinct functional properties. We, for the first time, demonstrate that Cp190 is critical for correct regulation of the bithorax complex and show that Cp190 is required at an exceptionally strong Fub insulator to partition the bithorax complex into two topological domains. PMID:26715665

Topological strings in d < 1

NASA Astrophysics Data System (ADS)

Dijkgraaf, Robbert; Verlinde, Herman; Verlinde, Erik

1991-03-01

We calculate correlation functions in minimal topological field theories. These twisted versions of N = 2 minimal models have recently been proposed to describe d < 1 matrix models, once coupled to topological gravity. In our calculation we make use of the Landau-Ginzburg formulation of the N = 2 models, and we find a direct relation between the Landau-Ginzburg superpotential and the KdV differential operator. Using this correspondence we show that the minimal topological models are in perfect agreement with the matrix models as solved in terms of the KdV hierarchy. This proves the equivalence at tree-level of topological and ordinary string thoery in d < 1.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bergen, Ben; Moss, Nicholas; Charest, Marc Robert Joseph

FleCSI is a compile-time configurable framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. Current support includes multi-dimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures. FleCSI also introduces a functional programming model with control, execution, and data abstractions that are consistent with both MPI and state-of-the-art task-based runtimes such as Legion and Charm++. The FleCSI abstraction layer providesmore » the developer with insulation from the underlying runtime, while allowing support for multiple runtime systems, including conventional models like asynchronous MPI. The intent is to give developers a concrete set of user-friendly programming tools that can be used now, while allowing flexibility in choosing runtime implementations and optimizations that can be applied to architectures and runtimes that arise in the future. The control and execution models in FleCSI also provide formal nomenclature for describing poorly understood concepts like kernels and tasks.« less

Entropy and optimality in river deltas

NASA Astrophysics Data System (ADS)

Tejedor, Alejandro; Longjas, Anthony; Edmonds, Douglas A.; Zaliapin, Ilya; Georgiou, Tryphon T.; Rinaldo, Andrea; Foufoula-Georgiou, Efi

2017-10-01

The form and function of river deltas is intricately linked to the evolving structure of their channel networks, which controls how effectively deltas are nourished with sediments and nutrients. Understanding the coevolution of deltaic channels and their flux organization is crucial for guiding maintenance strategies of these highly stressed systems from a range of anthropogenic activities. To date, however, a unified theory explaining how deltas self-organize to distribute water and sediment up to the shoreline remains elusive. Here, we provide evidence for an optimality principle underlying the self-organized partition of fluxes in delta channel networks. By introducing a suitable nonlocal entropy rate (nER) and by analyzing field and simulated deltas, we suggest that delta networks achieve configurations that maximize the diversity of water and sediment flux delivery to the shoreline. We thus suggest that prograding deltas attain dynamically accessible optima of flux distributions on their channel network topologies, thus effectively decoupling evolutionary time scales of geomorphology and hydrology. When interpreted in terms of delta resilience, high nER configurations reflect an increased ability to withstand perturbations. However, the distributive mechanism responsible for both diversifying flux delivery to the shoreline and dampening possible perturbations might lead to catastrophic events when those perturbations exceed certain intensity thresholds.

Molecular docking of superantigens with class II major histocompatibility complex proteins.

PubMed

Olson, M A; Cuff, L

1997-01-01

The molecular recognition of two superantigens with class II major histocompatibility complex molecules was simulated by using protein-protein docking. Superantigens studied were staphylococcal enterotoxin B (SEB) and toxic shock syndrome toxin-1 (TSST-1) in their crystallographic assemblies with HLA-DR1. Rigid-body docking was performed sampling configurational space of the interfacial surfaces by employing a strategy of partitioning the contact regions on HLA-DR1 into separate molecular recognition units. Scoring of docked conformations was based on an electrostatic continuum model evaluated with the finite-difference Poisson-Boltzmann method. Estimates of nonpolar contributions were derived from the buried molecular surface areas. We found for both superantigens that docking the HLA-DR1 surface complementary with the SEB and TSST-1 contact regions containing a homologous hydrophobic surface loop provided sufficient recognition for the reconstitution of native-like conformers exhibiting the highest-scoring free energies. For the SEB complex, the calculations were successful in reproducing the total association free energy. A comparison of the free-energy determinants of the conserved hydrophobic contact residue indicates functional similarity between the two proteins for this interface. Though both superantigens share a common global association mode, differences in binding topology distinguish the conformational specificities underlying recognition.

Exploring optimal topology of thermal cloaks by CMA-ES

NASA Astrophysics Data System (ADS)

Fujii, Garuda; Akimoto, Youhei; Takahashi, Masayuki

2018-02-01

This paper presents topology optimization for thermal cloaks expressed by level-set functions and explored using the covariance matrix adaptation evolution strategy (CMA-ES). Designed optimal configurations provide superior performances in thermal cloaks for the steady-state thermal conduction and succeed in realizing thermal invisibility, despite the structures being simply composed of iron and aluminum and without inhomogeneities caused by employing metamaterials. To design thermal cloaks, a prescribed objective function is used to evaluate the difference between the temperature field controlled by a thermal cloak and when no thermal insulator is present. The CMA-ES involves searches for optimal sets of level-set functions as design variables that minimize a regularized fitness involving a perimeter constraint. Through topology optimization subject to structural symmetries about four axes, we obtain a concept design of a thermal cloak that functions in an isotropic heat flux.

Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb)*

PubMed Central

Orfanoudaki, Georgia; Economou, Anastassios

2014-01-01

Cell compartmentalization serves both the isolation and the specialization of cell functions. After synthesis in the cytoplasm, over a third of all proteins are targeted to other subcellular compartments. Knowing how proteins are distributed within the cell and how they interact is a prerequisite for understanding it as a whole. Surface and secreted proteins are important pathogenicity determinants. Here we present the STEP database (STEPdb) that contains a comprehensive characterization of subcellular localization and topology of the complete proteome of Escherichia coli. Two widely used E. coli proteomes (K-12 and BL21) are presented organized into thirteen subcellular classes. STEPdb exploits the wealth of genetic, proteomic, biochemical, and functional information on protein localization, secretion, and targeting in E. coli, one of the best understood model organisms. Subcellular annotations were derived from a combination of bioinformatics prediction, proteomic, biochemical, functional, topological data and extensive literature re-examination that were refined through manual curation. Strong experimental support for the location of 1553 out of 4303 proteins was based on 426 articles and some experimental indications for another 526. Annotations were provided for another 320 proteins based on firm bioinformatic predictions. STEPdb is the first database that contains an extensive set of peripheral IM proteins (PIM proteins) and includes their graphical visualization into complexes, cellular functions, and interactions. It also summarizes all currently known protein export machineries of E. coli K-12 and pairs them, where available, with the secretory proteins that use them. It catalogs the Sec- and TAT-utilizing secretomes and summarizes their topological features such as signal peptides and transmembrane regions, transmembrane topologies and orientations. It also catalogs physicochemical and structural features that influence topology such as abundance, solubility, disorder, heat resistance, and structural domain families. Finally, STEPdb incorporates prediction tools for topology (TMHMM, SignalP, and Phobius) and disorder (IUPred) and implements the BLAST2STEP that performs protein homology searches against the STEPdb. PMID:25210196

Diagrammatic expansion for positive density-response spectra: Application to the electron gas

NASA Astrophysics Data System (ADS)

Uimonen, A.-M.; Stefanucci, G.; Pavlyukh, Y.; van Leeuwen, R.

2015-03-01

In a recent paper [Phys. Rev. B 90, 115134 (2014), 10.1103/PhysRevB.90.115134] we put forward a diagrammatic expansion for the self-energy which guarantees the positivity of the spectral function. In this work we extend the theory to the density-response function. We write the generic diagram for the density-response spectrum as the sum of "partitions." In a partition the original diagram is evaluated using time-ordered Green's functions on the left half of the diagram, antitime-ordered Green's functions on the right half of the diagram, and lesser or greater Green's function gluing the two halves. As there exists more than one way to cut a diagram in two halves, to every diagram corresponds more than one partition. We recognize that the most convenient diagrammatic objects for constructing a theory of positive spectra are the half-diagrams. Diagrammatic approximations obtained by summing the squares of half-diagrams do indeed correspond to a combination of partitions which, by construction, yield a positive spectrum. We develop the theory using bare Green's functions and subsequently extend it to dressed Green's functions. We further prove a connection between the positivity of the spectral function and the analytic properties of the polarizability. The general theory is illustrated with several examples and then applied to solve the long-standing problem of including vertex corrections without altering the positivity of the spectrum. In fact already the first-order vertex diagram, relevant to the study of gradient expansion, Friedel oscillations, etc., leads to spectra which are negative in certain frequency domain. We find that the simplest approximation to cure this deficiency is given by the sum of the zeroth-order bubble diagram, the first-order vertex diagram, and a partition of the second-order ladder diagram. We evaluate this approximation in the three-dimensional homogeneous electron gas and show the positivity of the spectrum for all frequencies and densities.

Exact deconstruction of the 6D (2,0) theory

NASA Astrophysics Data System (ADS)

Hayling, J.; Papageorgakis, C.; Pomoni, E.; Rodríguez-Gómez, D.

2017-06-01

The dimensional-deconstruction prescription of Arkani-Hamed, Cohen, Kaplan, Karch and Motl provides a mechanism for recovering the A-type (2,0) theories on T 2, starting from a four-dimensional N=2 circular-quiver theory. We put this conjecture to the test using two exact-counting arguments: in the decompactification limit, we compare the Higgs-branch Hilbert series of the 4D N=2 quiver to the "half-BPS" limit of the (2,0) superconformal index. We also compare the full partition function for the 4D quiver on S 4 to the (2,0) partition function on S 4 × T 2. In both cases we find exact agreement. The partition function calculation sets up a dictionary between exact results in 4D and 6D.

Partition functions with spin in AdS2 via quasinormal mode methods

DOE PAGES

Keeler, Cynthia; Lisbão, Pedro; Ng, Gim Seng

2016-10-12

We extend the results of [1], computing one loop partition functions for massive fields with spin half in AdS 2 using the quasinormal mode method proposed by Denef, Hartnoll, and Sachdev [2]. We find the finite representations of SO(2,1) for spin zero and spin half, consisting of a highest weight state |hi and descendants with non-unitary values of h. These finite representations capture the poles and zeroes of the one loop determinants. Together with the asymptotic behavior of the partition functions (which can be easily computed using a large mass heat kernel expansion), these are sufficient to determine the fullmore » answer for the one loop determinants. We also discuss extensions to higher dimensional AdS 2n and higher spins.« less

Topology-Optimized Multilayered Metaoptics

NASA Astrophysics Data System (ADS)

Lin, Zin; Groever, Benedikt; Capasso, Federico; Rodriguez, Alejandro W.; Lončar, Marko

2018-04-01

We propose a general topology-optimization framework for metasurface inverse design that can automatically discover highly complex multilayered metastructures with increased functionalities. In particular, we present topology-optimized multilayered geometries exhibiting angular phase control, including a single-piece nanophotonic metalens with angular aberration correction, as well as an angle-convergent metalens that focuses light onto the same focal spot regardless of the angle of incidence.

Asymmetry of Hemispheric Network Topology Reveals Dissociable Processes between Functional and Structural Brain Connectome in Community-Living Elders

PubMed Central

Sun, Yu; Li, Junhua; Suckling, John; Feng, Lei

2017-01-01

Human brain is structurally and functionally asymmetrical and the asymmetries of brain phenotypes have been shown to change in normal aging. Recent advances in graph theoretical analysis have showed topological lateralization between hemispheric networks in the human brain throughout the lifespan. Nevertheless, apparent discrepancies of hemispheric asymmetry were reported between the structural and functional brain networks, indicating the potentially complex asymmetry patterns between structural and functional networks in aging population. In this study, using multimodal neuroimaging (resting-state fMRI and structural diffusion tensor imaging), we investigated the characteristics of hemispheric network topology in 76 (male/female = 15/61, age = 70.08 ± 5.30 years) community-dwelling older adults. Hemispheric functional and structural brain networks were obtained for each participant. Graph theoretical approaches were then employed to estimate the hemispheric topological properties. We found that the optimal small-world properties were preserved in both structural and functional hemispheric networks in older adults. Moreover, a leftward asymmetry in both global and local levels were observed in structural brain networks in comparison with a symmetric pattern in functional brain network, suggesting a dissociable process of hemispheric asymmetry between structural and functional connectome in healthy older adults. Finally, the scores of hemispheric asymmetry in both structural and functional networks were associated with behavioral performance in various cognitive domains. Taken together, these findings provide new insights into the lateralized nature of multimodal brain connectivity, highlight the potentially complex relationship between structural and functional brain network alterations, and augment our understanding of asymmetric structural and functional specializations in normal aging. PMID:29209197

Practical deviations from Henry`s law for water/air partitioning of volatile organic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schabron, J.F.; Rovani, J.F. Jr.

A study was conducted to define parameters relating to the use of a down hole submersible photoionization detector (PID) probe to measure volatile organic compounds (VOCs) in an artificial headspace. The partitioning of toluene and trichloroethylene between water and air was studied as a function of analyte concentration and water temperature. The Henry`s law constant governing this partitioning represents an ideal condition at infinite dilution for a particular temperature. The results show that in practice. this partitioning is far from ideal. Conditions resulting in apparent, practical deviations from Henry`s law include temperature and VOC concentration. Thus, a single value ofmore » Henry`s law constant for a particular VOC such as toluene can provide only an approximation of concentration in the field. Detector response in saturated humidity environments as a function of water temperature and analyte concentration was studied also.« less

Dimerization controls the lipid raft partitioning of uPAR/CD87 and regulates its biological functions

PubMed Central

Cunningham, Orla; Andolfo, Annapaola; Santovito, Maria Lisa; Iuzzolino, Lucia; Blasi, Francesco; Sidenius, Nicolai

2003-01-01

The urokinase-type plasminogen activator receptor (uPAR/CD87) is a glycosylphosphatidylinositol-anchored membrane protein with multiple functions in extracellular proteolysis, cell adhesion, cell migration and proliferation. We now report that cell surface uPAR dimerizes and that dimeric uPAR partitions preferentially to detergent-resistant lipid rafts. Dimerization of uPAR did not require raft partitioning as the lowering of membrane cholesterol failed to reduce dimerization and as a transmembrane uPAR chimera, which does not partition to lipid rafts, also dimerized efficiently. While uPA bound to uPAR independently of its membrane localization and dimerization status, uPA-induced uPAR cleavage was strongly accelerated in lipid rafts. In contrast to uPA, the binding of Vn occurred preferentially to raft- associated dimeric uPAR and was completely blocked by cholesterol depletion. PMID:14609946

Different alterations in brain functional networks according to direct and indirect topological connections in patients with schizophrenia.

PubMed

Park, Chang-Hyun; Lee, Seungyup; Kim, Taewon; Won, Wang Yeon; Lee, Kyoung-Uk

2017-10-01

Schizophrenia displays connectivity deficits in the brain, but the literature has shown inconsistent findings about alterations in global efficiency of brain functional networks. We supposed that such inconsistency at the whole brain level may be due to a mixture of different portions of global efficiency at sub-brain levels. Accordingly, we considered measuring portions of global efficiency in two aspects: spatial portions by considering sub-brain networks and topological portions by considering contributions to global efficiency according to direct and indirect topological connections. We proposed adjacency and indirect adjacency as new network parameters attributable to direct and indirect topological connections, respectively, and applied them to graph-theoretical analysis of brain functional networks constructed from resting state fMRI data of 22 patients with schizophrenia and 22 healthy controls. Group differences in the network parameters were observed not for whole brain and hemispheric networks, but for regional networks. Alterations in adjacency and indirect adjacency were in opposite directions, such that adjacency increased, but indirect adjacency decreased in patients with schizophrenia. Furthermore, over connections in frontal and parietal regions, increased adjacency was associated with more severe negative symptoms, while decreased adjacency was associated with more severe positive symptoms of schizophrenia. This finding indicates that connectivity deficits associated with positive and negative symptoms of schizophrenia may involve topologically different paths in the brain. In patients with schizophrenia, although changes in global efficiency may not be clearly shown, different alterations in brain functional networks according to direct and indirect topological connections could be revealed at the regional level. Copyright © 2017 Elsevier B.V. All rights reserved.

Sizable band gap in organometallic topological insulator

NASA Astrophysics Data System (ADS)

Derakhshan, V.; Ketabi, S. A.

2017-01-01

Based on first principle calculation when Ceperley-Alder and Perdew-Burke-Ernzerh type exchange-correlation energy functional were adopted to LSDA and GGA calculation, electronic properties of organometallic honeycomb lattice as a two-dimensional topological insulator was calculated. In the presence of spin-orbit interaction bulk band gap of organometallic lattice with heavy metals such as Au, Hg, Pt and Tl atoms were investigated. Our results show that the organometallic topological insulator which is made of Mercury atom shows the wide bulk band gap of about ∼120 meV. Moreover, by fitting the conduction and valence bands to the band-structure which are produced by Density Functional Theory, spin-orbit interaction parameters were extracted. Based on calculated parameters, gapless edge states within bulk insulating gap are indeed found for finite width strip of two-dimensional organometallic topological insulators.

Complexity and dynamics of topological and community structure in complex networks

NASA Astrophysics Data System (ADS)

Berec, Vesna

2017-07-01

Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

Thermodynamic limit of random partitions and dispersionless Toda hierarchy

NASA Astrophysics Data System (ADS)

Takasaki, Kanehisa; Nakatsu, Toshio

2012-01-01

We study the thermodynamic limit of random partition models for the instanton sum of 4D and 5D supersymmetric U(1) gauge theories deformed by some physical observables. The physical observables correspond to external potentials in the statistical model. The partition function is reformulated in terms of the density function of Maya diagrams. The thermodynamic limit is governed by a limit shape of Young diagrams associated with dominant terms in the partition function. The limit shape is characterized by a variational problem, which is further converted to a scalar-valued Riemann-Hilbert problem. This Riemann-Hilbert problem is solved with the aid of a complex curve, which may be thought of as the Seiberg-Witten curve of the deformed U(1) gauge theory. This solution of the Riemann-Hilbert problem is identified with a special solution of the dispersionless Toda hierarchy that satisfies a pair of generalized string equations. The generalized string equations for the 5D gauge theory are shown to be related to hidden symmetries of the statistical model. The prepotential and the Seiberg-Witten differential are also considered.

Investigations of Topological Surface States in Sb (111) Ultrathin Films by STM/STS Experiments and DFT Calculations

NASA Astrophysics Data System (ADS)

Luo, Ziyu; Yao, Guanggeng; Xu, Wentao; Feng, Yuanping; Wang, Xue-Sen

2014-03-01

Bulk Sb was regarded as a semimetal with a nontrivial topological order. It is worth exploring whether the Sb ultrathin film has the potential to be an elementary topological insulator. In the presence of quantum confinement effect, we investigated the evolution of topological surface states in Sb (111) ultrathin films with different thickness by the scanning tunneling microscopy/ spectroscopy (STM/STS) experiments and density functional theory (DFT) calculations. By comparing the quasiparticle interference (QPI) patterns obtained from Fourier-transform scanning tunneling spectroscopy (FT-STS) and from DFT calculations, we successfully derive the spin properties of topological surface states on Sb (111) ultrathin films. In addition, based on the DFT calculations, the 8BL Sb (111) ultrathin film was proved to possess up to 30% spinseparated topological surface states within the bandgap. Therefore, the highquality 8BL Sb (111) ultrathin film could be regarded as an elementary topological insulator.

Monochromatic Transmittance/Radiance Computations

DTIC Science & Technology

1974-12-31

In the infrared region, these tran- sitions are normally between various vibration -rotation states. There are usually a large number of possible...energy level of the transition, and Q (e,m.) and Q (0,m.) are respectively the ratio of the vibrational and rotational partition function at...values used are listed in Table 2 (Ref. 2). For source conditions, the vibrational partition function cannot be ignored and has been calculated 4

Phase diagram of q-deformed Yang-Mills theory on S 2 at non-zero θ-angle

NASA Astrophysics Data System (ADS)

Okuyama, Kazumi

2018-04-01

We study the phase diagram of q-deformed Yang-Mills theory on S 2 at non-zero θ-angle using the exact partition function at finite N . By evaluating the exact partition function numerically, we find evidence for the existence of a series of phase transitions at non-zero θ-angle as conjectured in [hep-th/0509004

GPS/INS integration by functional partitioning

NASA Astrophysics Data System (ADS)

Diesel, John W.

It is shown that a GPS/INS system integrated by functional partitioning can satisfy all of the RTCA navigation requirements and goals. This is accomplished by accurately calibrating the INS using GPS after the inertial instruments are thermally stabilized and by exploiting the very slow subsequent error growth in the INS information. In this way, autonomous integrity monitoring can be achieved using only existing or presently planned systems.

Quantized charge transport in chiral Majorana edge modes

NASA Astrophysics Data System (ADS)

Rachel, Stephan; Mascot, Eric; Cocklin, Sagen; Vojta, Matthias; Morr, Dirk K.

2017-11-01

Majorana fermions can be realized as quasiparticles in topological superconductors, with potential applications in topological quantum computing. Recently, lattices of magnetic adatoms deposited on the surface of s -wave superconductors—Shiba lattices—have been proposed as a new platform for topological superconductivity. These systems possess the great advantage that they are accessible via scanning-probe techniques and thus enable the local manipulation and detection of Majorana modes. Using a nonequilibrium Green's function technique we demonstrate that the topological Majorana edge modes of nanoscopic Shiba islands display universal electronic and transport properties. Most remarkably, these Majorana modes possess a quantized charge conductance that is proportional to the topological Chern number, C , and carry a supercurrent whose chirality reflects the sign of C . These results establish nanoscopic Shiba islands as promising components in future topology-based devices.

Discriminating topology in galaxy distributions using network analysis

NASA Astrophysics Data System (ADS)

Hong, Sungryong; Coutinho, Bruno C.; Dey, Arjun; Barabási, Albert-L.; Vogelsberger, Mark; Hernquist, Lars; Gebhardt, Karl

2016-07-01

The large-scale distribution of galaxies is generally analysed using the two-point correlation function. However, this statistic does not capture the topology of the distribution, and it is necessary to resort to higher order correlations to break degeneracies. We demonstrate that an alternate approach using network analysis can discriminate between topologically different distributions that have similar two-point correlations. We investigate two galaxy point distributions, one produced by a cosmological simulation and the other by a Lévy walk. For the cosmological simulation, we adopt the redshift z = 0.58 slice from Illustris and select galaxies with stellar masses greater than 108 M⊙. The two-point correlation function of these simulated galaxies follows a single power law, ξ(r) ˜ r-1.5. Then, we generate Lévy walks matching the correlation function and abundance with the simulated galaxies. We find that, while the two simulated galaxy point distributions have the same abundance and two-point correlation function, their spatial distributions are very different; most prominently, filamentary structures, absent in Lévy fractals. To quantify these missing topologies, we adopt network analysis tools and measure diameter, giant component, and transitivity from networks built by a conventional friends-of-friends recipe with various linking lengths. Unlike the abundance and two-point correlation function, these network quantities reveal a clear separation between the two simulated distributions; therefore, the galaxy distribution simulated by Illustris is not a Lévy fractal quantitatively. We find that the described network quantities offer an efficient tool for discriminating topologies and for comparing observed and theoretical distributions.

A New Approach to Investigate the Association between Brain Functional Connectivity and Disease Characteristics of Attention-Deficit/Hyperactivity Disorder: Topological Neuroimaging Data Analysis.

PubMed

Kyeong, Sunghyon; Park, Seonjeong; Cheon, Keun-Ah; Kim, Jae-Jin; Song, Dong-Ho; Kim, Eunjoo

2015-01-01

Attention-deficit/hyperactivity disorder (ADHD) is currently diagnosed by a diagnostic interview, mainly based on subjective reports from parents or teachers. It is necessary to develop methods that rely on objectively measureable neurobiological data to assess brain-behavior relationship in patients with ADHD. We investigated the application of a topological data analysis tool, Mapper, to analyze the brain functional connectivity data from ADHD patients. To quantify the disease severity using the neuroimaging data, the decomposition of individual functional networks into normal and disease components by the healthy state model (HSM) was performed, and the magnitude of the disease component (MDC) was computed. Topological data analysis using Mapper was performed to distinguish children with ADHD (n = 196) from typically developing controls (TDC) (n = 214). In the topological data analysis, the partial clustering results of patients with ADHD and normal subjects were shown in a chain-like graph. In the correlation analysis, the MDC showed a significant increase with lower intelligence scores in TDC. We also found that the rates of comorbidity in ADHD significantly increased when the deviation of the functional connectivity from HSM was large. In addition, a significant correlation between ADHD symptom severity and MDC was found in part of the dataset. The application of HSM and topological data analysis methods in assessing the brain functional connectivity seem to be promising tools to quantify ADHD symptom severity and to reveal the hidden relationship between clinical phenotypic variables and brain connectivity.

An Integrative Object-Based Image Analysis Workflow for Uav Images

NASA Astrophysics Data System (ADS)

Yu, Huai; Yan, Tianheng; Yang, Wen; Zheng, Hong

2016-06-01

In this work, we propose an integrative framework to process UAV images. The overall process can be viewed as a pipeline consisting of the geometric and radiometric corrections, subsequent panoramic mosaicking and hierarchical image segmentation for later Object Based Image Analysis (OBIA). More precisely, we first introduce an efficient image stitching algorithm after the geometric calibration and radiometric correction, which employs a fast feature extraction and matching by combining the local difference binary descriptor and the local sensitive hashing. We then use a Binary Partition Tree (BPT) representation for the large mosaicked panoramic image, which starts by the definition of an initial partition obtained by an over-segmentation algorithm, i.e., the simple linear iterative clustering (SLIC). Finally, we build an object-based hierarchical structure by fully considering the spectral and spatial information of the super-pixels and their topological relationships. Moreover, an optimal segmentation is obtained by filtering the complex hierarchies into simpler ones according to some criterions, such as the uniform homogeneity and semantic consistency. Experimental results on processing the post-seismic UAV images of the 2013 Ya'an earthquake demonstrate the effectiveness and efficiency of our proposed method.

Architecture of the ParF*ParG protein complex involved in prokaryotic DNA segregation.

PubMed

Barillà, Daniela; Hayes, Finbarr

2003-07-01

The mechanism by which low copy number plasmids are segregated at cell division involves the concerted action of two plasmid-encoded proteins that assemble on a centromere-like site. This study explores the topology of the DNA segregation machinery specified by the parFG locus of TP228, a partition system which is phylogenetically distinct from more well-characterized archetypes. A variety of genetic, biochemical and biophysical strategies revealed that the ParG protein is dimeric. ParF, which is more closely related to the cell division regulator MinD than to the prototypical ParA partition protein of plasmid P1, is instead multimeric and its polymeric state appears to be modulated by ATP which correlates with the proposed ATP-binding activity of ParF. ParG interacts in a sequence-specific manner with the DNA region upstream of the parFG locus and this binding is modulated by ParF. Intriguingly, the ParF and ParG proteins form at least two types of discrete complex in the absence of this region suggesting that the assembly dynamics of these proteins onto DNA is intricate.

Distributed k-Means Algorithm and Fuzzy c-Means Algorithm for Sensor Networks Based on Multiagent Consensus Theory.

PubMed

Qin, Jiahu; Fu, Weiming; Gao, Huijun; Zheng, Wei Xing

2016-03-03

This paper is concerned with developing a distributed k-means algorithm and a distributed fuzzy c-means algorithm for wireless sensor networks (WSNs) where each node is equipped with sensors. The underlying topology of the WSN is supposed to be strongly connected. The consensus algorithm in multiagent consensus theory is utilized to exchange the measurement information of the sensors in WSN. To obtain a faster convergence speed as well as a higher possibility of having the global optimum, a distributed k-means++ algorithm is first proposed to find the initial centroids before executing the distributed k-means algorithm and the distributed fuzzy c-means algorithm. The proposed distributed k-means algorithm is capable of partitioning the data observed by the nodes into measure-dependent groups which have small in-group and large out-group distances, while the proposed distributed fuzzy c-means algorithm is capable of partitioning the data observed by the nodes into different measure-dependent groups with degrees of membership values ranging from 0 to 1. Simulation results show that the proposed distributed algorithms can achieve almost the same results as that given by the centralized clustering algorithms.

Community Detection in Signed Networks: the Role of Negative ties in Different Scales

PubMed Central

Esmailian, Pouya; Jalili, Mahdi

2015-01-01

Extracting community structure of complex network systems has many applications from engineering to biology and social sciences. There exist many algorithms to discover community structure of networks. However, it has been significantly under-explored for networks with positive and negative links as compared to unsigned ones. Trying to fill this gap, we measured the quality of partitions by introducing a Map Equation for signed networks. It is based on the assumption that negative relations weaken positive flow from a node towards a community, and thus, external (internal) negative ties increase the probability of staying inside (escaping from) a community. We further extended the Constant Potts Model, providing a map spectrum for signed networks. Accordingly, a partition is selected through balancing between abridgment and expatiation of a signed network. Most importantly, multi-scale spectrum of signed networks revealed how informative are negative ties in different scales, and quantified the topological placement of negative ties between dense positive ones. Moreover, an inconsistency was found in the signed Modularity: as the number of negative ties increases, the density of positive ties is neglected more. These results shed lights on the community structure of signed networks. PMID:26395815

Spacecraft On-Board Information Extraction Computer (SOBIEC)

NASA Technical Reports Server (NTRS)

Eisenman, David; Decaro, Robert E.; Jurasek, David W.

1994-01-01

The Jet Propulsion Laboratory is the Technical Monitor on an SBIR Program issued for Irvine Sensors Corporation to develop a highly compact, dual use massively parallel processing node known as SOBIEC. SOBIEC couples 3D memory stacking technology provided by nCUBE. The node contains sufficient network Input/Output to implement up to an order-13 binary hypercube. The benefit of this network, is that it scales linearly as more processors are added, and it is a superset of other commonly used interconnect topologies such as: meshes, rings, toroids, and trees. In this manner, a distributed processing network can be easily devised and supported. The SOBIEC node has sufficient memory for most multi-computer applications, and also supports external memory expansion and DMA interfaces. The SOBIEC node is supported by a mature set of software development tools from nCUBE. The nCUBE operating system (OS) provides configuration and operational support for up to 8000 SOBIEC processors in an order-13 binary hypercube or any subset or partition(s) thereof. The OS is UNIX (USL SVR4) compatible, with C, C++, and FORTRAN compilers readily available. A stand-alone development system is also available to support SOBIEC test and integration.

Recent Performance Results of VPIC on Trinity

NASA Astrophysics Data System (ADS)

Nystrom, W. D.; Bergen, B.; Bird, R. F.; Bowers, K. J.; Daughton, W. S.; Guo, F.; Le, A.; Li, H.; Nam, H.; Pang, X.; Stark, D. J.; Rust, W. N., III; Yin, L.; Albright, B. J.

2017-10-01

Trinity is a new DOE compute resource now in production at Los Alamos National Laboratory. Trinity has several new and unique features including two compute partitions, one with dual socket Intel Haswell Xeon compute nodes and one with Intel Knights Landing (KNL) Xeon Phi compute nodes, use of on package high bandwidth memory (HBM) for KNL nodes, ability to configure KNL nodes with respect to HBM model and on die network topology in a variety of operational modes at run time, and use of solid state storage via burst buffer technology to reduce time required to perform I/O. An effort is in progress to optimize VPIC on Trinity by taking advantage of these new architectural features. Results of work will be presented on performance of VPIC on Haswell and KNL partitions for single node runs and runs at scale. Results include use of burst buffers at scale to optimize I/O, comparison of strategies for using MPI and threads, performance benefits using HBM and effectiveness of using intrinsics for vectorization. Work performed under auspices of U.S. Dept. of Energy by Los Alamos National Security, LLC Los Alamos National Laboratory under contract DE-AC52-06NA25396 and supported by LANL LDRD program.

Formal Specification and Validation of a Hybrid Connectivity Restoration Algorithm for Wireless Sensor and Actor Networks †

PubMed Central

Imran, Muhammad; Zafar, Nazir Ahmad

2012-01-01

Maintaining inter-actor connectivity is extremely crucial in mission-critical applications of Wireless Sensor and Actor Networks (WSANs), as actors have to quickly plan optimal coordinated responses to detected events. Failure of a critical actor partitions the inter-actor network into disjoint segments besides leaving a coverage hole, and thus hinders the network operation. This paper presents a Partitioning detection and Connectivity Restoration (PCR) algorithm to tolerate critical actor failure. As part of pre-failure planning, PCR determines critical/non-critical actors based on localized information and designates each critical node with an appropriate backup (preferably non-critical). The pre-designated backup detects the failure of its primary actor and initiates a post-failure recovery process that may involve coordinated multi-actor relocation. To prove the correctness, we construct a formal specification of PCR using Z notation. We model WSAN topology as a dynamic graph and transform PCR to corresponding formal specification using Z notation. Formal specification is analyzed and validated using the Z Eves tool. Moreover, we simulate the specification to quantitatively analyze the efficiency of PCR. Simulation results confirm the effectiveness of PCR and the results shown that it outperforms contemporary schemes found in the literature.

Influence function for robust phylogenetic reconstructions.

PubMed

Bar-Hen, Avner; Mariadassou, Mahendra; Poursat, Marie-Anne; Vandenkoornhuyse, Philippe

2008-05-01

Based on the computation of the influence function, a tool to measure the impact of each piece of sampled data on the statistical inference of a parameter, we propose to analyze the support of the maximum-likelihood (ML) tree for each site. We provide a new tool for filtering data sets (nucleotides, amino acids, and others) in the context of ML phylogenetic reconstructions. Because different sites support different phylogenic topologies in different ways, outlier sites, that is, sites with a very negative influence value, are important: they can drastically change the topology resulting from the statistical inference. Therefore, these outlier sites must be clearly identified and their effects accounted for before drawing biological conclusions from the inferred tree. A matrix containing 158 fungal terminals all belonging to Chytridiomycota, Zygomycota, and Glomeromycota is analyzed. We show that removing the strongest outlier from the analysis strikingly modifies the ML topology, with a loss of as many as 20% of the internal nodes. As a result, estimating the topology on the filtered data set results in a topology with enhanced bootstrap support. From this analysis, the polyphyletic status of the fungal phyla Chytridiomycota and Zygomycota is reinforced, suggesting the necessity of revisiting the systematics of these fungal groups. We show the ability of influence function to produce new evolution hypotheses.

EEG functional network topology is associated with disability in patients with amyotrophic lateral sclerosis

NASA Astrophysics Data System (ADS)

Fraschini, Matteo; Demuru, Matteo; Hillebrand, Arjan; Cuccu, Lorenza; Porcu, Silvia; di Stefano, Francesca; Puligheddu, Monica; Floris, Gianluca; Borghero, Giuseppe; Marrosu, Francesco

2016-12-01

Amyotrophic Lateral Sclerosis (ALS) is one of the most severe neurodegenerative diseases, which is known to affect upper and lower motor neurons. In contrast to the classical tenet that ALS represents the outcome of extensive and progressive impairment of a fixed set of motor connections, recent neuroimaging findings suggest that the disease spreads along vast non-motor connections. Here, we hypothesised that functional network topology is perturbed in ALS, and that this reorganization is associated with disability. We tested this hypothesis in 21 patients affected by ALS at several stages of impairment using resting-state electroencephalography (EEG) and compared the results to 16 age-matched healthy controls. We estimated functional connectivity using the Phase Lag Index (PLI), and characterized the network topology using the minimum spanning tree (MST). We found a significant difference between groups in terms of MST dissimilarity and MST leaf fraction in the beta band. Moreover, some MST parameters (leaf, hierarchy and kappa) significantly correlated with disability. These findings suggest that the topology of resting-state functional networks in ALS is affected by the disease in relation to disability. EEG network analysis may be of help in monitoring and evaluating the clinical status of ALS patients.

STRUCTURAL DYNAMICS OF METAL PARTITIONING TO MINERAL SURFACES

EPA Science Inventory

The conceptual understanding of surface complexation reactions that control trace element partitioning to mineral surfaces is limited by the assumption that the solid reactant possesses a finite, time-invariant population of surface functional groups. This assumption has limited...

The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?

PubMed Central

Murray, Gemma G. R.; Weinert, Lucy A.; Rhule, Emma L.; Welch, John J.

2016-01-01

Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives. PMID:26559010

Building supertrees: an empirical assessment using the grass family (Poaceae).

PubMed

Salamin, Nicolas; Hodkinson, Trevor R; Savolainen, Vincent

2002-02-01

Large and comprehensive phylogenetic trees are desirable for studying macroevolutionary processes and for classification purposes. Such trees can be obtained in two different ways. Either the widest possible range of taxa can be sampled and used in a phylogenetic analysis to produce a "big tree," or preexisting topologies can be used to create a supertree. Although large multigene analyses are often favored, combinable data are not always available, and supertrees offer a suitable solution. The most commonly used method of supertree reconstruction, matrix representation with parsimony (MRP), is presented here. We used a combined data set for the Poaceae to (1) assess the differences between an approach that uses combined data and one that uses different MRP modifications based on the character partitions and (2) investigate the advantages and disadvantages of these modifications. Baum and Ragan and Purvis modifications gave similar results. Incorporating bootstrap support associated with pre-existing topologies improved Baum and Ragan modification and its similarity with a combined analysis. Finally, we used the supertree reconstruction approach on 55 published phylogenies to build one of most comprehensive phylogenetic trees published for the grass family including 403 taxa and discuss its strengths and weaknesses in relation to other published hypotheses.

Investigating the topological structure of quenched lattice QCD with overlap fermions using a multi-probing approximation

NASA Astrophysics Data System (ADS)

Zou, You-Hao; Zhang, Jian-Bo; Xiong, Guang-Yi; Chen, Ying; Liu, Chuan; Liu, Yu-Bin; Ma, Jian-Ping

2017-10-01

The topological charge density and topological susceptibility are determined by a multi-probing approximation using overlap fermions in quenched SU(3) gauge theory. Then we investigate the topological structure of the quenched QCD vacuum, and compare it with results from the all-scale topological density. The results are consistent. Random permuted topological charge density is used to check whether these structures represent underlying ordered properties. The pseudoscalar glueball mass is extracted from the two-point correlation function of the topological charge density. We study 3 ensembles of different lattice spacing a with the same lattice volume 163×32. The results are compatible with the results of all-scale topological charge density, and the topological structures revealed by multi-probing are much closer to all-scale topological charge density than those from eigenmode expansion. Supported by National Natural Science Foundation of China (NSFC) (11335001, 11275169, 11075167), It is also supported in part by the DFG and the NSFC (11261130311) through funds provided to the Sino-German CRC 110 "Symmetries and the Emergence of Structure in QCD". This work was also funded in part by National Basic Research Program of China (973 Program) (2015CB856700)

High-temperature asymptotics of supersymmetric partition functions

DOE PAGES

Ardehali, Arash Arabi

2016-07-05

We study the supersymmetric partition function of 4d supersymmetric gauge theories with a U(1) R-symmetry on Euclidean S 3 × S β 1, with S 3 the unit-radius squashed three-sphere, and β the circumference of the circle. For superconformal theories, this partition function coincides (up to a Casimir energy factor) with the 4d superconformal index. The partition function can be computed exactly using the supersymmetric localization of the gauge theory path-integral. It takes the form of an elliptic hypergeometric integral, which may be viewed as a matrix-integral over the moduli space of the holonomies of the gauge fields around Smore » β 1. At high temperatures (β → 0, corresponding to the hyperbolic limit of the elliptic hypergeometric integral) we obtain from the matrix-integral a quantum effective potential for the holonomies. The effective potential is proportional to the temperature. Therefore the high-temperature limit further localizes the matrix-integral to the locus of the minima of the potential. If the effective potential is positive semi-definite, the leading high-temperature asymptotics of the partition function is given by the formula of Di Pietro and Komargodski, and the subleading asymptotics is connected to the Coulomb branch dynamics on R 3 × S 1. In theories where the effective potential is not positive semi-definite, the Di Pietro-Komargodski formula needs to be modified. In particular, this modification occurs in the SU(2) theory of Intriligator-Seiberg-Shenker, and the SO(N) theory of Brodie-Cho-Intriligator, both believed to exhibit “misleading” anomaly matchings, and both believed to yield interacting superconformal field theories with c < a. Lastly, two new simple tests for dualities between 4d supersymmetric gauge theories emerge as byproducts of our analysis.« less

The Topology Optimization Design Research for Aluminum Inner Panel of Automobile Engine Hood

NASA Astrophysics Data System (ADS)

Li, Minhao; Hu, Dongqing; Liu, Xiangzheng; Yuan, Huanquan

2017-11-01

This article discusses the topology optimization methods for automobile engine hood design. The aluminum inner panel of engine hood and mucilage glue regions are set as design areas, and the static performances of engine hood included modal frequency, lateral stiffness, torsional stiffness and indentation stiffness are set as the optimization objectives. The topology optimization results about different objective functions are contrasted for analysis. And based on the reasonable topology optimization result, a suited automobile engine hood designs are raised to further study. Finally, an automobile engine hood that good at all of static performances is designed, and a favorable topology optimization method is put forward for discussion.

Untangling the mechanics versus topology of overhand knots

NASA Astrophysics Data System (ADS)

Reis, Pedro; Jawed, Mohammad; Dieleman, Peter; Audoly, Basile

2015-03-01

We study the interplay between mechanics and topology of overhand knots in slender elastic rods. We perform precision desktop experiments of overhand knots with increasing values for the crossing number (our measure of topology) and characterize their mechanical response through tension-displacement tests. The tensile force required to tighten the knot is governed by an intricate balance between topology, bending, friction, and contact forces. Digital imaging is employed to characterize the configuration of the contact braid as a function of crossing number. A robust scaling law is found for the pulling force in terms of the geometric and topological parameters of the knot. A reduced theory is developed, which predictively rationalizes the process.

The H0 function, a new index for detecting structural/topological complexity information in undirected graphs

NASA Astrophysics Data System (ADS)

Buscema, Massimo; Asadi-Zeydabadi, Masoud; Lodwick, Weldon; Breda, Marco

2016-04-01

Significant applications such as the analysis of Alzheimer's disease differentiated from dementia, or in data mining of social media, or in extracting information of drug cartel structural composition, are often modeled as graphs. The structural or topological complexity or lack of it in a graph is quite often useful in understanding and more importantly, resolving the problem. We are proposing a new index we call the H0function to measure the structural/topological complexity of a graph. To do this, we introduce the concept of graph pruning and its associated algorithm that is used in the development of our measure. We illustrate the behavior of our measure, the H0 function, through different examples found in the appendix. These examples indicate that the H0 function contains information that is useful and important characteristics of a graph. Here, we restrict ourselves to undirected.

Topologically protected modes in non-equilibrium stochastic systems.

PubMed

Murugan, Arvind; Vaikuntanathan, Suriyanarayanan

2017-01-10

Non-equilibrium driving of biophysical processes is believed to enable their robust functioning despite the presence of thermal fluctuations and other sources of disorder. Such robust functions include sensory adaptation, enhanced enzymatic specificity and maintenance of coherent oscillations. Elucidating the relation between energy consumption and organization remains an important and open question in non-equilibrium statistical mechanics. Here we report that steady states of systems with non-equilibrium fluxes can support topologically protected boundary modes that resemble similar modes in electronic and mechanical systems. Akin to their electronic and mechanical counterparts, topological-protected boundary steady states in non-equilibrium systems are robust and are largely insensitive to local perturbations. We argue that our work provides a framework for how biophysical systems can use non-equilibrium driving to achieve robust function.

Topological Alterations of the Intrinsic Brain Network in Patients with Functional Dyspepsia.

PubMed

Nan, Jiaofen; Zhang, Li; Zhu, Fubao; Tian, Xiaorui; Zheng, Qian; Deneen, Karen M von; Liu, Jixin; Zhang, Ming

2016-01-31

Previous studies reported that integrated information in the brain ultimately determines the subjective experience of patients with chronic pain, but how the information is integrated in the brain connectome of functional dyspepsia (FD) patients remains largely unclear. The study aimed to quantify the topological changes of the brain network in FD patients. Small-world properties, network efficiency and nodal centrality were utilized to measure the changes in topological architecture in 25 FD patients and 25 healthy controls based on functional magnetic resonance imaging. Pearson's correlation assessed the relationship of each topological property with clinical symptoms. FD patients showed an increase of clustering coefficients and local efficiency relative to controls from the perspective of a whole network as well as elevated nodal centrality in the right orbital part of the inferior frontal gyrus, left anterior cingulate gyrus and left hippocampus, and decreased nodal centrality in the right posterior cingulate gyrus, left cuneus, right putamen, left middle occipital gyrus and right inferior occipital gyrus. Moreover, the centrality in the anterior cingulate gyrus was significantly associated with symptom severity and duration in FD patients. Nevertheless, the inclusion of anxiety and depression scores as covariates erased the group differences in nodal centralities in the orbital part of the inferior frontal gyrus and hippocampus. The results suggest topological disruption of the functional brain networks in FD patients, presumably in response to disturbances of sensory information integrated with emotion, memory, pain modulation, and selective attention in patients.

Anharmonic effects in the quantum cluster equilibrium method

NASA Astrophysics Data System (ADS)

von Domaros, Michael; Perlt, Eva

2017-03-01

The well-established quantum cluster equilibrium (QCE) model provides a statistical thermodynamic framework to apply high-level ab initio calculations of finite cluster structures to macroscopic liquid phases using the partition function. So far, the harmonic approximation has been applied throughout the calculations. In this article, we apply an important correction in the evaluation of the one-particle partition function and account for anharmonicity. Therefore, we implemented an analytical approximation to the Morse partition function and the derivatives of its logarithm with respect to temperature, which are required for the evaluation of thermodynamic quantities. This anharmonic QCE approach has been applied to liquid hydrogen chloride and cluster distributions, and the molar volume, the volumetric thermal expansion coefficient, and the isobaric heat capacity have been calculated. An improved description for all properties is observed if anharmonic effects are considered.

AGT/ℤ2

NASA Astrophysics Data System (ADS)

Le Floch, Bruno; Turiaci, Gustavo J.

2017-12-01

We relate Liouville/Toda CFT correlators on Riemann surfaces with boundaries and cross-cap states to supersymmetric observables in four-dimensional N=2 gauge theories. Our construction naturally involves four-dimensional theories with fields defined on different ℤ2 quotients of the sphere (hemisphere and projective space) but nevertheless interacting with each other. The six-dimensional origin is a ℤ2 quotient of the setup giving rise to the usual AGT correspondence. To test the correspondence, we work out the ℝℙ4 partition function of four-dimensional N=2 theories by combining a 3d lens space and a 4d hemisphere partition functions. The same technique reproduces known ℝℙ2 partition functions in a form that lets us easily check two-dimensional Seiberg-like dualities on this nonorientable space. As a bonus we work out boundary and cross-cap wavefunctions in Toda CFT.

Polynomial solution of quantum Grassmann matrices

NASA Astrophysics Data System (ADS)

Tierz, Miguel

2017-05-01

We study a model of quantum mechanical fermions with matrix-like index structure (with indices N and L) and quartic interactions, recently introduced by Anninos and Silva. We compute the partition function exactly with q-deformed orthogonal polynomials (Stieltjes-Wigert polynomials), for different values of L and arbitrary N. From the explicit evaluation of the thermal partition function, the energy levels and degeneracies are determined. For a given L, the number of states of different energy is quadratic in N, which implies an exponential degeneracy of the energy levels. We also show that at high-temperature we have a Gaussian matrix model, which implies a symmetry that swaps N and L, together with a Wick rotation of the spectral parameter. In this limit, we also write the partition function, for generic L and N, in terms of a single generalized Hermite polynomial.

Determination of the topology of endoplasmic reticulum membrane proteins using redox-sensitive green-fluorescence protein fusions.

PubMed

Tsachaki, Maria; Birk, Julia; Egert, Aurélie; Odermatt, Alex

2015-07-01

Membrane proteins of the endoplasmic reticulum (ER) are involved in a wide array of essential cellular functions. Identification of the topology of membrane proteins can provide significant insight into their mechanisms of action and biological roles. This is particularly important for membrane enzymes, since their topology determines the subcellular site where a biochemical reaction takes place and the dependence on luminal or cytosolic co-factor pools and substrates. The methods currently available for the determination of topology of proteins are rather laborious and require post-lysis or post-fixation manipulation of cells. In this work, we have developed a simple method for defining intracellular localization and topology of ER membrane proteins in living cells, based on the fusion of the respective protein with redox-sensitive green-fluorescent protein (roGFP). We validated the method and demonstrated that roGFP fusion proteins constitute a reliable tool for the study of ER membrane protein topology, using as control microsomal 11β-hydroxysteroid dehydrogenase (11β-HSD) proteins whose topology has been resolved, and comparing with an independent approach. We then implemented this method to determine the membrane topology of six microsomal members of the 17β-hydroxysteroid dehydrogenase (17β-HSD) family. The results revealed a luminal orientation of the catalytic site for three enzymes, i.e. 17β-HSD6, 7 and 12. Knowledge of the intracellular location of the catalytic site of these enzymes will enable future studies on their biological functions and on the role of the luminal co-factor pool. Copyright © 2015 Elsevier B.V. All rights reserved.

Wind farm topology-finding algorithm considering performance, costs, and environmental impacts.

PubMed

Tazi, Nacef; Chatelet, Eric; Bouzidi, Youcef; Meziane, Rachid

2017-06-05

Optimal power in wind farms turns to be a modern problem for investors and decision makers; onshore wind farms are subject to performance and economic and environmental constraints. The aim of this work is to define the best installed capacity (best topology) with maximum performance and profits and consider environmental impacts as well. In this article, we continue the work recently done on wind farm topology-finding algorithm. The proposed resolution technique is based on finding the best topology of the system that maximizes the wind farm performance (availability) under the constraints of costs and capital investments. Global warming potential of wind farm is calculated and taken into account in the results. A case study is done using data and constraints similar to those collected from wind farm constructors, managers, and maintainers. Multi-state systems (MSS), universal generating function (UGF), wind, and load charge functions are applied. An economic study was conducted to assess the wind farm investment. Net present value (NPV) and levelized cost of energy (LCOE) were calculated for best topologies found.

Non-local electron transport through normal and topological ladder-like atomic systems

NASA Astrophysics Data System (ADS)

Kurzyna, Marcin; Kwapiński, Tomasz

2018-05-01

We propose a locally protected ladder-like atomic system (nanoconductor) on a substrate that is insensitive to external perturbations. The system corresponds to coupled atomic chains fabricated on different surfaces. Electron transport properties of such conductors are studied theoretically using the model tight-binding Su-Schriffer-Hegger (SSH) Hamiltonian and Green's function formalism. We have found that the conductance of the system is almost insensitive to single adatoms and oscillates as a function of the side chain length with very large periods. Non-local character of the electron transport was observed also for topological SSH chains where nontrivial end states survive in the presence of disturbances as well as for different substrates. We have found that the careful inspection of the density of states or charge waves can provide the information about the atom energy levels and hopping amplitudes. Moreover, the ladder-like geometry allows one to distinguish between normal and topological zero-energy states. It is important that topological chains do not reveal Friedel oscillations which are observed in non-topological chains.

Analysis of the morphology, stability, and folding pathways of ring polymers with supramolecular topological constraints using molecular simulation and nonlinear manifold learning

NASA Astrophysics Data System (ADS)

Wang, Jiang; Ferguson, Andrew

Ring polymers offer a wide range of natural and engineered functions and applications, including as circular bacterial DNA, crown ethers for cation chelation, and ``molecular machines'' such as mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and degree of polymerization of the ring, and intramolecular and supramolecular topological constraints such as knots or mechanically-interlocked rings. We perform molecular dynamics simulations of polyethylene ring polymers as a function of degree of polymerization and in different topological states, including a knotted state, catenane state (two interlocked rings), and borromean state (three interlocked rings). Applying nonlinear manifold learning to our all-atom simulation trajectories, we extract low-dimensional free energy surfaces governing the accessible conformational states and their relative thermodynamic stability. The free energy surfaces reveal how degree of polymerization and topological constraints affect the thermally accessible conformations, chiral symmetry breaking, and folding and collapse pathways of the rings, and present a means to rationally engineer ring size and topology to preferentially stabilize particular conformational states.

Strain-induced topological quantum phase transition in phosphorene oxide

NASA Astrophysics Data System (ADS)

Kang, Seoung-Hun; Park, Jejune; Woo, Sungjong; Kwon, Young-Kyun

Using ab initio density functional theory, we investigate the structural stability and electronic properties of phosphorene oxides (POx) with different oxygen compositions x. A variety of configurations are modeled and optimized geometrically to search for the equilibrium structure for each x value. Our electronic structure calculations on the equilibrium configuration obtained for each x reveal that the band gap tends to increase with the oxygen composition of x < 0.5, and then to decrease with x > 0.5. We further explore the strain effect on the electronic structure of the fully oxidized phosphorene, PO, with x = 1. At a particular strain without spin-orbit coupling (SOC) is observed a band gap closure near the Γ point in the k space. We further find the strain in tandem with SOC induces an interesting band inversion with a reopened very small band gap (5 meV), and thus gives rise to a topological quantum phase transition from a normal insulator to a topological insulator. Such a topological phase transition is confirmed by the wave function analysis and the band topology identified by the Z2 invariant calculation.

Cognitive performance in mid-stage Parkinson's disease: functional connectivity under chronic antiparkinson treatment.

PubMed

Vancea, Roxana; Simonyan, Kristina; Petracca, Maria; Brys, Miroslaw; Di Rocco, Alessandro; Ghilardi, Maria Felice; Inglese, Matilde

2017-09-23

Cognitive impairment in Parkinson's disease (PD) is related to the reorganization of brain topology. Although drug challenge studies have proven how levodopa treatment can modulate functional connectivity in brain circuits, the role of chronic dopaminergic therapy on cognitive status and functional connectivity has never been investigated. We sought to characterize brain functional topology in mid-stage PD patients under chronic antiparkinson treatment and explore the presence of correlation between reorganization of brain architecture and specific cognitive deficits. We explored networks topology and functional connectivity in 16 patients with PD and 16 matched controls through a graph theoretical analysis of resting state-functional MRI data, and evaluated the relationships between network metrics and cognitive performance. PD patients showed a preserved small-world network topology but a lower clustering coefficient in comparison with healthy controls. Locally, PD patients showed lower degree of connectivity and local efficiency in many hubs corresponding to functionally relevant areas. Four disconnected subnetworks were also identified in regions responsible for executive control, sensory-motor control and planning, motor coordination and visual elaboration. Executive functions and information processing speed were directly correlated with degree of connectivity and local efficiency in frontal, parietal and occipital areas. While functional reorganization appears in both motor and cognitive areas, the clinical expression of network imbalance seems to be partially compensated by the chronic levodopa treatment with regards to the motor but not to the cognitive performance. In a context of reduced network segregation, the presence of higher local efficiency in hubs regions correlates with a better cognitive performance.

Computer program for calculating and fitting thermodynamic functions

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford

1992-01-01

A computer program is described which (1) calculates thermodynamic functions (heat capacity, enthalpy, entropy, and free energy) for several optional forms of the partition function, (2) fits these functions to empirical equations by means of a least-squares fit, and (3) calculates, as a function of temperture, heats of formation and equilibrium constants. The program provides several methods for calculating ideal gas properties. For monatomic gases, three methods are given which differ in the technique used for truncating the partition function. For diatomic and polyatomic molecules, five methods are given which differ in the corrections to the rigid-rotator harmonic-oscillator approximation. A method for estimating thermodynamic functions for some species is also given.

Evaluation of Hierarchical Clustering Algorithms for Document Datasets

DTIC Science & Technology

2002-06-03

link, complete-link, and group average ( UPGMA )) and a new set of merging criteria derived from the six partitional criterion functions. Overall, we...used the single-link, complete-link, and UPGMA schemes, as well as, the various partitional criterion functions described in Section 3.1. The single-link...other (complete-link approach). The UPGMA scheme [16] (also known as group average) overcomes these problems by measuring the similarity of two clusters

Topological Properties of Some Integrated Circuits for Very Large Scale Integration Chip Designs

NASA Astrophysics Data System (ADS)

Swanson, S.; Lanzerotti, M.; Vernizzi, G.; Kujawski, J.; Weatherwax, A.

2015-03-01

This talk presents topological properties of integrated circuits for Very Large Scale Integration chip designs. These circuits can be implemented in very large scale integrated circuits, such as those in high performance microprocessors. Prior work considered basic combinational logic functions and produced a mathematical framework based on algebraic topology for integrated circuits composed of logic gates. Prior work also produced an historically-equivalent interpretation of Mr. E. F. Rent's work for today's complex circuitry in modern high performance microprocessors, where a heuristic linear relationship was observed between the number of connections and number of logic gates. This talk will examine topological properties and connectivity of more complex functionally-equivalent integrated circuits. The views expressed in this article are those of the author and do not reflect the official policy or position of the United States Air Force, Department of Defense or the U.S. Government.

3D Topology Preserving Flows for Viewpoint-Based Cortical Unfolding

PubMed Central

Rocha, Kelvin R.; Sundaramoorthi, Ganesh; Yezzi, Anthony J.; Prince, Jerry L.

2009-01-01

We present a variational method for unfolding of the cortex based on a user-chosen point of view as an alternative to more traditional global flattening methods, which incur more distortion around the region of interest. Our approach involves three novel contributions. The first is an energy function and its corresponding gradient flow to measure the average visibility of a region of interest of a surface with respect to a given viewpoint. The second is an additional energy function and flow designed to preserve the 3D topology of the evolving surface. The third is a method that dramatically improves the computational speed of the 3D topology preservation approach by creating a tree structure of the 3D surface and using a recursion technique. Experiments results show that the proposed approach can successfully unfold highly convoluted surfaces such as the cortex while preserving their topology. PMID:19960105

A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space.

PubMed

Wu, Yao; Dai, Xiaodong; Huang, Niu; Zhao, Lifeng

2013-06-05

In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function-based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high-level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function-based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function-based weighting method may be applied in developing any types of force field parameters. Copyright © 2013 Wiley Periodicals, Inc.

Statistical Systems with Z

NASA Astrophysics Data System (ADS)

William, Peter

In this dissertation several two dimensional statistical systems exhibiting discrete Z(n) symmetries are studied. For this purpose a newly developed algorithm to compute the partition function of these models exactly is utilized. The zeros of the partition function are examined in order to obtain information about the observable quantities at the critical point. This occurs in the form of critical exponents of the order parameters which characterize phenomena at the critical point. The correlation length exponent is found to agree very well with those computed from strong coupling expansions for the mass gap and with Monte Carlo results. In Feynman's path integral formalism the partition function of a statistical system can be related to the vacuum expectation value of the time ordered product of the observable quantities of the corresponding field theoretic model. Hence a generalization of ordinary scale invariance in the form of conformal invariance is focussed upon. This principle is very suitably applicable, in the case of two dimensional statistical models undergoing second order phase transitions at criticality. The conformal anomaly specifies the universality class to which these models belong. From an evaluation of the partition function, the free energy at criticality is computed, to determine the conformal anomaly of these models. The conformal anomaly for all the models considered here are in good agreement with the predicted values.

Elastic network model of learned maintained contacts to predict protein motion

PubMed Central

Putz, Ines

2017-01-01

We present a novel elastic network model, lmcENM, to determine protein motion even for localized functional motions that involve substantial changes in the protein’s contact topology. Existing elastic network models assume that the contact topology remains unchanged throughout the motion and are thus most appropriate to simulate highly collective function-related movements. lmcENM uses machine learning to differentiate breaking from maintained contacts. We show that lmcENM accurately captures functional transitions unexplained by the classical ENM and three reference ENM variants, while preserving the simplicity of classical ENM. We demonstrate the effectiveness of our approach on a large set of proteins covering different motion types. Our results suggest that accurately predicting a “deformation-invariant” contact topology offers a promising route to increase the general applicability of ENMs. We also find that to correctly predict this contact topology a combination of several features seems to be relevant which may vary slightly depending on the protein. Additionally, we present case studies of two biologically interesting systems, Ferric Citrate membrane transporter FecA and Arachidonate 15-Lipoxygenase. PMID:28854238

Triangular Quantum Loop Topography for Machine Learning

NASA Astrophysics Data System (ADS)

Zhang, Yi; Kim, Eun-Ah

Despite rapidly growing interest in harnessing machine learning in the study of quantum many-body systems there has been little success in training neural networks to identify topological phases. The key challenge is in efficiently extracting essential information from the many-body Hamiltonian or wave function and turning the information into an image that can be fed into a neural network. When targeting topological phases, this task becomes particularly challenging as topological phases are defined in terms of non-local properties. Here we introduce triangular quantum loop (TQL) topography: a procedure of constructing a multi-dimensional image from the ''sample'' Hamiltonian or wave function using two-point functions that form triangles. Feeding the TQL topography to a fully-connected neural network with a single hidden layer, we demonstrate that the architecture can be effectively trained to distinguish Chern insulator and fractional Chern insulator from trivial insulators with high fidelity. Given the versatility of the TQL topography procedure that can handle different lattice geometries, disorder, interaction and even degeneracy our work paves the route towards powerful applications of machine learning in the study of topological quantum matters.

Two-dimensional ferroelectric topological insulators in functionalized atomically thin bismuth layers

NASA Astrophysics Data System (ADS)

Kou, Liangzhi; Fu, Huixia; Ma, Yandong; Yan, Binghai; Liao, Ting; Du, Aijun; Chen, Changfeng

2018-02-01

We introduce a class of two-dimensional (2D) materials that possess coexisting ferroelectric and topologically insulating orders. Such ferroelectric topological insulators (FETIs) occur in noncentrosymmetric atomic layer structures with strong spin-orbit coupling (SOC). We showcase a prototype 2D FETI in an atomically thin bismuth layer functionalized by C H2OH , which exhibits a large ferroelectric polarization that is switchable by a ligand molecule rotation mechanism and a strong SOC that drives a band inversion leading to the topologically insulating state. An external electric field that switches the ferroelectric polarization also tunes the spin texture in the underlying atomic lattice. Moreover, the functionalized bismuth layer exhibits an additional quantum order driven by the valley splitting at the K and K' points in the Brillouin zone stemming from the symmetry breaking and strong SOC in the system, resulting in a remarkable state of matter with the simultaneous presence of the quantum spin Hall and quantum valley Hall effect. These phenomena are predicted to exist in other similarly constructed 2D FETIs, thereby offering a unique quantum material platform for discovering novel physics and exploring innovative applications.

Topological phase diagram and saddle point singularity in a tunable topological crystalline insulator

DOE PAGES

Neupane, Madhab; Xu, Su-Yang; Sankar, R.; ...

2015-08-20

Here we report the evolution of the surface electronic structure and surface material properties of a topological crystalline insulator (TCI), Pb 1more » $${-}$$xSnxSe, as a function of various material parameters including composition x, temperature T , and crystal structure. Our spectroscopic data demonstrate the electronic ground-state condition for the saddle point singularity, the tunability of surface chemical potential, and the surface states’ response to circularly polarized light. Our results show that each material parameter can tune the system between the trivial and topological phase in a distinct way, unlike that seen in Bi 2Se 3 and related compounds, leading to a rich topological phase diagram. Our systematic studies of the TCI Pb 1$${-}$$xSnxSe are a valuable materials guide to realize new topological phenomena.« less

Network topology and resilience analysis of South Korean power grid

NASA Astrophysics Data System (ADS)

Kim, Dong Hwan; Eisenberg, Daniel A.; Chun, Yeong Han; Park, Jeryang

2017-01-01

In this work, we present topological and resilience analyses of the South Korean power grid (KPG) with a broad voltage level. While topological analysis of KPG only with high-voltage infrastructure shows an exponential degree distribution, providing another empirical evidence of power grid topology, the inclusion of low voltage components generates a distribution with a larger variance and a smaller average degree. This result suggests that the topology of a power grid may converge to a highly skewed degree distribution if more low-voltage data is considered. Moreover, when compared to ER random and BA scale-free networks, the KPG has a lower efficiency and a higher clustering coefficient, implying that highly clustered structure does not necessarily guarantee a functional efficiency of a network. Error and attack tolerance analysis, evaluated with efficiency, indicate that the KPG is more vulnerable to random or degree-based attacks than betweenness-based intentional attack. Cascading failure analysis with recovery mechanism demonstrates that resilience of the network depends on both tolerance capacity and recovery initiation time. Also, when the two factors are fixed, the KPG is most vulnerable among the three networks. Based on our analysis, we propose that the topology of power grids should be designed so the loads are homogeneously distributed, or functional hubs and their neighbors have high tolerance capacity to enhance resilience.

Phylogeny, paleontology, and primates: do incomplete fossils bias the tree of life?

PubMed

Pattinson, David J; Thompson, Richard S; Piotrowski, Aleks K; Asher, Robert J

2015-03-01

Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here, we apply a heuristic means to assess how a fossil's incompleteness detracts from inferring its phylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon's molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was defined by those present in a given fossil (the template). By measuring congruence between a well-corroborated phylogeny to those incorporating artificial fossils, and by comparing real vs. random character distributions and states, we tested the information content of paleontological datasets and determined if extinction of a living species leads to bias in phylogeny reconstruction. We found a positive correlation between fossil completeness and topological congruence. Real fossil templates sampled for 36 or more of the 360 available morphological characters (including dental) performed significantly better than similarly complete templates with random states. Templates dominated by only one partition performed worse than templates with randomly sampled characters across partitions. The template based on the Eocene primate Darwinius masillae performs better than most other templates with a similar number of sampled characters, likely due to preservation of data across multiple partitions. Our results support the interpretation that Darwinius is strepsirhine, not haplorhine, and suggest that paleontological datasets are reliable in primate phylogeny reconstruction. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Topology of molecular interaction networks.

PubMed

Winterbach, Wynand; Van Mieghem, Piet; Reinders, Marcel; Wang, Huijuan; de Ridder, Dick

2013-09-16

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks.Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs.Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes.Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further.

Topology of molecular interaction networks

PubMed Central

2013-01-01

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks. Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs. Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes. Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further. PMID:24041013

Many-body formalism for fermions: The partition function

NASA Astrophysics Data System (ADS)

Watson, D. K.

2017-09-01

The partition function, a fundamental tenet in statistical thermodynamics, contains in principle all thermodynamic information about a system. It encapsulates both microscopic information through the quantum energy levels and statistical information from the partitioning of the particles among the available energy levels. For identical particles, this statistical accounting is complicated by the symmetry requirements of the allowed quantum states. In particular, for Fermi systems, the enforcement of the Pauli principle is typically a numerically demanding task, responsible for much of the cost of the calculations. The interplay of these three elements—the structure of the many-body spectrum, the statistical partitioning of the N particles among the available levels, and the enforcement of the Pauli principle—drives the behavior of mesoscopic and macroscopic Fermi systems. In this paper, we develop an approach for the determination of the partition function, a numerically difficult task, for systems of strongly interacting identical fermions and apply it to a model system of harmonically confined, harmonically interacting fermions. This approach uses a recently introduced many-body method that is an extension of the symmetry-invariant perturbation method (SPT) originally developed for bosons. It uses group theory and graphical techniques to avoid the heavy computational demands of conventional many-body methods which typically scale exponentially with the number of particles. The SPT application of the Pauli principle is trivial to implement since it is done "on paper" by imposing restrictions on the normal-mode quantum numbers at first order in the perturbation. The method is applied through first order and represents an extension of the SPT method to excited states. Our method of determining the partition function and various thermodynamic quantities is accurate and efficient and has the potential to yield interesting insight into the role played by the Pauli principle and the influence of large degeneracies on the emergence of the thermodynamic behavior of large-N systems.

Functional integrative levels in the human interactome recapitulate organ organization.

PubMed

Souiai, Ouissem; Becker, Emmanuelle; Prieto, Carlos; Benkahla, Alia; De las Rivas, Javier; Brun, Christine

2011-01-01

Interactome networks represent sets of possible physical interactions between proteins. They lack spatio-temporal information by construction. However, the specialized functions of the differentiated cell types which are assembled into tissues or organs depend on the combinatorial arrangements of proteins and their physical interactions. Is tissue-specificity, therefore, encoded within the interactome? In order to address this question, we combined protein-protein interactions, expression data, functional annotations and interactome topology. We first identified a subnetwork formed exclusively of proteins whose interactions were observed in all tested tissues. These are mainly involved in housekeeping functions and are located at the topological center of the interactome. This 'Largest Common Interactome Network' represents a 'functional interactome core'. Interestingly, two types of tissue-specific interactions are distinguished when considering function and network topology: tissue-specific interactions involved in regulatory and developmental functions are central whereas tissue-specific interactions involved in organ physiological functions are peripheral. Overall, the functional organization of the human interactome reflects several integrative levels of functions with housekeeping and regulatory tissue-specific functions at the center and physiological tissue-specific functions at the periphery. This gradient of functions recapitulates the organization of organs, from cells to organs. Given that several gradients have already been identified across interactomes, we propose that gradients may represent a general principle of protein-protein interaction network organization.

Critic: a new program for the topological analysis of solid-state electron densities

NASA Astrophysics Data System (ADS)

Otero-de-la-Roza, A.; Blanco, M. A.; Pendás, A. Martín; Luaña, Víctor

2009-01-01

In this paper we introduce CRITIC, a new program for the topological analysis of the electron densities of crystalline solids. Two different versions of the code are provided, one adapted to the LAPW (Linear Augmented Plane Wave) density calculated by the WIEN2K package and the other to the ab initio Perturbed Ion ( aiPI) density calculated with the PI7 code. Using the converged ground state densities, CRITIC can locate their critical points, determine atomic basins and integrate properties within them, and generate several graphical representations which include topological atomic basins and primary bundles, contour maps of ρ and ∇ρ, vector maps of ∇ρ, chemical graphs, etc. Program summaryProgram title: CRITIC Catalogue identifier: AECB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL, version 3 No. of lines in distributed program, including test data, etc.: 1 206 843 No. of bytes in distributed program, including test data, etc.: 12 648 065 Distribution format: tar.gz Programming language: FORTRAN 77 and 90 Computer: Any computer capable of compiling Fortran Operating system: Unix, GNU/Linux Classification: 7.3 Nature of problem: Topological analysis of the electron density in periodic solids. Solution method: The automatic localization of the electron density critical points is based on a recursive partitioning of the Wigner-Seitz cell into tetrahedra followed by a Newton search from significant points on each tetrahedra. Plotting of and integration on the atomic basins is currently based on a new implementation of Keith's promega algorithm. Running time: Variable, depending on the task. From seconds to a few minutes for the localization of critical points. Hours to days for the determination of the atomic basins shape and properties. Times correspond to a typical 2007 PC.

Network analysis of functional brain connectivity in borderline personality disorder using resting-state fMRI

PubMed Central

Xu, Tingting; Cullen, Kathryn R.; Mueller, Bryon; Schreiner, Mindy W.; Lim, Kelvin O.; Schulz, S. Charles; Parhi, Keshab K.

2016-01-01

Borderline personality disorder (BPD) is associated with symptoms such as affect dysregulation, impaired sense of self, and self-harm behaviors. Neuroimaging research on BPD has revealed structural and functional abnormalities in specific brain regions and connections. However, little is known about the topological organizations of brain networks in BPD. We collected resting-state functional magnetic resonance imaging (fMRI) data from 20 patients with BPD and 10 healthy controls, and constructed frequency-specific functional brain networks by correlating wavelet-filtered fMRI signals from 82 cortical and subcortical regions. We employed graph-theory based complex network analysis to investigate the topological properties of the brain networks, and employed network-based statistic to identify functional dysconnections in patients. In the 0.03–0.06 Hz frequency band, compared to controls, patients with BPD showed significantly larger measures of global network topology, including the size of largest connected graph component, clustering coefficient, small-worldness, and local efficiency, indicating increased local cliquishness of the functional brain network. Compared to controls, patients showed lower nodal centrality at several hub nodes but greater centrality at several non-hub nodes in the network. Furthermore, an interconnected subnetwork in 0.03–0.06 Hz frequency band was identified that showed significantly lower connectivity in patients. The links in the subnetwork were mainly long-distance connections between regions located at different lobes; and the mean connectivity of this subnetwork was negatively correlated with the increased global topology measures. Lastly, the key network measures showed high correlations with several clinical symptom scores, and classified BPD patients against healthy controls with high accuracy based on linear discriminant analysis. The abnormal topological properties and connectivity found in this study may add new knowledge to the current understanding of functional brain networks in BPD. However, due to limitation of small sample sizes, the results of the current study should be viewed as exploratory and need to be validated on large samples in future works. PMID:26977400

Network analysis of functional brain connectivity in borderline personality disorder using resting-state fMRI.

PubMed

Xu, Tingting; Cullen, Kathryn R; Mueller, Bryon; Schreiner, Mindy W; Lim, Kelvin O; Schulz, S Charles; Parhi, Keshab K

2016-01-01

Borderline personality disorder (BPD) is associated with symptoms such as affect dysregulation, impaired sense of self, and self-harm behaviors. Neuroimaging research on BPD has revealed structural and functional abnormalities in specific brain regions and connections. However, little is known about the topological organizations of brain networks in BPD. We collected resting-state functional magnetic resonance imaging (fMRI) data from 20 patients with BPD and 10 healthy controls, and constructed frequency-specific functional brain networks by correlating wavelet-filtered fMRI signals from 82 cortical and subcortical regions. We employed graph-theory based complex network analysis to investigate the topological properties of the brain networks, and employed network-based statistic to identify functional dysconnections in patients. In the 0.03-0.06 Hz frequency band, compared to controls, patients with BPD showed significantly larger measures of global network topology, including the size of largest connected graph component, clustering coefficient, small-worldness, and local efficiency, indicating increased local cliquishness of the functional brain network. Compared to controls, patients showed lower nodal centrality at several hub nodes but greater centrality at several non-hub nodes in the network. Furthermore, an interconnected subnetwork in 0.03-0.06 Hz frequency band was identified that showed significantly lower connectivity in patients. The links in the subnetwork were mainly long-distance connections between regions located at different lobes; and the mean connectivity of this subnetwork was negatively correlated with the increased global topology measures. Lastly, the key network measures showed high correlations with several clinical symptom scores, and classified BPD patients against healthy controls with high accuracy based on linear discriminant analysis. The abnormal topological properties and connectivity found in this study may add new knowledge to the current understanding of functional brain networks in BPD. However, due to limitation of small sample sizes, the results of the current study should be viewed as exploratory and need to be validated on large samples in future works.

Graph Theory Approach for Studying Food Webs

NASA Astrophysics Data System (ADS)

Longjas, A.; Tejedor, A.; Foufoula-Georgiou, E.

2017-12-01

Food webs are complex networks of feeding interactions among species in ecological communities. Metrics describing food web structure have been proposed to compare and classify food webs ranging from food chain length, connectance, degree distribution, centrality measures, to the presence of motifs (distinct compartments), among others. However, formal methodologies for studying both food web topology and the dynamic processes operating on them are still lacking. Here, we utilize a quantitative framework using graph theory within which a food web is represented by a directed graph, i.e., a collection of vertices (species or trophic species defined as sets of species sharing the same predators and prey) and directed edges (predation links). This framework allows us to identify apex (environmental "source" node) to outlet (top predators) subnetworks and compute the steady-state flux (e.g., carbon, nutrients, energy etc.) in the food web. We use this framework to (1) construct vulnerability maps that quantify the relative change of flux delivery to the top predators in response to perturbations in prey species (2) identify keystone species, whose loss would precipitate further species extinction, and (3) introduce a suite of graph-theoretic metrics to quantify the topologic (imposed by food web connectivity) and dynamic (dictated by the flux partitioning and distribution) components of a food web's complexity. By projecting food webs into a 2D Topodynamic Complexity Space whose coordinates are given by Number of alternative paths (topologic) and Leakage Index (dynamic), we show that this space provides a basis for food web comparison and provide physical insights into their dynamic behavior.

Reconstruction of a piecewise constant conductivity on a polygonal partition via shape optimization in EIT

NASA Astrophysics Data System (ADS)

Beretta, Elena; Micheletti, Stefano; Perotto, Simona; Santacesaria, Matteo

2018-01-01

In this paper, we develop a shape optimization-based algorithm for the electrical impedance tomography (EIT) problem of determining a piecewise constant conductivity on a polygonal partition from boundary measurements. The key tool is to use a distributed shape derivative of a suitable cost functional with respect to movements of the partition. Numerical simulations showing the robustness and accuracy of the method are presented for simulated test cases in two dimensions.

Partition of some key regulating services in terrestrial ecosystems: Meta-analysis and review.

PubMed

Viglizzo, E F; Jobbágy, E G; Ricard, M F; Paruelo, J M

2016-08-15

Our knowledge about the functional foundations of ecosystem service (ES) provision is still limited and more research is needed to elucidate key functional mechanisms. Using a simplified eco-hydrological scheme, in this work we analyzed how land-use decisions modify the partition of some essential regulatory ES by altering basic relationships between biomass stocks and water flows. A comprehensive meta-analysis and review was conducted based on global, regional and local data from peer-reviewed publications. We analyzed five datasets comprising 1348 studies and 3948 records on precipitation (PPT), aboveground biomass (AGB), AGB change, evapotranspiration (ET), water yield (WY), WY change, runoff (R) and infiltration (I). The conceptual framework was focused on ES that are associated with the ecological functions (e.g., intermediate ES) of ET, WY, R and I. ES included soil protection, carbon sequestration, local climate regulation, water-flow regulation and water recharge. To address the problem of data normality, the analysis included both parametric and non-parametric regression analysis. Results demonstrate that PPT is a first-order biophysical factor that controls ES release at the broader scales. At decreasing scales, ES are partitioned as result of PPT interactions with other biophysical and anthropogenic factors. At intermediate scales, land-use change interacts with PPT modifying ES partition as it the case of afforestation in dry regions, where ET and climate regulation may be enhanced at the expense of R and water-flow regulation. At smaller scales, site-specific conditions such as topography interact with PPT and AGB displaying different ES partition formats. The probable implications of future land-use and climate change on some key ES production and partition are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

A Locally Optimal Algorithm for Estimating a Generating Partition from an Observed Time Series and Its Application to Anomaly Detection.

PubMed

Ghalyan, Najah F; Miller, David J; Ray, Asok

2018-06-12

Estimation of a generating partition is critical for symbolization of measurements from discrete-time dynamical systems, where a sequence of symbols from a (finite-cardinality) alphabet may uniquely specify the underlying time series. Such symbolization is useful for computing measures (e.g., Kolmogorov-Sinai entropy) to identify or characterize the (possibly unknown) dynamical system. It is also useful for time series classification and anomaly detection. The seminal work of Hirata, Judd, and Kilminster (2004) derives a novel objective function, akin to a clustering objective, that measures the discrepancy between a set of reconstruction values and the points from the time series. They cast estimation of a generating partition via the minimization of their objective function. Unfortunately, their proposed algorithm is nonconvergent, with no guarantee of finding even locally optimal solutions with respect to their objective. The difficulty is a heuristic-nearest neighbor symbol assignment step. Alternatively, we develop a novel, locally optimal algorithm for their objective. We apply iterative nearest-neighbor symbol assignments with guaranteed discrepancy descent, by which joint, locally optimal symbolization of the entire time series is achieved. While most previous approaches frame generating partition estimation as a state-space partitioning problem, we recognize that minimizing the Hirata et al. (2004) objective function does not induce an explicit partitioning of the state space, but rather the space consisting of the entire time series (effectively, clustering in a (countably) infinite-dimensional space). Our approach also amounts to a novel type of sliding block lossy source coding. Improvement, with respect to several measures, is demonstrated over popular methods for symbolizing chaotic maps. We also apply our approach to time-series anomaly detection, considering both chaotic maps and failure application in a polycrystalline alloy material.

Surface alloy engineering in 2D trigonal lattice: giant Rashba spin splitting and two large topological gaps

NASA Astrophysics Data System (ADS)

Liu, Zhao; Jin, Yingdi; Yang, Yuchen; Wang, Z. F.; Yang, Jinlong

2018-02-01

We demonstrate that sp 2 based trigonal lattice can exhibit giant Rashba splitting and two large topological gaps simultaneously. First, an effective tight binding model is developed to describe the Rashba spin-orbit coupling (SOC) on a real surface and give a topological phase diagram based on two independent SOC parameters. Second, based on density functional theory calculations, it is proposed that Au/Si(111)-\\sqrt{3}× \\sqrt{3} surface with 1/3 monolayer Bi coverage is a good material candidate to realize both giant Rashba splitting and two large topological gaps. These results would inspire great research interests for searching two-dimensional topological insulator and manipulating Rashba spin splitting through surface alloy engineering.

Entanglement entropy and entanglement spectrum of triplet topological superconductors.

PubMed

Oliveira, T P; Ribeiro, P; Sacramento, P D

2014-10-22

We analyze the entanglement entropy properties of a 2D p-wave superconductor with Rashba spin-orbit coupling, which displays a rich phase-space that supports non-trivial topological phases, as the chemical potential and the Zeeman term are varied. We show that the entanglement entropy and its derivatives clearly signal the topological transitions and we find numerical evidence that for this model the derivative with respect to the magnetization provides a sensible signature of each topological phase. Following the area law for the entanglement entropy, we systematically analyze the contributions that are proportional to or independent of the perimeter of the system, as a function of the Hamiltonian coupling constants and the geometry of the finite subsystem. For this model, we show that even though the topological entanglement entropy vanishes, it signals the topological phase transitions in a finite system. We also observe a relationship between a topological contribution to the entanglement entropy in a half-cylinder geometry and the number of edge states, and that the entanglement spectrum has robust modes associated with each edge state, as in other topological systems.

Algorithms for the automatic generation of 2-D structured multi-block grids

NASA Technical Reports Server (NTRS)

Schoenfeld, Thilo; Weinerfelt, Per; Jenssen, Carl B.

1995-01-01

Two different approaches to the fully automatic generation of structured multi-block grids in two dimensions are presented. The work aims to simplify the user interactivity necessary for the definition of a multiple block grid topology. The first approach is based on an advancing front method commonly used for the generation of unstructured grids. The original algorithm has been modified toward the generation of large quadrilateral elements. The second method is based on the divide-and-conquer paradigm with the global domain recursively partitioned into sub-domains. For either method each of the resulting blocks is then meshed using transfinite interpolation and elliptic smoothing. The applicability of these methods to practical problems is demonstrated for typical geometries of fluid dynamics.

The Impact of the Network Topology on the Viral Prevalence: A Node-Based Approach

PubMed Central

Yang, Lu-Xing; Draief, Moez; Yang, Xiaofan

2015-01-01

This paper addresses the impact of the structure of the viral propagation network on the viral prevalence. For that purpose, a new epidemic model of computer virus, known as the node-based SLBS model, is proposed. Our analysis shows that the maximum eigenvalue of the underlying network is a key factor determining the viral prevalence. Specifically, the value range of the maximum eigenvalue is partitioned into three subintervals: viruses tend to extinction very quickly or approach extinction or persist depending on into which subinterval the maximum eigenvalue of the propagation network falls. Consequently, computer virus can be contained by adjusting the propagation network so that its maximum eigenvalue falls into the desired subinterval. PMID:26222539

Performance Comparison of a Set of Periodic and Non-Periodic Tridiagonal Solvers on SP2 and Paragon Parallel Computers

NASA Technical Reports Server (NTRS)

Sun, Xian-He; Moitra, Stuti

1996-01-01

Various tridiagonal solvers have been proposed in recent years for different parallel platforms. In this paper, the performance of three tridiagonal solvers, namely, the parallel partition LU algorithm, the parallel diagonal dominant algorithm, and the reduced diagonal dominant algorithm, is studied. These algorithms are designed for distributed-memory machines and are tested on an Intel Paragon and an IBM SP2 machines. Measured results are reported in terms of execution time and speedup. Analytical study are conducted for different communication topologies and for different tridiagonal systems. The measured results match the analytical results closely. In addition to address implementation issues, performance considerations such as problem sizes and models of speedup are also discussed.

Confinement and Mayer cluster expansions

NASA Astrophysics Data System (ADS)

Bourgine, Jean-Emile

2014-05-01

In this paper, we study a class of grand-canonical partition functions with a kernel depending on a small parameter ɛ. This class is directly relevant to Nekrasov partition functions of 𝒩 = 2 SUSY gauge theories on the 4d Ω-background, for which ɛ is identified with one of the equivariant deformation parameter. In the Nekrasov-Shatashvili limit ɛ→0, we show that the free energy is given by an on-shell effective action. The equations of motion take the form of a TBA equation. The free energy is identified with the Yang-Yang functional of the corresponding system of Bethe roots. We further study the associated canonical model that takes the form of a generalized matrix model. Confinement of the eigenvalues by the short-range potential is observed. In the limit where this confining potential becomes weak, the collective field theory formulation is recovered. Finally, we discuss the connection with the alternative expression of instanton partition functions as sums over Young tableaux.

BPS/CFT Correspondence III: Gauge Origami Partition Function and qq-Characters

NASA Astrophysics Data System (ADS)

Nekrasov, Nikita

2018-03-01

We study generalized gauge theories engineered by taking the low energy limit of the Dp branes wrapping {X × {T}^{p-3}}, with X a possibly singular surface in a Calabi-Yau fourfold Z. For toric Z and X the partition function can be computed by localization, making it a statistical mechanical model, called the gauge origami. The random variables are the ensembles of Young diagrams. The building block of the gauge origami is associated with a tetrahedron, whose edges are colored by vector spaces. We show the properly normalized partition function is an entire function of the Coulomb moduli, for generic values of the {Ω} -background parameters. The orbifold version of the theory defines the qq-character operators, with and without the surface defects. The analytic properties are the consequence of a relative compactness of the moduli spaces M({ěc n}, k) of crossed and spiked instantons, demonstrated in "BPS/CFT correspondence II: instantons at crossroads, moduli and compactness theorem".

Matrix quantum mechanics on S1 /Z2

NASA Astrophysics Data System (ADS)

Betzios, P.; Gürsoy, U.; Papadoulaki, O.

2018-03-01

We study Matrix Quantum Mechanics on the Euclidean time orbifold S1 /Z2. Upon Wick rotation to Lorentzian time and taking the double-scaling limit this theory provides a toy model for a big-bang/big crunch universe in two dimensional non-critical string theory where the orbifold fixed points become cosmological singularities. We derive the MQM partition function both in the canonical and grand canonical ensemble in two different formulations and demonstrate agreement between them. We pinpoint the contribution of twisted states in both of these formulations either in terms of bi-local operators acting at the end-points of time or branch-cuts on the complex plane. We calculate, in the matrix model, the contribution of the twisted states to the torus level partition function explicitly and show that it precisely matches the world-sheet result, providing a non-trivial test of the proposed duality. Finally we discuss some interesting features of the partition function and the possibility of realising it as a τ-function of an integrable hierarchy.

PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape

PubMed Central

Wang, Yong; Tang, Chun; Wang, Erkang; Wang, Jin

2014-01-01

Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages. PMID:24992446

PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape.

PubMed

Wang, Yong; Tang, Chun; Wang, Erkang; Wang, Jin

2014-07-01

Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.

Topologically massive gravity and galilean conformal algebra: a study of correlation functions

NASA Astrophysics Data System (ADS)

Bagchi, Arjun

2011-02-01

The Galilean Conformal Algebra (GCA) arises from the conformal algebra in the non-relativistic limit. In two dimensions, one can view it as a limit of linear combinations of the two copies Virasoro algebra. Recently, it has been argued that Topologically Massive Gravity (TMG) realizes the quantum 2d GCA in a particular scaling limit of the gravitational Chern-Simons term. To add strength to this claim, we demonstrate a matching of correlation functions on both sides of this correspondence. A priori looking for spatially dependent correlators seems to force us to deal with high spin operators in the bulk. We get around this difficulty by constructing the non-relativistic Energy-Momentum tensor and considering its correlation functions. On the gravity side, our analysis makes heavy use of recent results of Holographic Renormalization in Topologically Massive Gravity.

Z/sub n/ Baxter model: symmetries and the Belavin parametrization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richey, M.P.; Tracy, C.A.

1986-02-01

The Z/sub n/ Baxter model is an exactly solvable lattice model in the special case of the Belavin parametrization. For this parametrization the authors calculate the partition function in an antiferromagnetic region and the order parameter in a ferromagnetic region. They find that the order parameter is expressible in terms of a modular function of level n which for n=2 is the Onsager-Yang-Baxter result. In addition they determine the symmetry group of the finite lattice partition function for the general Z/sub n/ Baxter model.

Using maximum topology matching to explore differences in species distribution models

USGS Publications Warehouse

Poco, Jorge; Doraiswamy, Harish; Talbert, Marian; Morisette, Jeffrey; Silva, Claudio

2015-01-01

Species distribution models (SDM) are used to help understand what drives the distribution of various plant and animal species. These models are typically high dimensional scalar functions, where the dimensions of the domain correspond to predictor variables of the model algorithm. Understanding and exploring the differences between models help ecologists understand areas where their data or understanding of the system is incomplete and will help guide further investigation in these regions. These differences can also indicate an important source of model to model uncertainty. However, it is cumbersome and often impractical to perform this analysis using existing tools, which allows for manual exploration of the models usually as 1-dimensional curves. In this paper, we propose a topology-based framework to help ecologists explore the differences in various SDMs directly in the high dimensional domain. In order to accomplish this, we introduce the concept of maximum topology matching that computes a locality-aware correspondence between similar extrema of two scalar functions. The matching is then used to compute the similarity between two functions. We also design a visualization interface that allows ecologists to explore SDMs using their topological features and to study the differences between pairs of models found using maximum topological matching. We demonstrate the utility of the proposed framework through several use cases using different data sets and report the feedback obtained from ecologists.

Handedness- and brain size-related efficiency differences in small-world brain networks: a resting-state functional magnetic resonance imaging study.

PubMed

Li, Meiling; Wang, Junping; Liu, Feng; Chen, Heng; Lu, Fengmei; Wu, Guorong; Yu, Chunshui; Chen, Huafu

2015-05-01

The human brain has been described as a complex network, which integrates information with high efficiency. However, the relationships between the efficiency of human brain functional networks and handedness and brain size remain unclear. Twenty-one left-handed and 32 right-handed healthy subjects underwent a resting-state functional magnetic resonance imaging scan. The whole brain functional networks were constructed by thresholding Pearson correlation matrices of 90 cortical and subcortical regions. Graph theory-based methods were employed to further analyze their topological properties. As expected, all participants demonstrated small-world topology, suggesting a highly efficient topological structure. Furthermore, we found that smaller brains showed higher local efficiency, whereas larger brains showed higher global efficiency, reflecting a suitable efficiency balance between local specialization and global integration of brain functional activity. Compared with right-handers, significant alterations in nodal efficiency were revealed in left-handers, involving the anterior and median cingulate gyrus, middle temporal gyrus, angular gyrus, and amygdala. Our findings indicated that the functional network organization in the human brain was associated with handedness and brain size.

A 3d-3d appetizer

DOE PAGES

Pei, Du; Ye, Ke

2016-11-02

Here, we test the 3d-3d correspondence for theories that are labeled by Lens spaces. We find a full agreement between the index of the 3d N=2 “Lens space theory” T [L(p, 1)] and the partition function of complex Chern-Simons theory on L(p, 1). In particular, for p = 1, we show how the familiar S 3 partition function of Chern-Simons theory arises from the index of a free theory. For large p, we find that the index of T[L(p, 1)] becomes a constant independent of p. In addition, we study T[L(p, 1)] on the squashed three-sphere S b 3. Thismore » enables us to see clearly, at the level of partition function, to what extent G C complex Chern-Simons theory can be thought of as two copies of Chern-Simons theory with compact gauge group G.« less

Differences in graph theory functional connectivity in left and right temporal lobe epilepsy.

PubMed

Chiang, Sharon; Stern, John M; Engel, Jerome; Levin, Harvey S; Haneef, Zulfi

2014-12-01

To investigate lateralized differences in limbic system functional connectivity between left and right temporal lobe epilepsy (TLE) using graph theory. Interictal resting state fMRI was performed in 14 left TLE patients, 11 right TLE patients, and 12 controls. Graph theory analysis of 10 bilateral limbic regions of interest was conducted. Changes in edgewise functional connectivity, network topology, and regional topology were quantified, and then left and right TLE were compared. Limbic edgewise functional connectivity was predominantly reduced in both left and right TLE. More regional connections were reduced in right TLE, most prominently involving reduced interhemispheric connectivity between the bilateral insula and bilateral hippocampi. A smaller number of limbic connections were increased in TLE, more so in left than in right TLE. Topologically, the most pronounced change was a reduction in average network betweenness centrality and concurrent increase in left hippocampal betweenness centrality in right TLE. In contrast, left TLE exhibited a weak trend toward increased right hippocampal betweenness centrality, with no change in average network betweenness centrality. Limbic functional connectivity is predominantly reduced in both left and right TLE, with more pronounced reductions in right TLE. In contrast, left TLE exhibits both edgewise and topological changes that suggest a tendency toward reorganization. Network changes in TLE and lateralized differences thereof may have important diagnostic and prognostic implications. Published by Elsevier B.V.

Relevance of the DFT method to study expanded porphyrins with different topologies.

PubMed

Torrent-Sucarrat, Miquel; Navarro, Sara; Cossío, Fernando P; Anglada, Josep M; Luis, Josep M

2017-12-15

Meso-aryl expanded porphyrins present a structural versatility that allows them to achieve different topologies with distinct aromaticities. Several studies appeared in the literature studying these topological switches from an experimental and theoretical point of view. Most of these publications include density functional theory calculations, being the B3LYP the most used methodology. In this work, we show that the selection of the functional has a critical role on the geometric, energetic, and magnetic results of these expanded porphyrins, and that the use of an inadequate methodology can even generate spurious stationary points on the potential energy surface. To illustrate these aspects, in this article we have studied different molecular distortions of two expanded porphyrins, [32]-heptaphyrin and [26]-hexaphyrin using 11 DFT functionals and performing single point energy calculations at the local pair natural orbital coupled cluster DLPNO-CCSD(T) method, which have been carried out for benchmarking purposes. For some selected functionals, the dispersion effects have also been evaluated using the D3-Grimme's dispersion correction with Becke-Johnson damping. Our results let us to conclude that the CAM-B3LYP, M05-2X, and M06-2X functionals are the methodologies that provide a more consistent description of these topological switches, while other methods, such as B3LYP, BPE, and BP86, show a biased description. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The Reorganization of Human Brain Networks Modulated by Driving Mental Fatigue.

PubMed

Chunlin Zhao; Min Zhao; Yong Yang; Junfeng Gao; Nini Rao; Pan Lin

2017-05-01

The organization of the brain functional network is associated with mental fatigue, but little is known about the brain network topology that is modulated by the mental fatigue. In this study, we used the graph theory approach to investigate reconfiguration changes in functional networks of different electroen-cephalography (EEG) bands from 16 subjects performing a simulated driving task. Behavior and brain functional networks were compared between the normal and driving mental fatigue states. The scores of subjective self-reports indicated that 90 min of simulated driving-induced mental fatigue. We observed that coherence was significantly increased in the frontal, central, and temporal brain regions. Furthermore, in the brain network topology metric, significant increases were observed in the clustering coefficient (Cp) for beta, alpha, and delta bands and the character path length (Lp) for all EEG bands. The normalized measures γ showed significant increases in beta, alpha, and delta bands, and λ showed similar patterns in beta and theta bands. These results indicate that functional network topology can shift the network topology structure toward a more economic but less efficient configuration, which suggests low wiring costs in functional networks and disruption of the effective interactions between and across cortical regions during mental fatigue states. Graph theory analysis might be a useful tool for further understanding the neural mechanisms of driving mental fatigue.

Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers.

PubMed

Da, Yang

2015-12-18

The amount of functional genomic information has been growing rapidly but remains largely unused in genomic selection. Genomic prediction and estimation using haplotypes in genome regions with functional elements such as all genes of the genome can be an approach to integrate functional and structural genomic information for genomic selection. Towards this goal, this article develops a new haplotype approach for genomic prediction and estimation. A multi-allelic haplotype model treating each haplotype as an 'allele' was developed for genomic prediction and estimation based on the partition of a multi-allelic genotypic value into additive and dominance values. Each additive value is expressed as a function of h - 1 additive effects, where h = number of alleles or haplotypes, and each dominance value is expressed as a function of h(h - 1)/2 dominance effects. For a sample of q individuals, the limit number of effects is 2q - 1 for additive effects and is the number of heterozygous genotypes for dominance effects. Additive values are factorized as a product between the additive model matrix and the h - 1 additive effects, and dominance values are factorized as a product between the dominance model matrix and the h(h - 1)/2 dominance effects. Genomic additive relationship matrix is defined as a function of the haplotype model matrix for additive effects, and genomic dominance relationship matrix is defined as a function of the haplotype model matrix for dominance effects. Based on these results, a mixed model implementation for genomic prediction and variance component estimation that jointly use haplotypes and single markers is established, including two computing strategies for genomic prediction and variance component estimation with identical results. The multi-allelic genetic partition fills a theoretical gap in genetic partition by providing general formulations for partitioning multi-allelic genotypic values and provides a haplotype method based on the quantitative genetics model towards the utilization of functional and structural genomic information for genomic prediction and estimation.

Introduction of functionality, selection of topology, and enhancement of gas adsorption in multivariate metal-organic framework-177.

PubMed

Zhang, Yue-Biao; Furukawa, Hiroyasu; Ko, Nakeun; Nie, Weixuan; Park, Hye Jeong; Okajima, Satoshi; Cordova, Kyle E; Deng, Hexiang; Kim, Jaheon; Yaghi, Omar M

2015-02-25

Metal-organic framework-177 (MOF-177) is one of the most porous materials whose structure is composed of octahedral Zn4O(-COO)6 and triangular 1,3,5-benzenetribenzoate (BTB) units to make a three-dimensional extended network based on the qom topology. This topology violates a long-standing thesis where highly symmetric building units are expected to yield highly symmetric networks. In the case of octahedron and triangle combinations, MOFs based on pyrite (pyr) and rutile (rtl) nets were expected instead of qom. In this study, we have made 24 MOF-177 structures with different functional groups on the triangular BTB linker, having one or more functionalities. We find that the position of the functional groups on the BTB unit allows the selection for a specific net (qom, pyr, and rtl), and that mixing of functionalities (-H, -NH2, and -C4H4) is an important strategy for the incorporation of a specific functionality (-NO2) into MOF-177 where otherwise incorporation of such functionality would be difficult. Such mixing of functionalities to make multivariate MOF-177 structures leads to enhancement of hydrogen uptake by 25%.

Introduction of Functionality, Selection of Topology, and Enhancement of Gas Adsorption in Multivariate Metal–Organic Framework-177

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yue-Biao; Furukawa, Hiroyasu; Ko, Nakeun

2015-02-25

Metal–organic framework-177 (MOF-177) is one of the most porous materials whose structure is composed of octahedral Zn 4O(-COO) 6 and triangular 1,3,5-benzenetribenzoate (BTB) units to make a three-dimensional extended network based on the qom topology. This topology violates a long-standing thesis where highly symmetric building units are expected to yield highly symmetric networks. In the case of octahedron and triangle combinations, MOFs based on pyrite (pyr) and rutile (rtl) nets were expected instead of qom. In this study, we have made 24 MOF-177 structures with different functional groups on the triangular BTB linker, having one or more functionalities. We findmore » that the position of the functional groups on the BTB unit allows the selection for a specific net (qom, pyr, and rtl), and that mixing of functionalities (-H, -NH 2, and -C 4H 4) is an important strategy for the incorporation of a specific functionality (-NO 2) into MOF-177 where otherwise incorporation of such functionality would be difficult. Such mixing of functionalities to make multivariate MOF-177 structures leads to enhancement of hydrogen uptake by 25%.« less

Efficient O(N) integration for all-electron electronic structure calculation using numeric basis functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Havu, V.; Fritz Haber Institute of the Max Planck Society, Berlin; Blum, V.

2009-12-01

We consider the problem of developing O(N) scaling grid-based operations needed in many central operations when performing electronic structure calculations with numeric atom-centered orbitals as basis functions. We outline the overall formulation of localized algorithms, and specifically the creation of localized grid batches. The choice of the grid partitioning scheme plays an important role in the performance and memory consumption of the grid-based operations. Three different top-down partitioning methods are investigated, and compared with formally more rigorous yet much more expensive bottom-up algorithms. We show that a conceptually simple top-down grid partitioning scheme achieves essentially the same efficiency as themore » more rigorous bottom-up approaches.« less

A Meinardus Theorem with Multiple Singularities

NASA Astrophysics Data System (ADS)

Granovsky, Boris L.; Stark, Dudley

2012-09-01

Meinardus proved a general theorem about the asymptotics of the number of weighted partitions, when the Dirichlet generating function for weights has a single pole on the positive real axis. Continuing (Granovsky et al., Adv. Appl. Math. 41:307-328, 2008), we derive asymptotics for the numbers of three basic types of decomposable combinatorial structures (or, equivalently, ideal gas models in statistical mechanics) of size n, when their Dirichlet generating functions have multiple simple poles on the positive real axis. Examples to which our theorem applies include ones related to vector partitions and quantum field theory. Our asymptotic formula for the number of weighted partitions disproves the belief accepted in the physics literature that the main term in the asymptotics is determined by the rightmost pole.

Multimaterial topology optimization of contact problems using phase field regularization

NASA Astrophysics Data System (ADS)

Myśliński, Andrzej

2018-01-01

The numerical method to solve multimaterial topology optimization problems for elastic bodies in unilateral contact with Tresca friction is developed in the paper. The displacement of the elastic body in contact is governed by elliptic equation with inequality boundary conditions. The body is assumed to consists from more than two distinct isotropic elastic materials. The materials distribution function is chosen as the design variable. Since high contact stress appears during the contact phenomenon the aim of the structural optimization problem is to find such topology of the domain occupied by the body that the normal contact stress along the boundary of the body is minimized. The original cost functional is regularized using the multiphase volume constrained Ginzburg-Landau energy functional rather than the perimeter functional. The first order necessary optimality condition is recalled and used to formulate the generalized gradient flow equations of Allen-Cahn type. The optimal topology is obtained as the steady state of the phase transition governed by the generalized Allen-Cahn equation. As the interface width parameter tends to zero the transition of the phase field model to the level set model is studied. The optimization problem is solved numerically using the operator splitting approach combined with the projection gradient method. Numerical examples confirming the applicability of the proposed method are provided and discussed.

Topological entanglement entropy of fracton stabilizer codes

NASA Astrophysics Data System (ADS)

Ma, Han; Schmitz, A. T.; Parameswaran, S. A.; Hermele, Michael; Nandkishore, Rahul M.

2018-03-01

Entanglement entropy provides a powerful characterization of two-dimensional gapped topological phases of quantum matter, intimately tied to their description by topological quantum field theories (TQFTs). Fracton topological orders are three-dimensional gapped topologically ordered states of matter that lack a TQFT description. We show that three-dimensional fracton phases are nevertheless characterized, at least partially, by universal structure in the entanglement entropy of their ground-state wave functions. We explicitly compute the entanglement entropy for two archetypal fracton models, the "X-cube model" and "Haah's code," and demonstrate the existence of a nonlocal contribution that scales linearly in subsystem size. We show via Schrieffer-Wolff transformations that this piece of the entanglement entropy of fracton models is robust against arbitrary local perturbations of the Hamiltonian. Finally, we argue that these results may be extended to characterize localization-protected fracton topological order in excited states of disordered fracton models.

Disrupted topological organization of resting-state functional brain network in subcortical vascular mild cognitive impairment.

PubMed

Yi, Li-Ye; Liang, Xia; Liu, Da-Ming; Sun, Bo; Ying, Sun; Yang, Dong-Bo; Li, Qing-Bin; Jiang, Chuan-Lu; Han, Ying

2015-10-01

Neuroimaging studies have demonstrated both structural and functional abnormalities in widespread brain regions in patients with subcortical vascular mild cognitive impairment (svMCI). However, whether and how these changes alter functional brain network organization remains largely unknown. We recruited 21 patients with svMCI and 26 healthy control (HC) subjects who underwent resting-state functional magnetic resonance imaging scans. Graph theory-based network analyses were used to investigate alterations in the topological organization of functional brain networks. Compared with the HC individuals, the patients with svMCI showed disrupted global network topology with significantly increased path length and modularity. Modular structure was also impaired in the svMCI patients with a notable rearrangement of the executive control module, where the parietal regions were split out and grouped as a separate module. The svMCI patients also revealed deficits in the intra- and/or intermodule connectivity of several brain regions. Specifically, the within-module degree was decreased in the middle cingulate gyrus while it was increased in the left anterior insula, medial prefrontal cortex and cuneus. Additionally, increased intermodule connectivity was observed in the inferior and superior parietal gyrus, which was associated with worse cognitive performance in the svMCI patients. Together, our results indicate that svMCI patients exhibit dysregulation of the topological organization of functional brain networks, which has important implications for understanding the pathophysiological mechanism of svMCI. © 2015 John Wiley & Sons Ltd.

Accurate Classification of RNA Structures Using Topological Fingerprints

PubMed Central

Li, Kejie; Gribskov, Michael

2016-01-01

While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint. PMID:27755571

Semiclassical electron transport at the edge of a two-dimensional topological insulator: Interplay of protected and unprotected modes

NASA Astrophysics Data System (ADS)

Khalaf, E.; Skvortsov, M. A.; Ostrovsky, P. M.

2016-03-01

We study electron transport at the edge of a generic disordered two-dimensional topological insulator, where some channels are topologically protected from backscattering. Assuming the total number of channels is large, we consider the edge as a quasi-one-dimensional quantum wire and describe it in terms of a nonlinear sigma model with a topological term. Neglecting localization effects, we calculate the average distribution function of transmission probabilities as a function of the sample length. We mainly focus on the two experimentally relevant cases: a junction between two quantum Hall (QH) states with different filling factors (unitary class) and a relatively thick quantum well exhibiting quantum spin Hall (QSH) effect (symplectic class). In a QH sample, the presence of topologically protected modes leads to a strong suppression of diffusion in the other channels already at scales much shorter than the localization length. On the semiclassical level, this is accompanied by the formation of a gap in the spectrum of transmission probabilities close to unit transmission, thereby suppressing shot noise and conductance fluctuations. In the case of a QSH system, there is at most one topologically protected edge channel leading to weaker transport effects. In order to describe `topological' suppression of nearly perfect transparencies, we develop an exact mapping of the semiclassical limit of the one-dimensional sigma model onto a zero-dimensional sigma model of a different symmetry class, allowing us to identify the distribution of transmission probabilities with the average spectral density of a certain random-matrix ensemble. We extend our results to other symmetry classes with topologically protected edges in two dimensions.

Nonequilibrium partitioning during rapid solidification of SiAs alloys

NASA Astrophysics Data System (ADS)

Kittl, J. A.; Aziz, M. J.; Brunco, D. P.; Thompson, M. O.

1995-02-01

The velocity dependence of the partition coefficient was measured for rapid solidification of polycrystalline Si-4.5 at% As and Si-9 at% As alloys induced by pulsed laser melting. The results constitute the first test of partitioning models both for the high velocity regime and for non-dilute alloys. The continuous growth model (CGM) of Aziz and Kaplan fits the data well, but with an unusually low diffusive speed of 0.46 m/s. The data show negligible dependence of partitioning on concentration, also consistent with the CGM. The predictions of the Hillert-Sundman model are inconsistent with partitioning results. Using the aperiodic stepwise growth model (ASGM) of Goldman and Aziz, an average over crystallographic orientations with parameters from independent single-crystal experiments is shown to be reasonably consistent with these polycrystalline partitioning results. The results, combined with others, indicate that the CGM without solute drag and its extension to lateral ledge motion, the ASGM, are the only models that fit the data for both solute partioning and kinetic undercooling interface response functions. No current solute drag models can match both partitioning and undercooling measurements.

Aberrant topological organization of the functional brain network associated with prior overt hepatic encephalopathy in cirrhotic patients.

PubMed

Chen, Hua-Jun; Chen, Qiu-Feng; Yang, Zhe-Ting; Shi, Hai-Bin

2018-05-30

A higher risk of cognitive impairments has been found after an overt hepatic encephalopathy (OHE) episode in cirrhotic patients. We investigated the effect of prior OHE episodes on the topological organization of the functional brain network and its association with the relevant cognitive impairments. Resting-state functional MRI data were acquired from 41 cirrhotic patients (19 with prior OHE (Prior-OHE) and 22 without (Non-Prior-OHE)) and 21 healthy controls (HC). A Psychometric Hepatic Encephalopathy Score (PHES) assessed cognition. The whole-brain functional network was constructed by thresholding functional correlation matrices of 90 brain regions (derived from the Automated Anatomic Labeling atlas). The topological properties of the brain network, including small-worldness, network efficiency, and nodal efficiency, were examined using graph theory-based analysis. Globally, the Prior-OHE group had a significantly decreased clustering coefficient and local efficiency, compared with the controls. Locally, the nodal efficiency in the bilateral medial superior frontal gyrus and the right postcentral gyrus decreased in the Prior-OHE group, while the nodal efficiency in the bilateral anterior cingulate/paracingulate gyri and right superior parietal gyrus increased in the Prior-OHE group. The alterations of global and regional network parameters progressed from Non-Prior-OHE to Prior-OHE and the clustering coefficient and local efficiency values were significantly correlated with PHES results. In conclusion, cirrhosis leads to the reduction of brain functional network efficiency, which could be aggravated by a prior OHE episode. Aberrant topological organization of the functional brain network may contribute to a higher risk of cognitive impairments in Prior-OHE patients.

Effective vacua for Floquet topological phases: A numerical perspective on the switch-function formalism

NASA Astrophysics Data System (ADS)

Tauber, C.

2018-05-01

We propose a general edge index definition for two-dimensional Floquet topological phases based on a switch-function formalism. When the Floquet operator has a spectral gap, the index covers both clean and disordered phases, anomalous or not, and does not require the bulk to be fully localized. It is interpreted as a nonadiabatic charge pumping that is quantized when the sample is placed next to an effective vacuum. This vacuum is gap-dependent and obtained from a Floquet Hamiltonian. The choice of a vacuum provides a simple and alternative gap-selection mechanism. Inspired by the model from Rudner et al. we then illustrate these concepts on Floquet disordered phases. Switch-function formalism is usually restricted to infinite samples in the thermodynamic limit. Here we circumvent this issue and propose a numerical implementation of the edge index that could be adapted to any bulk or edge index expressed in terms of switch functions, already existing for many topological phases.

Fermionic Approach to Weighted Hurwitz Numbers and Topological Recursion

NASA Astrophysics Data System (ADS)

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

NASA Astrophysics Data System (ADS)

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.

Tunable Electronic and Topological Properties of Germanene by Functional Group Modification

PubMed Central

Ren, Ceng-Ceng; Zhang, Shu-Feng; Ji, Wei-Xiao; Zhang, Chang-Wen; Li, Ping; Wang, Pei-Ji

2018-01-01

Electronic and topological properties of two-dimensional germanene modified by functional group X (X = H, F, OH, CH3) at full coverage are studied with first-principles calculation. Without considering the effect of spin-orbit coupling (SOC), all functionalized configurations become semiconductors, removing the Dirac cone at K point in pristine germanene. We also find that their band gaps can be especially well tuned by an external strain. When the SOC is switched on, GeX (X = H, CH3) is a normal insulator and strain leads to a phase transition to a topological insulator (TI) phase. However, GeX (X = F, OH) becomes a TI with a large gap of 0.19 eV for X = F and 0.24 eV for X = OH, even without external strains. More interestingly, when all these functionalized monolayers form a bilayer structure, semiconductor-metal states are observed. All these results suggest a possible route of modulating the electronic properties of germanene and promote applications in nanoelectronics. PMID:29509699

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

PubMed Central

Guo, Ya; Xu, Quan; Canzio, Daniele; Shou, Jia; Li, Jinhuan; Gorkin, David U.; Jung, Inkyung; Wu, Haiyang; Zhai, Yanan; Tang, Yuanxiao; Lu, Yichao; Wu, Yonghu; Jia, Zhilian; Li, Wei; Zhang, Michael Q.; Ren, Bing; Krainer, Adrian R.; Maniatis, Tom; Wu, Qiang

2015-01-01

SUMMARY CTCF/cohesin play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters, and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. The findings reveal how 3D chromosome architecture can be encoded by genome sequence. PMID:26276636

Gene network interconnectedness and the generalized topological overlap measure

PubMed Central

Yip, Andy M; Horvath, Steve

2007-01-01

Background Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency) between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz et al. [1] can be interpreted as a measure of agreement between the m = 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness. Results We generalize the topological overlap measure from m = 1 step neighborhoods to m ≥ 2 step neighborhoods. This allows us to define the m-th order generalized topological overlap measure (GTOM) by (i) counting the number of m-step neighbors that a pair of nodes share and (ii) normalizing it to take a value between 0 and 1. Using theoretical arguments, a yeast co-expression network application, and a fly protein network application, we illustrate the usefulness of the proposed measure for module detection and gene neighborhood analysis. Conclusion Topological overlap can serve as an important filter to counter the effects of spurious or missing connections between network nodes. The m-th order topological overlap measure allows one to trade-off sensitivity versus specificity when it comes to defining pairwise interconnectedness and network modules. PMID:17250769

Altered Cerebral Blood Flow Covariance Network in Schizophrenia.

PubMed

Liu, Feng; Zhuo, Chuanjun; Yu, Chunshui

2016-01-01

Many studies have shown abnormal cerebral blood flow (CBF) in schizophrenia; however, it remains unclear how topological properties of CBF network are altered in this disorder. Here, arterial spin labeling (ASL) MRI was employed to measure resting-state CBF in 96 schizophrenia patients and 91 healthy controls. CBF covariance network of each group was constructed by calculating across-subject CBF covariance between 90 brain regions. Graph theory was used to compare intergroup differences in global and nodal topological measures of the network. Both schizophrenia patients and healthy controls had small-world topology in CBF covariance networks, implying an optimal balance between functional segregation and integration. Compared with healthy controls, schizophrenia patients showed reduced small-worldness, normalized clustering coefficient and local efficiency of the network, suggesting a shift toward randomized network topology in schizophrenia. Furthermore, schizophrenia patients exhibited altered nodal centrality in the perceptual-, affective-, language-, and spatial-related regions, indicating functional disturbance of these systems in schizophrenia. This study demonstrated for the first time that schizophrenia patients have disrupted topological properties in CBF covariance network, which provides a new perspective (efficiency of blood flow distribution between brain regions) for understanding neural mechanisms of schizophrenia.

Correspondence between spanning trees and the Ising model on a square lattice

NASA Astrophysics Data System (ADS)

Viswanathan, G. M.

2017-06-01

An important problem in statistical physics concerns the fascinating connections between partition functions of lattice models studied in equilibrium statistical mechanics on the one hand and graph theoretical enumeration problems on the other hand. We investigate the nature of the relationship between the number of spanning trees and the partition function of the Ising model on the square lattice. The spanning tree generating function T (z ) gives the spanning tree constant when evaluated at z =1 , while giving the lattice green function when differentiated. It is known that for the infinite square lattice the partition function Z (K ) of the Ising model evaluated at the critical temperature K =Kc is related to T (1 ) . Here we show that this idea in fact generalizes to all real temperatures. We prove that [Z(K ) s e c h 2 K ] 2=k exp[T (k )] , where k =2 tanh(2 K )s e c h (2 K ) . The identical Mahler measure connects the two seemingly disparate quantities T (z ) and Z (K ) . In turn, the Mahler measure is determined by the random walk structure function. Finally, we show that the the above correspondence does not generalize in a straightforward manner to nonplanar lattices.

Current-induced switching of magnetic molecules on topological insulator surfaces

NASA Astrophysics Data System (ADS)

Locane, Elina; Brouwer, Piet W.

2017-03-01

Electrical currents at the surface or edge of a topological insulator are intrinsically spin polarized. We show that such surface or edge currents can be used to switch the orientation of a molecular magnet weakly coupled to the surface or edge of a topological insulator. For the edge of a two-dimensional topological insulator as well as for the surface of a three-dimensional topological insulator the application of a well-chosen surface or edge current can lead to a complete polarization of the molecule if the molecule's magnetic anisotropy axis is appropriately aligned with the current direction. For a generic orientation of the molecule a nonzero but incomplete polarization is obtained. We calculate the probability distribution of the magnetic states and the switching rates as a function of the applied current.

Topological protection of multiparticle dissipative transport

NASA Astrophysics Data System (ADS)

Loehr, Johannes; Loenne, Michael; Ernst, Adrian; de Las Heras, Daniel; Fischer, Thomas M.

2016-06-01

Topological protection allows robust transport of localized phenomena such as quantum information, solitons and dislocations. The transport can be either dissipative or non-dissipative. Here, we experimentally demonstrate and theoretically explain the topologically protected dissipative motion of colloidal particles above a periodic hexagonal magnetic pattern. By driving the system with periodic modulation loops of an external and spatially homogeneous magnetic field, we achieve total control over the motion of diamagnetic and paramagnetic colloids. We can transport simultaneously and independently each type of colloid along any of the six crystallographic directions of the pattern via adiabatic or deterministic ratchet motion. Both types of motion are topologically protected. As an application, we implement an automatic topologically protected quality control of a chemical reaction between functionalized colloids. Our results are relevant to other systems with the same symmetry.

A Single Polar Residue and Distinct Membrane Topologies Impact the Function of the Infectious Bronchitis Coronavirus E Protein

PubMed Central

Ruch, Travis R.; Machamer, Carolyn E.

2012-01-01

The coronavirus E protein is a small membrane protein with a single predicted hydrophobic domain (HD), and has a poorly defined role in infection. The E protein is thought to promote virion assembly, which occurs in the Golgi region of infected cells. It has also been implicated in the release of infectious particles after budding. The E protein has ion channel activity in vitro, although a role for channel activity in infection has not been established. Furthermore, the membrane topology of the E protein is of considerable debate, and the protein may adopt more than one topology during infection. We previously showed that the HD of the infectious bronchitis virus (IBV) E protein is required for the efficient release of infectious virus, an activity that correlated with disruption of the secretory pathway. Here we report that a single residue within the hydrophobic domain, Thr16, is required for secretory pathway disruption. Substitutions of other residues for Thr16 were not tolerated. Mutations of Thr16 did not impact virus assembly as judged by virus-like particle production, suggesting that alteration of secretory pathway and assembly are independent activities. We also examined how the membrane topology of IBV E affected its function by generating mutant versions that adopted either a transmembrane or membrane hairpin topology. We found that a transmembrane topology was required for disrupting the secretory pathway, but was less efficient for virus-like particle production. The hairpin version of E was unable to disrupt the secretory pathway or produce particles. The findings reported here identify properties of the E protein that are important for its function, and provide insight into how the E protein may perform multiple roles during infection. PMID:22570613

Effects of Lewis number on the statistics of the invariants of the velocity gradient tensor and local flow topologies in turbulent premixed flames

NASA Astrophysics Data System (ADS)

Wacks, Daniel; Konstantinou, Ilias; Chakraborty, Nilanjan

2018-04-01

The behaviours of the three invariants of the velocity gradient tensor and the resultant local flow topologies in turbulent premixed flames have been analysed using three-dimensional direct numerical simulation data for different values of the characteristic Lewis number ranging from 0.34 to 1.2. The results have been analysed to reveal the statistical behaviours of the invariants and the flow topologies conditional upon the reaction progress variable. The behaviours of the invariants have been explained in terms of the relative strengths of the thermal and mass diffusions, embodied by the influence of the Lewis number on turbulent premixed combustion. Similarly, the behaviours of the flow topologies have been explained in terms not only of the Lewis number but also of the likelihood of the occurrence of individual flow topologies in the different flame regions. Furthermore, the sensitivity of the joint probability density function of the second and third invariants and the joint probability density functions of the mean and Gaussian curvatures to the variation in Lewis number have similarly been examined. Finally, the dependences of the scalar-turbulence interaction term on augmented heat release and of the vortex-stretching term on flame-induced turbulence have been explained in terms of the Lewis number, flow topology and reaction progress variable.

Effects of Lewis number on the statistics of the invariants of the velocity gradient tensor and local flow topologies in turbulent premixed flames

PubMed Central

Konstantinou, Ilias; Chakraborty, Nilanjan

2018-01-01

The behaviours of the three invariants of the velocity gradient tensor and the resultant local flow topologies in turbulent premixed flames have been analysed using three-dimensional direct numerical simulation data for different values of the characteristic Lewis number ranging from 0.34 to 1.2. The results have been analysed to reveal the statistical behaviours of the invariants and the flow topologies conditional upon the reaction progress variable. The behaviours of the invariants have been explained in terms of the relative strengths of the thermal and mass diffusions, embodied by the influence of the Lewis number on turbulent premixed combustion. Similarly, the behaviours of the flow topologies have been explained in terms not only of the Lewis number but also of the likelihood of the occurrence of individual flow topologies in the different flame regions. Furthermore, the sensitivity of the joint probability density function of the second and third invariants and the joint probability density functions of the mean and Gaussian curvatures to the variation in Lewis number have similarly been examined. Finally, the dependences of the scalar--turbulence interaction term on augmented heat release and of the vortex-stretching term on flame-induced turbulence have been explained in terms of the Lewis number, flow topology and reaction progress variable. PMID:29740257

Functional network organizations of two contrasting temperament groups in dimensions of novelty seeking and harm avoidance.

PubMed

Kyeong, Sunghyon; Kim, Eunjoo; Park, Hae-Jeong; Hwang, Dong-Uk

2014-08-05

Novelty seeking (NS) and harm avoidance (HA) are two major dimensions of temperament in Cloninger׳s neurobiological model of personality. Previous neurofunctional and biological studies on temperament dimensions of HA and NS suggested that the temperamental traits have significant correlations with cortical and subcortical brain regions. However, no study to date has investigated the functional network modular organization as a function of the temperament dimension. The temperament dimensions were originally proposed to be independent of one another. However, a meta-analysis based on 16 published articles found a significant negative correlation between HA and NS (Miettunen et al., 2008). Based on this negative correlation, the current study revealed the whole-brain connectivity modular architecture for two contrasting temperament groups. The k-means clustering algorithm, with the temperamental traits of HA and NS as an input, was applied to divide the 40 subjects into two temperament groups: 'high HA and low NS' versus 'low HA and high NS'. Using the graph theoretical framework, we found a functional segregation of whole brain network architectures derived from resting-state functional MRI. In the 'high HA and low NS' group, the regulatory brain regions, such as the prefrontal cortex (PFC), are clustered together with the limbic system. In the 'low HA and high NS' group, however, brain regions lying on the dopaminergic pathways, such as the PFC and basal ganglia, are partitioned together. These findings suggest that the neural basis of inhibited, passive, and inactive behaviors in the 'high HA and low NS' group was derived from the increased network associations between the PFC and limbic clusters. In addition, supporting evidence of topological differences between the two temperament groups was found by analyzing the functional connectivity density and gray matter volume, and by computing the relationships between the morphometry and function of the brain. Copyright © 2014 Elsevier B.V. All rights reserved.

Detecting phenotype-driven transitions in regulatory network structure.

PubMed

Padi, Megha; Quackenbush, John

2018-01-01

Complex traits and diseases like human height or cancer are often not caused by a single mutation or genetic variant, but instead arise from functional changes in the underlying molecular network. Biological networks are known to be highly modular and contain dense "communities" of genes that carry out cellular processes, but these structures change between tissues, during development, and in disease. While many methods exist for inferring networks and analyzing their topologies separately, there is a lack of robust methods for quantifying differences in network structure. Here, we describe ALPACA (ALtered Partitions Across Community Architectures), a method for comparing two genome-scale networks derived from different phenotypic states to identify condition-specific modules. In simulations, ALPACA leads to more nuanced, sensitive, and robust module discovery than currently available network comparison methods. As an application, we use ALPACA to compare transcriptional networks in three contexts: angiogenic and non-angiogenic subtypes of ovarian cancer, human fibroblasts expressing transforming viral oncogenes, and sexual dimorphism in human breast tissue. In each case, ALPACA identifies modules enriched for processes relevant to the phenotype. For example, modules specific to angiogenic ovarian tumors are enriched for genes associated with blood vessel development, and modules found in female breast tissue are enriched for genes involved in estrogen receptor and ERK signaling. The functional relevance of these new modules suggests that not only can ALPACA identify structural changes in complex networks, but also that these changes may be relevant for characterizing biological phenotypes.

Discretized torsional dynamics and the folding of an RNA chain.

PubMed

Fernández, A; Salthú, R; Cendra, H

1999-08-01

The aim of this work is to implement a discrete coarse codification of local torsional states of the RNA chain backbone in order to explore the long-time limit dynamics and ultimately obtain a coarse solution to the RNA folding problem. A discrete representation of the soft-mode dynamics is turned into an algorithm for a rough structure prediction. The algorithm itself is inherently parallel, as it evaluates concurrent folding possibilities by pattern recognition, but it may be implemented in a personal computer as a chain of perturbation-translation-renormalization cycles performed on a binary matrix of local topological constraints. This requires suitable representational tools and a periodic quenching of the dynamics for system renormalization. A binary coding of local topological constraints associated with each structural motif is introduced, with each local topological constraint corresponding to a local torsional state. This treatment enables us to adopt a computation time step far larger than hydrodynamic drag time scales. Accordingly, the solvent is no longer treated as a hydrodynamic drag medium. Instead we incorporate its capacity for forming local conformation-dependent dielectric domains. Each translation of the matrix of local topological constraints (LTM's) depends on the conformation-dependent local dielectric created by a confined solvent. Folding pathways are resolved as transitions between patterns of locally encoded structural signals which change within the 1 ns-100 ms time scale range. These coarse folding pathways are generated by a search at regular intervals for structural patterns in the LTM. Each pattern is recorded as a base-pairing pattern (BPP) matrix, a consensus-evaluation operation subject to a renormalization feedback loop. Since several mutually conflicting consensus evaluations might occur at a given time, the need arises for a probabilistic approach appropriate for an ensemble of RNA molecules. Thus, a statistical dynamics of consensus formation is determined by the time evolution of the base pairing probability matrix. These dynamics are generated for a functional RNA molecule, a representative of the so-called group I ribozymes, in order to test the model. The resulting ensemble of conformations is sharply peaked and the most probable structure features the predominance of all phylogenetically conserved intrachain helices tantamount to ribozyme function. Furthermore, the magnesium-aided cooperativity that leads to the shaping of the catalytic core is elucidated. Once the predictive folding algorithm has been implemented, the validity of the so-called "adiabatic approximation" is tested. This approximation requires that conformational microstates be lumped up into BPP's which are treated as quasiequilibrium states, while folding pathways are coarsely represented as sequences of BPP transitions. To test the validity of this adiabatic ansatz, a computation of the coarse Shannon information entropy sigma associated to the specific partition of conformation space into BPP's is performed taking into account the LTM evolution and contrasted with the adiabatic computation. The results reveal a subordination of torsional microstate dynamics to BPP transitions within time scales relevant to folding. This adiabatic entrainment in the long-time limit is thus identified as responsible for the expediency of the folding process.

Constructing topological models by symmetrization: A projected entangled pair states study

NASA Astrophysics Data System (ADS)

Fernández-González, Carlos; Mong, Roger S. K.; Landon-Cardinal, Olivier; Pérez-García, David; Schuch, Norbert

2016-10-01

Symmetrization of topologically ordered wave functions is a powerful method for constructing new topological models. Here we study wave functions obtained by symmetrizing quantum double models of a group G in the projected entangled pair states (PEPS) formalism. We show that symmetrization naturally gives rise to a larger symmetry group G ˜ which is always non-Abelian. We prove that by symmetrizing on sufficiently large blocks, one can always construct wave functions in the same phase as the double model of G ˜. In order to understand the effect of symmetrization on smaller patches, we carry out numerical studies for the toric code model, where we find strong evidence that symmetrizing on individual spins gives rise to a critical model which is at the phase transitions of two inequivalent toric codes, obtained by anyon condensation from the double model of G ˜.

Synchrotron Micro-XANES Measurements of Vanadium Oxidation State in Glasses as a Function of Oxygen Fugacity: Experimental Calibration of Data Relevant to Partition Coefficient Determination

NASA Technical Reports Server (NTRS)

Delaney, J. S.; Sutton, S. R.; Newville, M.; Jones, J. H.; Hanson, B.; Dyar, M. D.; Schreiber, H.

2000-01-01

Oxidation state microanalyses for V in glass have been made by calibrating XANES spectral features with optical spectroscopic measurements. The oxidation state change with fugacity of O2 will strongly influence partitioning results.

Topological Reorganization of the Default Mode Network in Severe Male Obstructive Sleep Apnea

PubMed Central

Chen, Liting; Fan, Xiaole; Li, Haijun; Ye, Chenglong; Yu, Honghui; Gong, Honghan; Zeng, Xianjun; Peng, Dechang; Yan, Liping

2018-01-01

Impaired spontaneous regional activity and altered topology of the brain network have been observed in obstructive sleep apnea (OSA). However, the mechanisms of disrupted functional connectivity (FC) and topological reorganization of the default mode network (DMN) in patients with OSA remain largely unknown. We explored whether the FC is altered within the DMN and examined topological changes occur in the DMN in patients with OSA using a graph theory analysis of resting-state functional magnetic resonance imaging data and evaluated the relationship between neuroimaging measures and clinical variables. Resting-state data were obtained from 46 male patients with untreated severe OSA and 46 male good sleepers (GSs). We specifically selected 20 DMN subregions to construct the DMN architecture. The disrupted FC and topological properties of the DMN in patients with OSA were characterized using graph theory. The OSA group showed significantly decreased FC of the anterior–posterior DMN and within the posterior DMN, and also showed increased FC within the DMN. The DMN exhibited small-world topology in both OSA and GS groups. Compared to GSs, patients with OSA showed a decreased clustering coefficient (Cp) and local efficiency, and decreased nodal centralities in the left posterior cingulate cortex and dorsal medial prefrontal cortex, and increased nodal centralities in the ventral medial prefrontal cortex and the right parahippocampal cortex. Finally, the abnormal DMN FC was significantly related to Cp, path length, global efficiency, and Montreal cognitive assessment score. OSA showed disrupted FC within the DMN, which may have contributed to the observed topological reorganization. These findings may provide further evidence of cognitive deficits in patients with OSA.

Functional Integrative Levels in the Human Interactome Recapitulate Organ Organization

PubMed Central

Prieto, Carlos; Benkahla, Alia; De Las Rivas, Javier; Brun, Christine

2011-01-01

Interactome networks represent sets of possible physical interactions between proteins. They lack spatio-temporal information by construction. However, the specialized functions of the differentiated cell types which are assembled into tissues or organs depend on the combinatorial arrangements of proteins and their physical interactions. Is tissue-specificity, therefore, encoded within the interactome? In order to address this question, we combined protein-protein interactions, expression data, functional annotations and interactome topology. We first identified a subnetwork formed exclusively of proteins whose interactions were observed in all tested tissues. These are mainly involved in housekeeping functions and are located at the topological center of the interactome. This ‘Largest Common Interactome Network’ represents a ‘functional interactome core’. Interestingly, two types of tissue-specific interactions are distinguished when considering function and network topology: tissue-specific interactions involved in regulatory and developmental functions are central whereas tissue-specific interactions involved in organ physiological functions are peripheral. Overall, the functional organization of the human interactome reflects several integrative levels of functions with housekeeping and regulatory tissue-specific functions at the center and physiological tissue-specific functions at the periphery. This gradient of functions recapitulates the organization of organs, from cells to organs. Given that several gradients have already been identified across interactomes, we propose that gradients may represent a general principle of protein-protein interaction network organization. PMID:21799769

Exploring nonlinear topological states of matter with exciton-polaritons: Edge solitons in kagome lattice.

PubMed

Gulevich, D R; Yudin, D; Skryabin, D V; Iorsh, I V; Shelykh, I A

2017-05-11

Matter in nontrivial topological phase possesses unique properties, such as support of unidirectional edge modes on its interface. It is the existence of such modes which is responsible for the wonderful properties of a topological insulator - material which is insulating in the bulk but conducting on its surface, along with many of its recently proposed photonic and polaritonic analogues. We show that exciton-polariton fluid in a nontrivial topological phase in kagome lattice, supports nonlinear excitations in the form of solitons built up from wavepackets of topological edge modes - topological edge solitons. Our theoretical and numerical results indicate the appearance of bright, dark and grey solitons dwelling in the vicinity of the boundary of a lattice strip. In a parabolic region of the dispersion the solitons can be described by envelope functions satisfying the nonlinear Schrödinger equation. Upon collision, multiple topological edge solitons emerge undistorted, which proves them to be true solitons as opposed to solitary waves for which such requirement is waived. Importantly, kagome lattice supports topological edge mode with zero group velocity unlike other types of truncated lattices. This gives a finer control over soliton velocity which can take both positive and negative values depending on the choice of forming it topological edge modes.

WKB solutions of difference equations and reconstruction by the topological recursion

NASA Astrophysics Data System (ADS)

Marchal, Olivier

2018-01-01

The purpose of this article is to analyze the connection between Eynard-Orantin topological recursion and formal WKB solutions of a \\hbar -difference equation: \\Psi(x+\\hbar)=≤ft(e\\hbar\\fracd{dx}\\right) \\Psi(x)=L(x;\\hbar)\\Psi(x) with L(x;\\hbar)\\in GL_2( ({C}(x))[\\hbar]) . In particular, we extend the notion of determinantal formulas and topological type property proposed for formal WKB solutions of \\hbar -differential systems to this setting. We apply our results to a specific \\hbar -difference system associated to the quantum curve of the Gromov-Witten invariants of {P}1 for which we are able to prove that the correlation functions are reconstructed from the Eynard-Orantin differentials computed from the topological recursion applied to the spectral curve y=\\cosh-1\\frac{x}{2} . Finally, identifying the large x expansion of the correlation functions, proves a recent conjecture made by Dubrovin and Yang regarding a new generating series for Gromov-Witten invariants of {P}1 .

Impact of topology in foliated quantum Einstein gravity.

PubMed

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.

Topological Structures in Multiferroics - Domain Walls, Skyrmions and Vortices

DOE PAGES

Seidel, Jan; Vasudevan, Rama K.; Valanoor, Nagarajan

2015-12-15

Topological structures in multiferroic materials have recently received considerable attention because of their potential use as nanoscale functional elements. Their reduced size in conjunction with exotic arrangement of the ferroic order parameter and potential order parameter coupling allows for emergent and unexplored phenomena in condensed matter and functional materials systems. This will lead to exciting new fundamental discoveries as well as application concepts that exploit their response to external stimuli such as mechanical strain, electric and magnetic fields. In this review we capture the current development of this rapidly moving field with specific emphasis on key achievements that have castmore » light on how such topological structures in multiferroic materials systems can be exploited for use in complex oxide nanoelectronics and spintronics.« less

Determination of partition coefficients using 1 H NMR spectroscopy and time domain complete reduction to amplitude-frequency table (CRAFT) analysis.

PubMed

Soulsby, David; Chica, Jeryl A M

2017-08-01

We have developed a simple, direct and novel method for the determination of partition coefficients and partitioning behavior using 1 H NMR spectroscopy combined with time domain complete reduction to amplitude-frequency tables (CRAFT). After partitioning into water and 1-octanol using standard methods, aliquots from each layer are directly analyzed using either proton or selective excitation NMR experiments. Signal amplitudes for each compound from each layer are then extracted directly from the time domain data in an automated fashion and analyzed using the CRAFT software. From these amplitudes, log P and log D 7.4 values can be calculated directly. Phase, baseline and internal standard issues, which can be problematic when Fourier transformed data are used, are unimportant when using time domain data. Furthermore, analytes can contain impurities because only a single resonance is examined and need not be UV active. Using this approach, we examined a variety of pharmaceutically relevant compounds and determined partition coefficients that are in excellent agreement with literature values. To demonstrate the utility of this approach, we also examined salicylic acid in more detail demonstrating an aggregation effect as a function of sample loading and partition coefficient behavior as a function of pH value. This method provides a valuable addition to the medicinal chemist toolbox for determining these important constants. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. II. Relationships between chemical model and partition function algorithm.

PubMed

Fisicaro, E; Braibanti, A; Lamb, J D; Oscarson, J L

1990-05-01

The relationships between the chemical properties of a system and the partition function algorithm as applied to the description of multiple equilibria in solution are explained. The partition functions ZM, ZA, and ZH are obtained from powers of the binary generating functions Jj = (1 + kappa j gamma j,i[Y])i tau j, where i tau j = p tau j, q tau j, or r tau j represent the maximum number of sites in sites in class j, for Y = M, A, or H, respectively. Each term of the generating function can be considered an element (ij) of a vector Jj and each power of the cooperativity factor gamma ij,i can be considered an element of a diagonal cooperativity matrix gamma j. The vectors Jj are combined in tensor product matrices L tau = (J1) [J2]...[Jj]..., thus representing different receptor-ligand combinations. The partition functions are obtained by summing elements of the tensor matrices. The relationship of the partition functions with the total chemical amounts TM, TA, and TH has been found. The aim is to describe the total chemical amounts TM, TA, and TH as functions of the site affinity constants kappa j and cooperativity coefficients bj. The total amounts are calculated from the sum of elements of tensor matrices Ll. Each set of indices (pj..., qj..., rj...) represents one element of a tensor matrix L tau and defines each term of the summation. Each term corresponds to the concentration of a chemical microspecies. The distinction between microspecies MpjAqjHrj with ligands bound on specific sites and macrospecies MpAqHR corresponding to a chemical stoichiometric composition is shown. The translation of the properties of chemical model schemes into the algorithms for the generation of partition functions is illustrated with reference to a series of examples of gradually increasing complexity. The equilibria examined concern: (1) a unique class of sites; (2) the protonation of a base with two classes of sites; (3) the simultaneous binding of ligand A and proton H to a macromolecule or receptor M with four classes of sites; and (4) the binding to a macromolecule M of ligand A which is in turn a receptor for proton H. With reference to a specific example, it is shown how a computer program for least-squares refinement of variables kappa j and bj can be organized. The chemical model from the free components M, A, and H to the saturated macrospecies MpAQHR, with possible complex macrospecies MpAq and AHR, is defined first.(ABSTRACT TRUNCATED AT 250 WORDS)

Divergent evapotranspiration partition dynamics between shrubs and grasses in a shrub-encroached steppe ecosystem.

PubMed

Wang, Pei; Li, Xiao-Yan; Wang, Lixin; Wu, Xiuchen; Hu, Xia; Fan, Ying; Tong, Yaqin

2018-06-04

Previous evapotranspiration (ET) partitioning studies have usually neglected competitions and interactions between antagonistic plant functional types. This study investigated whether shrubs and grasses have divergent ET partition dynamics impacted by different water-use patterns, canopy structures, and physiological properties in a shrub-encroached steppe ecosystem in Inner Mongolia, China. The soil water-use patterns of shrubs and grasses have been quantified by an isotopic tracing approach and coupled into an improved multisource energy balance model to partition ET fluxes into soil evaporation, grass transpiration, and shrub transpiration. The mean fractional contributions to total ET were 24 ± 13%, 20 ± 4%, and 56 ± 16% for shrub transpiration, grass transpiration, and soil evaporation respectively during the growing season. Difference in ecohydrological connectivity and leaf development both contributed to divergent transpiration partitioning between shrubs and grasses. Shrub-encroachment processes result in larger changes in the ET components than in total ET flux, which could be well explained by changes in canopy resistance, an ecosystem function dominated by the interaction of soil water-use patterns and ecosystem structure. The analyses presented here highlight the crucial effects of vegetation structural changes on the processes of land-atmosphere interaction and climate feedback. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Hybrid Topological Lie-Hamiltonian Learning in Evolving Energy Landscapes

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

In this Chapter, a novel bidirectional algorithm for hybrid (discrete + continuous-time) Lie-Hamiltonian evolution in adaptive energy landscape-manifold is designed and its topological representation is proposed. The algorithm is developed within a geometrically and topologically extended framework of Hopfield's neural nets and Haken's synergetics (it is currently designed in Mathematica, although with small changes it could be implemented in Symbolic C++ or any other computer algebra system). The adaptive energy manifold is determined by the Hamiltonian multivariate cost function H, based on the user-defined vehicle-fleet configuration matrix W, which represents the pseudo-Riemannian metric tensor of the energy manifold. Search for the global minimum of H is performed using random signal differential Hebbian adaptation. This stochastic gradient evolution is driven (or, pulled-down) by `gravitational forces' defined by the 2nd Lie derivatives of H. Topological changes of the fleet matrix W are observed during the evolution and its topological invariant is established. The evolution stops when the W-topology breaks down into several connectivity-components, followed by topology-breaking instability sequence (i.e., a series of phase transitions).

Thermalization of topological entropy after a quantum quench

NASA Astrophysics Data System (ADS)

Zeng, Yu; Hamma, Alioscia; Fan, Heng

2016-09-01

Topologically ordered quantum phases are robust in the sense that perturbations in the Hamiltonian of the system will not change the topological nature of the ground-state wave function. However, in order to exploit topological order for applications such as self-correcting quantum memories and information processing, these states need to be also robust both dynamically and at finite temperature in the presence of an environment. It is well known that systems like the toric code in two spatial dimensions are fragile in temperature. In this paper, we show a completely analytic treatment of the toric code away from equilibrium, after a quantum quench of the system Hamiltonian. We show that, despite being subject to unitary evolution (and at zero temperature), the long-time behavior of the topological entropy is thermal, therefore vanishing. If the quench preserves a local gauge structure, there is a residual long-lived topological entropy. This also is the thermal behavior in presence of such gauge constraints. The result is obtained by studying the time evolution of the topological 2-Rényi entropy in a fully analytical, exact way.

Beyond Group: Multiple Person Tracking via Minimal Topology-Energy-Variation.

PubMed

Gao, Shan; Ye, Qixiang; Xing, Junliang; Kuijper, Arjan; Han, Zhenjun; Jiao, Jianbin; Ji, Xiangyang

2017-12-01

Tracking multiple persons is a challenging task when persons move in groups and occlude each other. Existing group-based methods have extensively investigated how to make group division more accurately in a tracking-by-detection framework; however, few of them quantify the group dynamics from the perspective of targets' spatial topology or consider the group in a dynamic view. Inspired by the sociological properties of pedestrians, we propose a novel socio-topology model with a topology-energy function to factor the group dynamics of moving persons and groups. In this model, minimizing the topology-energy-variance in a two-level energy form is expected to produce smooth topology transitions, stable group tracking, and accurate target association. To search for the strong minimum in energy variation, we design the discrete group-tracklet jump moves embedded in the gradient descent method, which ensures that the moves reduce the energy variation of group and trajectory alternately in the varying topology dimension. Experimental results on both RGB and RGB-D data sets show the superiority of our proposed model for multiple person tracking in crowd scenes.

Fully gapped superconductivity in In-doped topological crystalline insulator Pb 0.5Sn 0.5Te

DOE PAGES

Du, Guan; Gu, G. D.; Du, Zengyi; ...

2015-07-27

In this study, superconductors derived from topological insulators and topological crystalline insulators by chemical doping have long been considered to be candidates as topological superconductors. Pb 0.5Sn 0.5Te is a topological crystalline insulator with mirror symmetry protected surface states on (001)-, (011)-, and (111)-oriented surfaces. The superconductor (Pb 0.5Sn 0.5) 0.7In 0.3Te is produced by In doping in Pb 0.5Sn 0.5Te, and is thought to be a topological superconductor. Here we report scanning tunneling spectroscopy measurements of the superconducting state as well as the superconducting energy gap in (Pb 0.5Sn 0.5) 0.7In 0.3Te on a (001)-oriented surface. The spectrum canmore » be well fitted by an anisotropic s-wave gap function of Δ = 0.72 + 0.18cos4θ meV using Dynes model. The results show that the superconductor seems to be a fully gapped one without any in-gap states, in contradiction with the expectation of a topological superconductor.« less

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

PubMed Central

2017-01-01

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation. This representation reveals hidden structure-function relationships in biomolecules. We further integrate ESPH and deep convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the deep learning limitations from small and noisy training sets, we propose a multi-task multichannel topological convolutional neural network (MM-TCNN). We demonstrate that TopologyNet outperforms the latest methods in the prediction of protein-ligand binding affinities, mutation induced globular protein folding free energy changes, and mutation induced membrane protein folding free energy changes. Availability: weilab.math.msu.edu/TDL/ PMID:28749969

DOE Office of Scientific and Technical Information (OSTI.GOV)

Argyres, Philip C.; Martone, Mario

In this paper we present a beautifully consistent web of evidence for the existence of interacting 4d rank-1more » $$ \\mathcal{N} $$ = 2 SCFTs obtained from gauging discrete subgroups of global symmetries of other existing 4d rank-1 $$ \\mathcal{N} $$ = 2 SCFTs. The global symmetries that can be gauged involve a non-trivial combination of discrete subgroups of the U(1) R, low-energy EM duality group SL(2,Z), and the outer automorphism group of the flavor symmetry algebra, Out(F ). The theories that we construct are remarkable in many ways: (i) two of them have exceptional F 4 and G 2 flavor groups; (ii) they substantially complete the picture of the landscape of rank-1 $$ \\mathcal{N} $$ = 2 SCFTs as they realize all but one of the remaining consistent rank-1 Seiberg-Witten geometries that we previously constructed but were not associated to known SCFTs; and (iii) some of them have enlarged $$ \\mathcal{N} $$ = 3 SUSY, and have not been previously constructed. They are also examples of SCFTs which violate the ShapereTachikawa relation between the conformal central charges and the scaling dimension of the Coulomb branch vev. Here, we propose a modification of the formulas computing these central charges from the topologically twisted Coulomb branch partition function which correctly compute them for discretely gauged theories.« less

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database

DOE PAGES

Mubarak, Misbah; Seol, Seegyoung; Lu, Qiukai; ...

2013-01-01

Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors are on different processors. This article presents a parallel algorithm of creating and deleting data copies, referred to as ghost copies, which localize neighborhood data for computation purposes while minimizing inter-process communication. The key characteristics of the algorithm are: (1) It can create ghost copies of any permissible topological order in amore » 1D, 2D or 3D mesh based on selected adjacencies. (2) It exploits neighborhood communication patterns during the ghost creation process thus eliminating all-to-all communication. (3) For applications that need neighbors of neighbors, the algorithm can create n number of ghost layers up to a point where the whole partitioned mesh can be ghosted. Strong and weak scaling results are presented for the IBM BG/P and Cray XE6 architectures up to a core count of 32,768 processors. The algorithm also leads to scalable results when used in a parallel super-convergent patch recovery error estimator, an application that frequently accesses neighborhood data to carry out computation.« less

N = 1 supersymmetric indices and the four-dimensional A-model

NASA Astrophysics Data System (ADS)

Closset, Cyril; Kim, Heeyeon; Willett, Brian

2017-08-01

We compute the supersymmetric partition function of N = 1 supersymmetric gauge theories with an R-symmetry on M_4\\cong M_{g,p}× {S}^1 , a principal elliptic fiber bundle of degree p over a genus- g Riemann surface, Σ g . Equivalently, we compute the generalized supersymmetric index I_{M}{_{g,p}, with the supersymmetric three-manifold M_{g,p} as the spatial slice. The ordinary N = 1 supersymmetric index on the round three-sphere is recovered as a special case. We approach this computation from the point of view of a topological A-model for the abelianized gauge fields on the base Σ g . This A-model — or A-twisted two-dimensional N = (2 , 2) gauge theory — encodes all the information about the generalized indices, which are viewed as expectations values of some canonically-defined surface defects wrapped on T 2 inside Σ g × T 2. Being defined by compactification on the torus, the A-model also enjoys natural modular properties, governed by the four-dimensional 't Hooft anomalies. As an application of our results, we provide new tests of Seiberg duality. We also present a new evaluation formula for the three-sphere index as a sum over two-dimensional vacua.

Analysing growth and development of plants jointly using developmental growth stages

PubMed Central

Dambreville, Anaëlle; Lauri, Pierre-Éric; Normand, Frédéric; Guédon, Yann

2015-01-01

Background and Aims Plant growth, the increase of organ dimensions over time, and development, the change in plant structure, are often studied as two separate processes. However, there is structural and functional evidence that these two processes are strongly related. The aim of this study was to investigate the co-ordination between growth and development using mango trees, which have well-defined developmental stages. Methods Developmental stages, determined in an expert way, and organ sizes, determined from objective measurements, were collected during the vegetative growth and flowering phases of two cultivars of mango, Mangifera indica. For a given cultivar and growth unit type (either vegetative or flowering), a multistage model based on absolute growth rate sequences deduced from the measurements was first built, and then growth stages deduced from the model were compared with developmental stages. Key Results Strong matches were obtained between growth stages and developmental stages, leading to a consistent definition of integrative developmental growth stages. The growth stages highlighted growth asynchronisms between two topologically connected organs, namely the vegetative axis and its leaves. Conclusions Integrative developmental growth stages emphasize that developmental stages are closely related to organ growth rates. The results are discussed in terms of the possible physiological processes underlying these stages, including plant hydraulics, biomechanics and carbohydrate partitioning. PMID:25452250

Detection of protein complex from protein-protein interaction network using Markov clustering

NASA Astrophysics Data System (ADS)

Ochieng, P. J.; Kusuma, W. A.; Haryanto, T.

2017-05-01

Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks.

Evolutionary Computation with Spatial Receding Horizon Control to Minimize Network Coding Resources

PubMed Central

Leeson, Mark S.

2014-01-01

The minimization of network coding resources, such as coding nodes and links, is a challenging task, not only because it is a NP-hard problem, but also because the problem scale is huge; for example, networks in real world may have thousands or even millions of nodes and links. Genetic algorithms (GAs) have a good potential of resolving NP-hard problems like the network coding problem (NCP), but as a population-based algorithm, serious scalability and applicability problems are often confronted when GAs are applied to large- or huge-scale systems. Inspired by the temporal receding horizon control in control engineering, this paper proposes a novel spatial receding horizon control (SRHC) strategy as a network partitioning technology, and then designs an efficient GA to tackle the NCP. Traditional network partitioning methods can be viewed as a special case of the proposed SRHC, that is, one-step-wide SRHC, whilst the method in this paper is a generalized N-step-wide SRHC, which can make a better use of global information of network topologies. Besides the SRHC strategy, some useful designs are also reported in this paper. The advantages of the proposed SRHC and GA for the NCP are illustrated by extensive experiments, and they have a good potential of being extended to other large-scale complex problems. PMID:24883371

Yeast cohesin complex embraces 2 micron plasmid sisters in a tri-linked catenane complex

PubMed Central

Ghosh, Santanu K.; Huang, Chu-Chun; Hajra, Sujata; Jayaram, Makkuni

2010-01-01

Sister chromatid cohesion, crucial for faithful segregation of replicated chromosomes in eukaryotes, is mediated by the multi-subunit protein complex cohesin. The Saccharomyces cerevisiae plasmid 2 micron circle mimics chromosomes in assembling cohesin at its partitioning locus. The plasmid is a multi-copy selfish DNA element that resides in the nucleus and propagates itself stably, presumably with assistance from cohesin. In metaphase cell lysates, or fractions enriched for their cohesed state by sedimentation, plasmid molecules are trapped topologically by the protein ring formed by cohesin. They can be released from cohesin’s embrace either by linearizing the DNA or by cleaving a cohesin subunit. Assays using two distinctly tagged cohesin molecules argue against the hand-cuff (an associated pair of monomeric cohesin rings) or the bracelet (a dimeric cohesin ring) model as responsible for establishing plasmid cohesion. Our cumulative results most easily fit a model in which a single monomeric cohesin ring, rather than a series of such rings, conjoins a pair of sister plasmids. These features of plasmid cohesion account for its sister-to-sister mode of segregation by cohesin disassembly during anaphase. The mechanistic similarities of cohesion between mini-chromosome sisters and 2 micron plasmid sisters suggest a potential kinship between the plasmid partitioning locus and centromeres. PMID:19920123

Topologically associating domains are stable units of replication-timing regulation.

PubMed

Pope, Benjamin D; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L; Wang, Yanli; Hansen, R Scott; Canfield, Theresa K; Thurman, Robert E; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H; Snyder, Michael P; Stamatoyannopoulos, John A; Taylor, James; Hardison, Ross C; Kahveci, Tamer; Ren, Bing; Gilbert, David M

2014-11-20

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae.

PubMed

Straub, Shannon C K; Moore, Michael J; Soltis, Pamela S; Soltis, Douglas E; Liston, Aaron; Livshultz, Tatyana

2014-11-01

Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value. Copyright © 2014 Elsevier Inc. All rights reserved.

Topologically-associating domains are stable units of replication-timing regulation

PubMed Central

Pope, Benjamin D.; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L.; Wang, Yanli; Hansen, R. Scott; Canfield, Theresa K.; Thurman, Robert E.; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H.; Snyder, Michael P.; Stamatoyannopoulos, John A.; Taylor, James; Hardison, Ross C.; Kahveci, Tamer; Ren, Bing; Gilbert, David M.

2014-01-01

Summary Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program1. During mammalian development, at least half the genome changes replication timing, primarily in units of 400–800 kb (“replication domains”; RDs), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements2–7. Early and late replication correlate strongly with open and closed chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, lamina-associated domains (LADs)4,5,8,9. Recent Hi-C mapping has unveiled a substructure of topologically-associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to RDs8,10. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale11,12. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure8,9,13. Here, we localize boundaries of RDs to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, RD boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure RD boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell type specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large-scale chromosome structure and function. PMID:25409831

Dimensionally regularized Tsallis' statistical mechanics and two-body Newton's gravitation

NASA Astrophysics Data System (ADS)

Zamora, J. D.; Rocca, M. C.; Plastino, A.; Ferri, G. L.

2018-05-01

Typical Tsallis' statistical mechanics' quantifiers like the partition function and the mean energy exhibit poles. We are speaking of the partition function Z and the mean energy 〈 U 〉 . The poles appear for distinctive values of Tsallis' characteristic real parameter q, at a numerable set of rational numbers of the q-line. These poles are dealt with dimensional regularization resources. The physical effects of these poles on the specific heats are studied here for the two-body classical gravitation potential.

Analysis of Different Cost Functions in the Geosect Airspace Partitioning Tool

NASA Technical Reports Server (NTRS)

Wong, Gregory L.

2010-01-01

A new cost function representing air traffic controller workload is implemented in the Geosect airspace partitioning tool. Geosect currently uses a combination of aircraft count and dwell time to select optimal airspace partitions that balance controller workload. This is referred to as the aircraft count/dwell time hybrid cost function. The new cost function is based on Simplified Dynamic Density, a measure of different aspects of air traffic controller workload. Three sectorizations are compared. These are the current sectorization, Geosect's sectorization based on the aircraft count/dwell time hybrid cost function, and Geosect s sectorization based on the Simplified Dynamic Density cost function. Each sectorization is evaluated for maximum and average workload along with workload balance using the Simplified Dynamic Density as the workload measure. In addition, the Airspace Concept Evaluation System, a nationwide air traffic simulator, is used to determine the capacity and delay incurred by each sectorization. The sectorization resulting from the Simplified Dynamic Density cost function had a lower maximum workload measure than the other sectorizations, and the sectorization based on the combination of aircraft count and dwell time did a better job of balancing workload and balancing capacity. However, the current sectorization had the lowest average workload, highest sector capacity, and the least system delay.

Allometric biomass partitioning under nitrogen enrichment: Evidence from manipulative experiments around the world.

PubMed

Peng, Yunfeng; Yang, Yuanhe

2016-06-28

Allometric and optimal hypotheses have been widely used to explain biomass partitioning in response to resource changes for individual plants; however, little evidence has been reported from measurements at the community level across a broad geographic scale. This study assessed the nitrogen (N) effect on community-level root to shoot (R/S) ratios and biomass partitioning functions by synthesizing global manipulative experiments. Results showed that, in aggregate, N addition decreased the R/S ratios in various biomes. However, the scaling slopes of the allometric equations were not significantly altered by the N enrichment, possibly indicating that N-induced reduction of the R/S ratio is a consequence of allometric allocation as a function of increasing plant size rather than an optimal partitioning model. To further illustrate this point, we developed power function models to explore the relationships between aboveground and belowground biomass for various biomes; then, we generated the predicted root biomass from the observed shoot biomass and predicted R/S ratios. The comparison of predicted and observed N-induced changes of the R/S ratio revealed no significant differences between each other, supporting the allometric allocation hypothesis. These results suggest that allometry, rather than optimal allocation, explains the N-induced reduction in the R/S ratio across global biomes.

Temperature and composition dependencies of trace element partitioning - Olivine/melt and low-Ca pyroxene/melt

NASA Technical Reports Server (NTRS)

Colson, R. O.; Mckay, G. A.; Taylor, L. A.

1988-01-01

This paper presents a systematic thermodynamic analysis of the effects of temperature and composition on olivine/melt and low-Ca pyroxene/melt partitioning. Experiments were conducted in several synthetic basalts with a wide range of Fe/Mg, determining partition coefficients for Eu, Ca, Mn, Fe, Ni, Sm, Cd, Y, Yb, Sc, Al, Zr, and Ti and modeling accurately the changes in free energy for trace element exchange between crystal and melt as functions of the trace element size and charge. On the basis of this model, partition coefficients for olivine/melt and low-Ca pyroxene/melt can be predicted for a wide range of elements over a variety of basaltic bulk compositions and temperatures. Moreover, variations in partition coeffeicients during crystallization or melting can be modeled on the basis of changes in temperature and major element chemistry.

High pressure breakdown of antigorite to spinifex-textured olivine and orthopyroxene, SE Spain

NASA Astrophysics Data System (ADS)

Trommsdorff, V.; Sánchez-Vizcaíno, V. López; Gómez-Pugnaire, M. T.; Müntener, O.

The prograde, high pressure, transition from antigorite serpentinite to enstatite-olivine rock occurs along a tectonically undisturbed profile at Cerro del Almirez, SE Spain. The reactant assemblage is antigorite + olivine with tremolite rimming precursor diopside. The product assemblage of tremolite + chlorite + enstatite + olivine has a spinifex-like texture with arborescent or radiating olivine elongated parallel to [001] and with radially grown enstatite. Product enstatite is very poor in Al2O3. Due to numerous oriented submicroscopic inclusions of chromian magnetite, product olivine has a brownish pleochroism and a bulk chromium content similar to precursor antigorite. Titanian clinohumite with a fluorine content of 0.45-0.50 wt% persisted beyond the breakdown of antigorite. The partitioning of iron and magnesium amongst the silicate phases is almost identical to that at lower pressures. Average Kd values Mn/Mg and Ni/Mg are 0.17 and 0.70 for antigorite-olivine pairs and 1.83 and 0.22 for orthopyroxene-olivine pairs, respectively. These data are useful in discriminating generations of olivine grown on each other. From the field data a phase diagram topology for a portion of the system CaO-MgO-SiO2-H2O is derived. This topology forms the basis for extrapolations into inaccessible P-T regions.

An object-oriented software approach for a distributed human tracking motion system

NASA Astrophysics Data System (ADS)

Micucci, Daniela L.

2003-06-01

Tracking is a composite job involving the co-operation of autonomous activities which exploit a complex information model and rely on a distributed architecture. Both information and activities must be classified and related in several dimensions: abstraction levels (what is modelled and how information is processed); topology (where the modelled entities are); time (when entities exist); strategy (why something happens); responsibilities (who is in charge of processing the information). A proper Object-Oriented analysis and design approach leads to a modular architecture where information about conceptual entities is modelled at each abstraction level via classes and intra-level associations, whereas inter-level associations between classes model the abstraction process. Both information and computation are partitioned according to level-specific topological models. They are also placed in a temporal framework modelled by suitable abstractions. Domain-specific strategies control the execution of the computations. Computational components perform both intra-level processing and intra-level information conversion. The paper overviews the phases of the analysis and design process, presents major concepts at each abstraction level, and shows how the resulting design turns into a modular, flexible and adaptive architecture. Finally, the paper sketches how the conceptual architecture can be deployed into a concrete distribute architecture by relying on an experimental framework.

Establishing non-Abelian topological order in Gutzwiller-projected Chern insulators via entanglement entropy and modular S-matrix

NASA Astrophysics Data System (ADS)

Zhang, Yi; Vishwanath, Ashvin

2013-04-01

We use entanglement entropy signatures to establish non-Abelian topological order in projected Chern-insulator wave functions. The simplest instance is obtained by Gutzwiller projecting a filled band with Chern number C=2, whose wave function may also be viewed as the square of the Slater determinant of a band insulator. We demonstrate that this wave function is captured by the SU(2)2 Chern-Simons theory coupled to fermions. This is established most persuasively by calculating the modular S-matrix from the candidate ground-state wave functions, following a recent entanglement-entropy-based approach. This directly demonstrates the peculiar non-Abelian braiding statistics of Majorana fermion quasiparticles in this state. We also provide microscopic evidence for the field theoretic generalization, that the Nth power of a Chern number C Slater determinant realizes the topological order of the SU(N)C Chern-Simons theory coupled to fermions, by studying the SU(2)3 (Read-Rezayi-type state) and the SU(3)2 wave functions. An advantage of our projected Chern-insulator wave functions is the relative ease with which physical properties, such as entanglement entropy and modular S-matrix, can be numerically calculated using Monte Carlo techniques.

Resting-State Network Topology Differentiates Task Signals across the Adult Life Span.

PubMed

Chan, Micaela Y; Alhazmi, Fahd H; Park, Denise C; Savalia, Neil K; Wig, Gagan S

2017-03-08

Brain network connectivity differs across individuals. For example, older adults exhibit less segregated resting-state subnetworks relative to younger adults (Chan et al., 2014). It has been hypothesized that individual differences in network connectivity impact the recruitment of brain areas during task execution. While recent studies have described the spatial overlap between resting-state functional correlation (RSFC) subnetworks and task-evoked activity, it is unclear whether individual variations in the connectivity pattern of a brain area (topology) relates to its activity during task execution. We report data from 238 cognitively normal participants (humans), sampled across the adult life span (20-89 years), to reveal that RSFC-based network organization systematically relates to the recruitment of brain areas across two functionally distinct tasks (visual and semantic). The functional activity of brain areas (network nodes) were characterized according to their patterns of RSFC: nodes with relatively greater connections to nodes in their own functional system ("non-connector" nodes) exhibited greater activity than nodes with relatively greater connections to nodes in other systems ("connector" nodes). This "activation selectivity" was specific to those brain systems that were central to each of the tasks. Increasing age was accompanied by less differentiated network topology and a corresponding reduction in activation selectivity (or differentiation) across relevant network nodes. The results provide evidence that connectional topology of brain areas quantified at rest relates to the functional activity of those areas during task. Based on these findings, we propose a novel network-based theory for previous reports of the "dedifferentiation" in brain activity observed in aging. SIGNIFICANCE STATEMENT Similar to other real-world networks, the organization of brain networks impacts their function. As brain network connectivity patterns differ across individuals, we hypothesized that individual differences in network connectivity would relate to differences in brain activity. Using functional MRI in a group of individuals sampled across the adult life span (20-89 years), we measured correlations at rest and related the functional connectivity patterns to measurements of functional activity during two independent tasks. Brain activity varied in relation to connectivity patterns revealed by large-scale network analysis. This relationship tracked the differences in connectivity patterns accompanied by older age, providing important evidence for a link between the topology of areal connectivity measured at rest and the functional recruitment of these areas during task performance. Copyright © 2017 Chan et al.

ADHM and the 4d quantum Hall effect

NASA Astrophysics Data System (ADS)

Barns-Graham, Alec; Dorey, Nick; Lohitsiri, Nakarin; Tong, David; Turner, Carl

2018-04-01

Yang-Mills instantons are solitonic particles in d = 4 + 1 dimensional gauge theories. We construct and analyse the quantum Hall states that arise when these particles are restricted to the lowest Landau level. We describe the ground state wavefunctions for both Abelian and non-Abelian quantum Hall states. Although our model is purely bosonic, we show that the excitations of this 4d quantum Hall state are governed by the Nekrasov partition function of a certain five dimensional supersymmetric gauge theory with Chern-Simons term. The partition function can also be interpreted as a variant of the Hilbert series of the instanton moduli space, counting holomorphic sections rather than holomorphic functions. It is known that the Hilbert series of the instanton moduli space can be rewritten using mirror symmetry of 3d gauge theories in terms of Coulomb branch variables. We generalise this approach to include the effect of a five dimensional Chern-Simons term. We demonstrate that the resulting Coulomb branch formula coincides with the corresponding Higgs branch Molien integral which, in turn, reproduces the standard formula for the Nekrasov partition function.

Restoring canonical partition functions from imaginary chemical potential

NASA Astrophysics Data System (ADS)

Bornyakov, V. G.; Boyda, D.; Goy, V.; Molochkov, A.; Nakamura, A.; Nikolaev, A.; Zakharov, V. I.

2018-03-01

Using GPGPU techniques and multi-precision calculation we developed the code to study QCD phase transition line in the canonical approach. The canonical approach is a powerful tool to investigate sign problem in Lattice QCD. The central part of the canonical approach is the fugacity expansion of the grand canonical partition functions. Canonical partition functions Zn(T) are coefficients of this expansion. Using various methods we study properties of Zn(T). At the last step we perform cubic spline for temperature dependence of Zn(T) at fixed n and compute baryon number susceptibility χB/T2 as function of temperature. After that we compute numerically ∂χ/∂T and restore crossover line in QCD phase diagram. We use improved Wilson fermions and Iwasaki gauge action on the 163 × 4 lattice with mπ/mρ = 0.8 as a sandbox to check the canonical approach. In this framework we obtain coefficient in parametrization of crossover line Tc(µ2B) = Tc(C-ĸµ2B/T2c) with ĸ = -0.0453 ± 0.0099.

Decreased Functional Brain Connectivity in Adolescents with Internet Addiction

PubMed Central

Hong, Soon-Beom; Zalesky, Andrew; Cocchi, Luca; Fornito, Alex; Choi, Eun-Jung; Kim, Ho-Hyun; Suh, Jeong-Eun; Kim, Chang-Dai; Kim, Jae-Won; Yi, Soon-Hyung

2013-01-01

Background Internet addiction has become increasingly recognized as a mental disorder, though its neurobiological basis is unknown. This study used functional neuroimaging to investigate whole-brain functional connectivity in adolescents diagnosed with internet addiction. Based on neurobiological changes seen in other addiction related disorders, it was predicted that connectivity disruptions in adolescents with internet addiction would be most prominent in cortico-striatal circuitry. Methods Participants were 12 adolescents diagnosed with internet addiction and 11 healthy comparison subjects. Resting-state functional magnetic resonance images were acquired, and group differences in brain functional connectivity were analyzed using the network-based statistic. We also analyzed network topology, testing for between-group differences in key graph-based network measures. Results Adolescents with internet addiction showed reduced functional connectivity spanning a distributed network. The majority of impaired connections involved cortico-subcortical circuits (∼24% with prefrontal and ∼27% with parietal cortex). Bilateral putamen was the most extensively involved subcortical brain region. No between-group difference was observed in network topological measures, including the clustering coefficient, characteristic path length, or the small-worldness ratio. Conclusions Internet addiction is associated with a widespread and significant decrease of functional connectivity in cortico-striatal circuits, in the absence of global changes in brain functional network topology. PMID:23451272

Analysis of Membrane Protein Topology in the Plant Secretory Pathway.

PubMed

Guo, Jinya; Miao, Yansong; Cai, Yi

2017-01-01

Topology of membrane proteins provides important information for the understanding of protein function and intermolecular associations. Integrate membrane proteins are generally transported from endoplasmic reticulum (ER) to Golgi and downstream compartments in the plant secretory pathway. Here, we describe a simple method to study membrane protein topology along the plant secretory pathway by transiently coexpressing a fluorescent protein (XFP)-tagged membrane protein and an ER export inhibitor protein, ARF1 (T31N), in tobacco BY-2 protoplast. By fractionation, microsome isolation, and trypsin digestion, membrane protein topology could be easily detected by either direct confocal microscopy imaging or western-blot analysis using specific XFP antibodies. A similar strategy in determining membrane protein topology could be widely adopted and applied to protein analysis in a broad range of eukaryotic systems, including yeast cells and mammalian cells.

The topology of large-scale structure. VI - Slices of the universe

NASA Astrophysics Data System (ADS)

Park, Changbom; Gott, J. R., III; Melott, Adrian L.; Karachentsev, I. D.

1992-03-01

Results of an investigation of the topology of large-scale structure in two observed slices of the universe are presented. Both slices pass through the Coma cluster and their depths are 100 and 230/h Mpc. The present topology study shows that the largest void in the CfA slice is divided into two smaller voids by a statistically significant line of galaxies. The topology of toy models like the white noise and bubble models is shown to be inconsistent with that of the observed slices. A large N-body simulation was made of the biased cloud dark matter model and the slices are simulated by matching them in selection functions and boundary conditions. The genus curves for these simulated slices are spongelike and have a small shift in the direction of a meatball topology like those of observed slices.